From samah.bouzidi at gmail.com Mon Feb 1 08:58:01 2016 From: samah.bouzidi at gmail.com (samah bouzidi) Date: Mon, 1 Feb 2016 14:58:01 +0100 Subject: [ITK] affine transform parameters Message-ID: Hi, I am running an Affine transform registration in 3D (using this example http://itk.org/Wiki/ITK/Examples/Registration/ImageRegistrationMethodAffine). I obtain 12 final parameters as : [ a b c d e f g h i j k l] assuming that j, k,l are the translation parameters where are the rotation parameters and how can I obtain the rotation angle ? my intial parameters are : R= [100 010 001] and tx=1 ty=1 tz=1 Thank you so much for your help, Samah -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Mon Feb 1 09:23:51 2016 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 1 Feb 2016 09:23:51 -0500 Subject: [ITK] http support on midas3.kitware.com In-Reply-To: References: Message-ID: <7C0008CB-D6E6-460E-B642-A68E2649E7DC@mail.nih.gov> Matt, There are a number of mirrors listed for the external data download to try [1]. Do all of these sites require https now? Do all of them have the full mirror of all the data? I think most of my machines don?t have SSL CMake. I imagine that they are pulling the data from the local cache right now. Is there a way we could push new data, or add a check, or produce a CMake warning of the needed CMake feature is not there? Thanks, Brad p.s. I think the Azure address not longer works [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/CMake/ITKExternalData.cmake#L34-L44 > On Jan 29, 2016, at 11:22 AM, Matt McCormick wrote: > > Hi folks, > > The server that hosts ITK data -- midas3.kitware.com now only supports > https, and does not support downloading via the http protocol. This > may result in build errors like: > > error: downloading > 'http://midas3.kitware.com/midas/download/bitstream/457653/castxml-linux.tar.gz' > failed > > status_code: 1 > status_string: "Unsupported protocol" > log: Trying 192.168.120.111... > > Connected to midas3.kitware.com (192.168.120.111) port 80 (#0) > > To address this error, the CMake client needs OpenSSL support. Newer > binaries from cmake.org have this support. When building from source, > this is not enabled by default -- enable the configuration option > CMAKE_USE_OPENSSL. > > Matt > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From matt.mccormick at kitware.com Mon Feb 1 11:19:51 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 1 Feb 2016 11:19:51 -0500 Subject: [ITK] affine transform parameters In-Reply-To: References: Message-ID: Hi Samah, By calling SetFixedParameters to specify the center of rotation and SetMatrix on a class that inherits from Rigid3DTransform [1], rotation angles can be obtained in the form desired, (Euler angles, versor, ...). But, SetMatrix will fail if the matrix is not orthogonal. Therefore, if a rigid transformation is desired, then the optimization should be performed with a VersorRigid3DTransform. Hope that helps, Matt [1] http://www.itk.org/Doxygen/html/classitk_1_1Rigid3DTransform.html On Mon, Feb 1, 2016 at 8:58 AM, samah bouzidi wrote: > Hi, > > I am running an Affine transform registration in 3D (using this example > http://itk.org/Wiki/ITK/Examples/Registration/ImageRegistrationMethodAffine). > I obtain 12 final parameters as : [ a b c d e f g h i j k l] assuming that > j, k,l are the translation parameters where are the rotation parameters and > how can I obtain the rotation angle ? > my intial parameters are : > R= [100 > 010 > 001] > and > tx=1 > ty=1 > tz=1 > Thank you so much for your help, > Samah > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From dzenanz at gmail.com Mon Feb 1 11:25:51 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 1 Feb 2016 11:25:51 -0500 Subject: [ITK] http support on midas3.kitware.com In-Reply-To: <7C0008CB-D6E6-460E-B642-A68E2649E7DC@mail.nih.gov> References: <7C0008CB-D6E6-460E-B642-A68E2649E7DC@mail.nih.gov> Message-ID: We should change the address from http:// to https://. That way CMake will give a more meaningful error (https protocol not supported). On Mon, Feb 1, 2016 at 9:23 AM, Bradley Lowekamp wrote: > Matt, > > There are a number of mirrors listed for the external data download to try > [1]. Do all of these sites require https now? Do all of them have the full > mirror of all the data? > > I think most of my machines don?t have SSL CMake. I imagine that they are > pulling the data from the local cache right now. Is there a way we could > push new data, or add a check, or produce a CMake warning of the needed > CMake feature is not there? > > Thanks, > Brad > > p.s. I think the Azure address not longer works > > > [1] > https://github.com/InsightSoftwareConsortium/ITK/blob/master/CMake/ITKExternalData.cmake#L34-L44 > > > On Jan 29, 2016, at 11:22 AM, Matt McCormick > wrote: > > > > Hi folks, > > > > The server that hosts ITK data -- midas3.kitware.com now only supports > > https, and does not support downloading via the http protocol. This > > may result in build errors like: > > > > error: downloading > > ' > http://midas3.kitware.com/midas/download/bitstream/457653/castxml-linux.tar.gz > ' > > failed > > > > status_code: 1 > > status_string: "Unsupported protocol" > > log: Trying 192.168.120.111... > > > > Connected to midas3.kitware.com (192.168.120.111) port 80 (#0) > > > > To address this error, the CMake client needs OpenSSL support. Newer > > binaries from cmake.org have this support. When building from source, > > this is not enabled by default -- enable the configuration option > > CMAKE_USE_OPENSSL. > > > > Matt > > _______________________________________________ > > Community mailing list > > Community at itk.org > > http://public.kitware.com/mailman/listinfo/community > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Feb 1 12:00:06 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 1 Feb 2016 12:00:06 -0500 Subject: [ITK] http support on midas3.kitware.com In-Reply-To: References: <7C0008CB-D6E6-460E-B642-A68E2649E7DC@mail.nih.gov> Message-ID: Hi, Since our Azure grant expired, we no longer have write access to our storage on their CDN. They were still providing read access, but that may have been discontinued. The resource is removed in this patch: http://review.source.kitware.com/#/c/20737/ Explicit listing of https for midas3.kitware.com to improve expectations and error messages is added here: http://review.source.kitware.com/#/c/20738/ The http://www.itk.org/files/ExternalData/ resource does support http. I added sync'ing of the InsightData tarball contents, which can be downloaded with every release, as part of the release process. However, data from External / Remote modules that is not uploaded via 'git gerrit-push' [1] is not uploaded there. And, resources like CastXML binaries are not uploaded here. The http://slicer.midas3.kitware.com/midas3/ archive does currently support http, but that support is being removed. A patch to update the URL is here: http://review.source.kitware.com/#/c/20739/ Thanks, Matt [1] http://www.itk.org/Wiki/ITK/Git/Develop/Data#Add_Data On Mon, Feb 1, 2016 at 11:25 AM, D?enan Zuki? wrote: > We should change the address from http:// to https://. That way CMake will > give a more meaningful error (https protocol not supported). > > On Mon, Feb 1, 2016 at 9:23 AM, Bradley Lowekamp > wrote: >> >> Matt, >> >> There are a number of mirrors listed for the external data download to try >> [1]. Do all of these sites require https now? Do all of them have the full >> mirror of all the data? >> >> I think most of my machines don?t have SSL CMake. I imagine that they are >> pulling the data from the local cache right now. Is there a way we could >> push new data, or add a check, or produce a CMake warning of the needed >> CMake feature is not there? >> >> Thanks, >> Brad >> >> p.s. I think the Azure address not longer works >> >> >> [1] >> https://github.com/InsightSoftwareConsortium/ITK/blob/master/CMake/ITKExternalData.cmake#L34-L44 >> >> > On Jan 29, 2016, at 11:22 AM, Matt McCormick >> > wrote: >> > >> > Hi folks, >> > >> > The server that hosts ITK data -- midas3.kitware.com now only supports >> > https, and does not support downloading via the http protocol. This >> > may result in build errors like: >> > >> > error: downloading >> > >> > 'http://midas3.kitware.com/midas/download/bitstream/457653/castxml-linux.tar.gz' >> > failed >> > >> > status_code: 1 >> > status_string: "Unsupported protocol" >> > log: Trying 192.168.120.111... >> > >> > Connected to midas3.kitware.com (192.168.120.111) port 80 (#0) >> > >> > To address this error, the CMake client needs OpenSSL support. Newer >> > binaries from cmake.org have this support. When building from source, >> > this is not enabled by default -- enable the configuration option >> > CMAKE_USE_OPENSSL. >> > >> > Matt >> > _______________________________________________ >> > Community mailing list >> > Community at itk.org >> > http://public.kitware.com/mailman/listinfo/community >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community > > From afs13 at imperial.ac.uk Mon Feb 1 12:39:39 2016 From: afs13 at imperial.ac.uk (=?UTF-8?Q?Andr=C3=A9_Ribeiro?=) Date: Mon, 1 Feb 2016 17:39:39 +0000 Subject: [ITK] cross-compiling ITK function to Windows Message-ID: Hi ITK community, I am trying to cross-compile an ITK code to windows from my linux machine, but without success. I am able to compile it if I use as the target system Linux (my machine) and the compilers x86_64-linux-gnu-gcc and x86_64-linux-gnu-g++ in the Toolchain cmake file. Yet, if i change the target system to Windows and the compilers to x86_64-w64-mingw32-gcc and x86_64-w64-mingw32-g++ the cmake runs without any problems but is unable to find any of the ITK libraries (I observed this by looking at the generated build.make file) Here goes the command line I am using for the cmake compilation: > cmake . -DCMAKE_TOOLCHAIN_FILE=./Toolchain-mingw32.cmake > -DCMAKE_INSTALL_PREFIX=/home/X/mingw-install -G "Unix Makefiles" Here goes one of the lines of the build.make file when the linux target is used > ThresholdImage: > /disk2/X/programs/InsightToolkit-4.8.2/ITK_4.8.2/lib/libITKIOTransformHDF5-4.8.so.1 Here goes the same line in the build.make file if the Windows is used as target > ThresholdImage.exe: ITKIOTransformHDF5-NOTFOUND Any help is appreciated. Regards, Andre Santos Ribeiro -------------- next part -------------- An HTML attachment was scrubbed... URL: From bakkari.abdelkhalek at hotmail.fr Mon Feb 1 13:06:45 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Mon, 1 Feb 2016 19:06:45 +0100 Subject: [ITK] [ITK-users] itk::ERROR: VarianceImageFilter(060CFF60): In-Reply-To: References: , Message-ID: Hi, How can I change the arguments to method have to be hanged as directed? Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland > Date: Thu, 28 Jan 2016 17:07:35 -0500 > Subject: Re: [ITK-users] itk::ERROR: VarianceImageFilter(060CFF60): > From: matt.mccormick at kitware.com > To: bakkari.abdelkhalek at hotmail.fr > CC: insight-users at itk.org > > Hi, > > > The signature of ThreadedGenerateData() has been changed in ITK v4 to use the ne > w ThreadIdType. " > > This means the type of the arguments to method have to be changed as directed. > > HTH, > Matt > > On Thu, Jan 28, 2016 at 4:58 PM, Abdelkhalek Bakkari > wrote: > > > > > > Hi ! > > > > I tried to adopt the itkImageVarianceFilter into my code. But, an error > > appears during execution : > > > > " Exception detected: itk::ERROR: MultiThreader(060E4078): Exception > > occurred duri > > ng SingleMethodExecute > > c:\itk 4.8.1\source\modules\core\common\include\itkImageSource.hxx:279: > > itk::ERROR: VarianceImageFilter(060CFF60): Subclass should override this > > method! > > !! > > The signature of ThreadedGenerateData() has been changed in ITK v4 to use > > the ne > > w ThreadIdType. " > > > > Any help, please! > > > > Best regards, > > > > Abdelkhalek Bakkari > > Ph.D candidate in Computer Science > > Institute of Applied Computer Science > > Lodz University of Technology, Poland > > > > > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From bakkari.abdelkhalek at hotmail.fr Mon Feb 1 13:50:39 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Mon, 1 Feb 2016 19:50:39 +0100 Subject: [ITK] [ITK-users] itk::ERROR: VarianceImageFilter(060CFF60): In-Reply-To: References: , , , Message-ID: threadId should be declared not as int but as ThreadIdType, like this: /** Does the real work. */ virtual void ThreadedGenerateData(const typename Superclass::OutputImageRegionType& outputRegionForThread, ThreadIdType threadId);Thank you D?enan Zuki? again ;) Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland From: bakkari.abdelkhalek at hotmail.fr To: matt.mccormick at kitware.com Date: Mon, 1 Feb 2016 19:06:45 +0100 CC: insight-users at itk.org Subject: Re: [ITK-users] itk::ERROR: VarianceImageFilter(060CFF60): Hi, How can I change the arguments to method have to be hanged as directed? Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland > Date: Thu, 28 Jan 2016 17:07:35 -0500 > Subject: Re: [ITK-users] itk::ERROR: VarianceImageFilter(060CFF60): > From: matt.mccormick at kitware.com > To: bakkari.abdelkhalek at hotmail.fr > CC: insight-users at itk.org > > Hi, > > > The signature of ThreadedGenerateData() has been changed in ITK v4 to use the ne > w ThreadIdType. " > > This means the type of the arguments to method have to be changed as directed. > > HTH, > Matt > > On Thu, Jan 28, 2016 at 4:58 PM, Abdelkhalek Bakkari > wrote: > > > > > > Hi ! > > > > I tried to adopt the itkImageVarianceFilter into my code. But, an error > > appears during execution : > > > > " Exception detected: itk::ERROR: MultiThreader(060E4078): Exception > > occurred duri > > ng SingleMethodExecute > > c:\itk 4.8.1\source\modules\core\common\include\itkImageSource.hxx:279: > > itk::ERROR: VarianceImageFilter(060CFF60): Subclass should override this > > method! > > !! > > The signature of ThreadedGenerateData() has been changed in ITK v4 to use > > the ne > > w ThreadIdType. " > > > > Any help, please! > > > > Best regards, > > > > Abdelkhalek Bakkari > > Ph.D candidate in Computer Science > > Institute of Applied Computer Science > > Lodz University of Technology, Poland > > > > > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Mon Feb 1 13:55:40 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 1 Feb 2016 13:55:40 -0500 Subject: [ITK] cross-compiling ITK function to Windows In-Reply-To: References: Message-ID: Hi Andre, When configuring the build for the ThresholdImage executable, make sure to set the ITK_DIR CMake configuration variable to the appropriate ITK build tree directory. For example, cmake . -DCMAKE_TOOLCHAIN_FILE=./Toolchain-mingw32.cmake -DCMAKE_INSTALL_PREFIX=/home/X/mingw-install -G "Unix Makefiles" -DITK_DIR=/home/X/ITK-build Hope this helps, Matt On Mon, Feb 1, 2016 at 12:39 PM, Andr? Ribeiro wrote: > Hi ITK community, > > I am trying to cross-compile an ITK code to windows from my linux machine, > but without success. > > I am able to compile it if I use as the target system Linux (my machine) and > the compilers x86_64-linux-gnu-gcc and x86_64-linux-gnu-g++ in the Toolchain > cmake file. > > Yet, if i change the target system to Windows and the compilers to > x86_64-w64-mingw32-gcc and x86_64-w64-mingw32-g++ the cmake runs without any > problems but is unable to find any of the ITK libraries (I observed this by > looking at the generated build.make file) > > > Here goes the command line I am using for the cmake compilation: >> >> cmake . -DCMAKE_TOOLCHAIN_FILE=./Toolchain-mingw32.cmake >> -DCMAKE_INSTALL_PREFIX=/home/X/mingw-install -G "Unix Makefiles" > > > Here goes one of the lines of the build.make file when the linux target is > used >> >> ThresholdImage: >> /disk2/X/programs/InsightToolkit-4.8.2/ITK_4.8.2/lib/libITKIOTransformHDF5-4.8.so.1 > > > Here goes the same line in the build.make file if the Windows is used as > target >> >> ThresholdImage.exe: ITKIOTransformHDF5-NOTFOUND > > > Any help is appreciated. > > > Regards, > Andre Santos Ribeiro > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From bakkari.abdelkhalek at hotmail.fr Mon Feb 1 14:20:21 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Mon, 1 Feb 2016 20:20:21 +0100 Subject: [ITK] ITK, VTK and QT crash Message-ID: Hi ! I have a problem using ITK, VTK and QT. When I tried to load a big data of Dicom images some functions into my interface does not working and the application crashed.Can you help me, please ? Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Mon Feb 1 14:47:46 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 1 Feb 2016 14:47:46 -0500 Subject: [ITK] [ITK-users] ITK, VTK and QT crash In-Reply-To: References: Message-ID: Hi Abdelkhalek, you have to be a lot more specific than that. How big are the files? 2GB, or 102GB? In which file/line does the crash finally manifest? Can you trace where the original exception occurred? Is it in ITK, VTK or Qt code? What is the error message? Try to produce a minimum working example (MWE), so we can take a look at it and offer help. Regards, D?enan On Mon, Feb 1, 2016 at 2:20 PM, Abdelkhalek Bakkari < bakkari.abdelkhalek at hotmail.fr> wrote: > > Hi ! > > I have a problem using ITK, VTK and QT. When I tried to load a big data of > Dicom images some functions into my interface does not working and the > application crashed. > Can you help me, please ? > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From samah.bouzidi at gmail.com Mon Feb 1 15:57:26 2016 From: samah.bouzidi at gmail.com (samah bouzidi) Date: Mon, 1 Feb 2016 21:57:26 +0100 Subject: [ITK] affine transform parameters In-Reply-To: References: Message-ID: Hi Matt, i will try to use the Rigid transform. But, i would like to know in that example what are these parameters in 2D (or 3D) ? are they the rotation angle the offset of the center and the translations parameters as it is described in the ITK software guide ( pdf page 490). regards, Samah. 2016-02-01 17:19 GMT+01:00 Matt McCormick : > Hi Samah, > > By calling SetFixedParameters to specify the center of rotation and > SetMatrix on a class that inherits from Rigid3DTransform [1], rotation > angles can be obtained in the form desired, (Euler angles, versor, > ...). But, SetMatrix will fail if the matrix is not orthogonal. > Therefore, if a rigid transformation is desired, then the optimization > should be performed with a VersorRigid3DTransform. > > Hope that helps, > Matt > > > [1] http://www.itk.org/Doxygen/html/classitk_1_1Rigid3DTransform.html > > On Mon, Feb 1, 2016 at 8:58 AM, samah bouzidi > wrote: > > Hi, > > > > I am running an Affine transform registration in 3D (using this example > > > http://itk.org/Wiki/ITK/Examples/Registration/ImageRegistrationMethodAffine > ). > > I obtain 12 final parameters as : [ a b c d e f g h i j k l] assuming > that > > j, k,l are the translation parameters where are the rotation parameters > and > > how can I obtain the rotation angle ? > > my intial parameters are : > > R= [100 > > 010 > > 001] > > and > > tx=1 > > ty=1 > > tz=1 > > Thank you so much for your help, > > Samah > > > > > > > > _______________________________________________ > > Community mailing list > > Community at itk.org > > http://public.kitware.com/mailman/listinfo/community > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Feb 1 16:44:49 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 1 Feb 2016 16:44:49 -0500 Subject: [ITK] affine transform parameters In-Reply-To: References: Message-ID: Hi Samah, As described in the class documentation [1], "the first (NDimension x NDimension) parameters defines the matrix in row-major order (where the column index varies the fastest). The last NDimension parameters defines the translation in each dimensions." HTH, Matt [1] http://www.itk.org/Doxygen/html/classitk_1_1AffineTransform.html On Mon, Feb 1, 2016 at 3:57 PM, samah bouzidi wrote: > Hi Matt, > > i will try to use the Rigid transform. But, i would like to know in that > example what are these parameters in 2D (or 3D) ? > are they the rotation angle the offset of the center and the translations > parameters as it is described in the ITK software guide ( pdf page 490). > > regards, > Samah. > > > > 2016-02-01 17:19 GMT+01:00 Matt McCormick : >> >> Hi Samah, >> >> By calling SetFixedParameters to specify the center of rotation and >> SetMatrix on a class that inherits from Rigid3DTransform [1], rotation >> angles can be obtained in the form desired, (Euler angles, versor, >> ...). But, SetMatrix will fail if the matrix is not orthogonal. >> Therefore, if a rigid transformation is desired, then the optimization >> should be performed with a VersorRigid3DTransform. >> >> Hope that helps, >> Matt >> >> >> [1] http://www.itk.org/Doxygen/html/classitk_1_1Rigid3DTransform.html >> >> On Mon, Feb 1, 2016 at 8:58 AM, samah bouzidi >> wrote: >> > Hi, >> > >> > I am running an Affine transform registration in 3D (using this example >> > >> > http://itk.org/Wiki/ITK/Examples/Registration/ImageRegistrationMethodAffine). >> > I obtain 12 final parameters as : [ a b c d e f g h i j k l] assuming >> > that >> > j, k,l are the translation parameters where are the rotation parameters >> > and >> > how can I obtain the rotation angle ? >> > my intial parameters are : >> > R= [100 >> > 010 >> > 001] >> > and >> > tx=1 >> > ty=1 >> > tz=1 >> > Thank you so much for your help, >> > Samah >> > >> > >> > >> > _______________________________________________ >> > Community mailing list >> > Community at itk.org >> > http://public.kitware.com/mailman/listinfo/community >> > > > From matt.mccormick at kitware.com Mon Feb 1 17:01:34 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 1 Feb 2016 17:01:34 -0500 Subject: [ITK] [ITK-dev] [Paraview] Retire expected builds In-Reply-To: <568BE9A6.4020303@ohio.edu> References: <568BE9A6.4020303@ohio.edu> Message-ID: Hi Kevin, Sorry to hear this, but thank you for your many helpful years of submissions! Best wishes as you begin your new job! Matt On Tue, Jan 5, 2016 at 11:04 AM, Kevin H. Hobbs wrote: > I'm moving to a new job, and will no longer be able to maintain my > nightly builds (even in their neglected state.) > > Please expect the expected builds from bubbles, murron, and k450e to > dissapear. > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html > > Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView > > Search the list archives at: http://markmail.org/search/?q=ParaView > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/paraview > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Mon Feb 1 17:07:09 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 1 Feb 2016 17:07:09 -0500 Subject: [ITK] [ITK-dev] Future of ITKApps In-Reply-To: References: <9DB0559B-F7FD-4FEB-8423-C7398659CBD4@uiowa.edu> Message-ID: Follow-up: the Docker image has come along well, but a little more work is required. We ran into a CMake issue that means we will not release ITKApps with 4.9.0 [1]. I will plan on releasing Docker versions of some of the ITKApps executables in the future. Matt [1] http://review.source.kitware.com/#/c/20730/ On Fri, Nov 20, 2015 at 11:53 AM, Matt McCormick wrote: > +1. > > I patched most of the apps for VTK 6, which is what we have in the > Superbuild, so I would like to get that merged. > > FLTK makes these building these quite finicky and hard to maintain. > There are many other better tools and demonstrations out there on how > to develop an app based on ITK. Yet, these apps still provide value > both in the functionality they provide and in the minimal, > self-contained demonstration of how to use ITK + VTK. > > There was a discussion recently on GitHub on how to use one of the > Apps on Windows [1]. Following that thread, I created a Docker image > to run the apps [2]. This runs on OSX / Linux / Windows, and can be > interacted with on all platforms, including tablets, phones. People > will be able to use the apps in perpetuity without requiring further > maintenance. > > I propose we create the create the Docker apps, then freeze > development. ITKApps released with ITK 4.9 would be the final > release. > > Thanks, > Matt > > > [1] https://github.com/InsightSoftwareConsortium/ITKDevelopmentEnvironment/issues/1 > > [2] https://github.com/thewtex/docker-opengl > > On Fri, Nov 20, 2015 at 10:49 AM, Johnson, Hans J > wrote: >> +10 ? That is not a typo. Really +10. >> >> The slicer extensions framework is one of many improved solutions over fltk apps. >> Heck? many of the demo apps could be easily re-written in SimpleITK with ipython notebook widgets. >> >> Hans >> >> >> On 11/20/15, 9:29 AM, "Insight-developers on behalf of Bill Lorensen" wrote: >> >>>Folks, >>> >>>ITKApps contains applications written a long time ago. We as a group >>>have been patching the apps, fixing compile errors as ITK and VTK >>>api's change. >>> >>>Also, many of the apps use an old version of FLTK as a gui. >>> >>>I think the maintenance cost is too much for these old applications. >>> >>>We should consider freezing it at VTK5.10 and the last ITK version >>>that works with it. >>> >>>As Matt has mentioned there are several modern apps like slicer and >>>SNAP that can provide users with a better experience. >>> >>>Thoughts? >>> >>>Bill >>> >>>-- >>>Unpaid intern in BillsBasement at noware dot com >>>_______________________________________________ >>>Powered by www.kitware.com >>> >>>Visit other Kitware open-source projects at >>>http://www.kitware.com/opensource/opensource.html >>> >>>Kitware offers ITK Training Courses, for more information visit: >>>http://kitware.com/products/protraining.php >>> >>>Please keep messages on-topic and check the ITK FAQ at: >>>http://www.itk.org/Wiki/ITK_FAQ >>> >>>Follow this link to subscribe/unsubscribe: >>>http://public.kitware.com/mailman/listinfo/insight-developers >> >> >> ________________________________ >> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. >> ________________________________ >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From g.bogle at auckland.ac.nz Tue Feb 2 00:25:21 2016 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 2 Feb 2016 05:25:21 +0000 Subject: [ITK] [ITK-users] Read a frame from a 3D image Message-ID: We want to work with a 3D TIFF that is much too big to fit in memory. It would be sufficient to be able to specify a 2D frame and read that. How can this be done? Thanks Gib -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From samah.bouzidi at gmail.com Tue Feb 2 03:54:32 2016 From: samah.bouzidi at gmail.com (samah bouzidi) Date: Tue, 2 Feb 2016 09:54:32 +0100 Subject: [ITK] affine transform parameters In-Reply-To: References: Message-ID: Hi Matt, My question is what are that first parameters " the first (NDimension x NDimension) parameters defines the matrix in row-major order (where the column index varies the fastest)" what they define here ? Regards Samah. 2016-02-01 22:44 GMT+01:00 Matt McCormick : > Hi Samah, > > As described in the class documentation [1], "the first (NDimension x > NDimension) parameters defines the matrix in row-major order (where > the column index varies the fastest). The last NDimension parameters > defines the translation in each dimensions." > > HTH, > Matt > > [1] http://www.itk.org/Doxygen/html/classitk_1_1AffineTransform.html > > On Mon, Feb 1, 2016 at 3:57 PM, samah bouzidi > wrote: > > Hi Matt, > > > > i will try to use the Rigid transform. But, i would like to know in that > > example what are these parameters in 2D (or 3D) ? > > are they the rotation angle the offset of the center and the translations > > parameters as it is described in the ITK software guide ( pdf page 490). > > > > regards, > > Samah. > > > > > > > > 2016-02-01 17:19 GMT+01:00 Matt McCormick : > >> > >> Hi Samah, > >> > >> By calling SetFixedParameters to specify the center of rotation and > >> SetMatrix on a class that inherits from Rigid3DTransform [1], rotation > >> angles can be obtained in the form desired, (Euler angles, versor, > >> ...). But, SetMatrix will fail if the matrix is not orthogonal. > >> Therefore, if a rigid transformation is desired, then the optimization > >> should be performed with a VersorRigid3DTransform. > >> > >> Hope that helps, > >> Matt > >> > >> > >> [1] http://www.itk.org/Doxygen/html/classitk_1_1Rigid3DTransform.html > >> > >> On Mon, Feb 1, 2016 at 8:58 AM, samah bouzidi > >> wrote: > >> > Hi, > >> > > >> > I am running an Affine transform registration in 3D (using this > example > >> > > >> > > http://itk.org/Wiki/ITK/Examples/Registration/ImageRegistrationMethodAffine > ). > >> > I obtain 12 final parameters as : [ a b c d e f g h i j k l] assuming > >> > that > >> > j, k,l are the translation parameters where are the rotation > parameters > >> > and > >> > how can I obtain the rotation angle ? > >> > my intial parameters are : > >> > R= [100 > >> > 010 > >> > 001] > >> > and > >> > tx=1 > >> > ty=1 > >> > tz=1 > >> > Thank you so much for your help, > >> > Samah > >> > > >> > > >> > > >> > _______________________________________________ > >> > Community mailing list > >> > Community at itk.org > >> > http://public.kitware.com/mailman/listinfo/community > >> > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Robert.Atwood at diamond.ac.uk Tue Feb 2 06:58:30 2016 From: Robert.Atwood at diamond.ac.uk (Robert.Atwood at diamond.ac.uk) Date: Tue, 2 Feb 2016 11:58:30 +0000 Subject: [ITK] [ITK-users] SimpleITK, Python, Local User, Anaconda -- how to install without messing up shared libraries? Message-ID: <6CCDD8FC6578314C902BBF87D511D9D8EA673F6A@EXCHMBX01.fed.cclrc.ac.uk> Hi, ITK people! I don't maintain the Python installation at work so I know little about all the intricacies of python modules and distributions and path searching and so on. What I do know is that if I follow the instructions for including SimpleITK as on the web page for Anacoda installation, everyone gets very angry. That is because it automatically resolves some dependencies in a way that breaks other people's applications, and it does this within the shared Python Anaconda installation on the cluster shared file system. It was suggested (strongly) that I "use the --user option of pip" . However I cannot get this to do anything by following the pip instruction on the SimpleITK web site, I know nothing of eggs and wheels nor pipit nor "more complicated commands. " Does anyone know the magic incantation to do what I want? Is there an Anaconda command that does it? Instructions from website with questions annotated: Wheels [ Recommended ] You need a recent version of pip ( >= 6.0, newer is better) to install wheels. Please go to pip homepage for more information about installation. Once you have pip, the package can be installed: $ pip install --allow-external SimpleITK --trusted-host www.simpleitk.org SimpleITK --timeout 30 SimpleITK Note: We do have window wheels hosted on pypi, but due to size and Linux binary restrictions neither OS X nor Linux are hosted on pipit, so the more complicated command is needed(1). However, you may need to manually download the file(2) from SourceForge. And specify it (3) on the command line if the automatic search does not work. (1) What is the 'more complicated command' ??? (2) Which file? An egg? Wheel? Huh? (3) Specify what? How (what is the syntax for specifying 'it' )? Output of session trying to follow the instructions. $ pip install --user --allow-external SimpleITK --trusted-host www.simpleitk.org SimpleITK --timeout 30 SimpleITK Double requirement given: SimpleITK (already in SimpleITK, name='SimpleITK') You are using pip version 7.1.2, however version 8.0.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [kny48981 at i12-ws011 6137]$ pip install --user --allow-external SimpleITK --trusted-host www.simpleitk.org --timeout 30 SimpleITK Collecting SimpleITK Could not find a version that satisfies the requirement SimpleITK (from versions: ) No matching distribution found for SimpleITK You are using pip version 7.1.2, however version 8.0.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [kny48981 at i12-ws011 6137]$ pip install --user --allow-external SimpleITK --trusted-host www.simpleitk.org SimpleITK Collecting SimpleITK Could not find a version that satisfies the requirement SimpleITK (from versions: ) No matching distribution found for SimpleITK You are using pip version 7.1.2, however version 8.0.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [kny48981 at i12-ws011 6137]$ pip install --user --allow-external --trusted-host www.simpleitk.org SimpleITK Collecting www.simpleitk.org Could not find a version that satisfies the requirement www.simpleitk.org (from versions: ) No matching distribution found for www.simpleitk.org You are using pip version 7.1.2, however version 8.0.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Tue Feb 2 07:44:45 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 2 Feb 2016 07:44:45 -0500 Subject: [ITK] affine transform parameters In-Reply-To: References: Message-ID: Hi Samah, if this is unclear to you, take a look at transform matrices . Regards, D?enan On Tue, Feb 2, 2016 at 3:54 AM, samah bouzidi wrote: > Hi Matt, > > My question is what are that first parameters " the first (NDimension x > NDimension) parameters defines the matrix in row-major order (where > the column index varies the fastest)" what they define here ? > > Regards > Samah. > > > > 2016-02-01 22:44 GMT+01:00 Matt McCormick : > >> Hi Samah, >> >> As described in the class documentation [1], "the first (NDimension x >> NDimension) parameters defines the matrix in row-major order (where >> the column index varies the fastest). The last NDimension parameters >> defines the translation in each dimensions." >> >> HTH, >> Matt >> >> [1] http://www.itk.org/Doxygen/html/classitk_1_1AffineTransform.html >> >> On Mon, Feb 1, 2016 at 3:57 PM, samah bouzidi >> wrote: >> > Hi Matt, >> > >> > i will try to use the Rigid transform. But, i would like to know in >> that >> > example what are these parameters in 2D (or 3D) ? >> > are they the rotation angle the offset of the center and the >> translations >> > parameters as it is described in the ITK software guide ( pdf page 490). >> > >> > regards, >> > Samah. >> > >> > >> > >> > 2016-02-01 17:19 GMT+01:00 Matt McCormick : >> >> >> >> Hi Samah, >> >> >> >> By calling SetFixedParameters to specify the center of rotation and >> >> SetMatrix on a class that inherits from Rigid3DTransform [1], rotation >> >> angles can be obtained in the form desired, (Euler angles, versor, >> >> ...). But, SetMatrix will fail if the matrix is not orthogonal. >> >> Therefore, if a rigid transformation is desired, then the optimization >> >> should be performed with a VersorRigid3DTransform. >> >> >> >> Hope that helps, >> >> Matt >> >> >> >> >> >> [1] http://www.itk.org/Doxygen/html/classitk_1_1Rigid3DTransform.html >> >> >> >> On Mon, Feb 1, 2016 at 8:58 AM, samah bouzidi > > >> >> wrote: >> >> > Hi, >> >> > >> >> > I am running an Affine transform registration in 3D (using this >> example >> >> > >> >> > >> http://itk.org/Wiki/ITK/Examples/Registration/ImageRegistrationMethodAffine >> ). >> >> > I obtain 12 final parameters as : [ a b c d e f g h i j k l] assuming >> >> > that >> >> > j, k,l are the translation parameters where are the rotation >> parameters >> >> > and >> >> > how can I obtain the rotation angle ? >> >> > my intial parameters are : >> >> > R= [100 >> >> > 010 >> >> > 001] >> >> > and >> >> > tx=1 >> >> > ty=1 >> >> > tz=1 >> >> > Thank you so much for your help, >> >> > Samah >> >> > >> >> > >> >> > >> >> > _______________________________________________ >> >> > Community mailing list >> >> > Community at itk.org >> >> > http://public.kitware.com/mailman/listinfo/community >> >> > >> > >> > >> > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From itkhelpacc at gmail.com Tue Feb 2 07:24:24 2016 From: itkhelpacc at gmail.com (vishal) Date: Tue, 2 Feb 2016 05:24:24 -0700 (MST) Subject: [ITK] [ITK-users] problem using VersorRigid3DTransform fo 2d/3d registration...Please advice?? Message-ID: <1454415864043-36714.post@n7.nabble.com> hi, Im currently working on registering 2d x ray image with 3d CT volume (2d/3d registration algorithm) and I have obtained pretty good results by using euler 3d transform, siddon Raycast interpolator, powell optimizer and NCG metric.. I read some post in the mailing list saying that using Versor 3d transform for such application is feasible and I tried it unfortunately Im not able to connect the Siddon ray cast interpolator to versor 3d transform... this the piece of the code where im initializing the interpolator const double dtr = ( atan(1.0) * 4.0 ) / 180.0; interpolator1->SetProjectionAngle( dtr*projAngle1 ); interpolator1->SetFocalPointToIsocenterDistance(scd); interpolator1->SetThreshold(threshold); interpolator1->SetTransform(transform); // this line the error occurs interpolator1->Initialize(); registration->SetInitialTransformParameters( transform->GetParameters() ); the error is as follows.. error C2664: 'itk::SiddonJacobsRayCastInterpolateImageFunction::SetTransform' : cannot convert parameter 1 from 'itk::SmartPointer' to 'itk::Euler3DTransform *' D:\Project_realted_example\MyOwnCodeRegistratonWithVersor\versor.cxx 696 IntelliSense: no suitable conversion function from "itk::SmartPointer>" to "itk::Euler3DTransform *" exists d:\Project_realted_example\MyOwnCodeRegistratonWithVersor\versor.cxx 696 its seems as though it is impossible to connect siddon ray casting interpolator to the versor 3d transform and IT ONLY WORKS with Euler3d transform... please give me some advice.. how can I solve this problem? Regards Vishal -- View this message in context: http://itk-users.7.n7.nabble.com/problem-using-VersorRigid3DTransform-fo-2d-3d-registration-Please-advice-tp36714.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Tue Feb 2 09:30:10 2016 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 2 Feb 2016 09:30:10 -0500 Subject: [ITK] [ITK-users] Read a frame from a 3D image In-Reply-To: References: Message-ID: <38328D60-A911-4755-9375-AC3E96C8C83A@mail.nih.gov> Gib, Currently the TIFFIO does not support streamed reading. Being able to just read a page is a straight forward first step. In fact when I refactored it I made sure it was clear how this could be done in the future [1]. The correct way to do it would be to upgrade TIFFImageIO with this feature. This would involve changing the parent class to StreamingImageIOBase, then overloading methods to disable streamed writing, and overloading the method ( GenerateStreamableReadRegionFromRequestedRegion ) to enable stream read such that the RequestedRegion is expanded to the whole slice, and verifying all the TIFF fields are valid for this operations. The tricky part would be to adapt existing tests, and test the new functionality. After that, the streaming would happen seamlessly with the ITK pipeline, giving there are stream compatible filters and all the features are configured correctly. Alternatively, there are utilities to split the pages of the TIFF in to separate files. HTH, Brad > On Feb 2, 2016, at 12:25 AM, Gib Bogle wrote: > > We want to work with a 3D TIFF that is much too big to fit in memory. It would be sufficient to be able to specify a 2D frame and read that. How can this be done? > > Thanks > Gib > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From bakkari.abdelkhalek at hotmail.fr Tue Feb 2 11:48:47 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Tue, 2 Feb 2016 17:48:47 +0100 Subject: [ITK] Region Adjacency Graph for voxels Message-ID: Hi ! How can I apply the region adjacency graph for voxels of a 3D image and obtain the adjacency list. Thank you in advance Regards, Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Tue Feb 2 14:28:12 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 2 Feb 2016 14:28:12 -0500 Subject: [ITK] [ITK-users] Region Adjacency Graph for voxels In-Reply-To: References: Message-ID: You could perhaps use neighborhood iterator over the image in question and for each iteration build a link between the pixel being iterated and the center pixel of the neighborhood. You will have to avoid duplicate links if the graph you are trying to build is undirected. HTH On Tue, Feb 2, 2016 at 11:48 AM, Abdelkhalek Bakkari < bakkari.abdelkhalek at hotmail.fr> wrote: > > Hi ! > > How can I apply the region adjacency graph for voxels of a 3D image and > obtain the adjacency list. > > Thank you in advance > > Regards, > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Tue Feb 2 15:36:04 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 2 Feb 2016 15:36:04 -0500 Subject: [ITK] [ITK-users] problem using VersorRigid3DTransform fo 2d/3d registration...Please advice?? In-Reply-To: <1454415864043-36714.post@n7.nabble.com> References: <1454415864043-36714.post@n7.nabble.com> Message-ID: Hi Vishal, you probably need to change the line in itkSiddonJacobsRayCastInterpolateImageFunction.h which says: typedef Euler3DTransform TransformType; If you make improvements, would you mind making a pull request to the repository so others can benefit from your work? Regards On Tue, Feb 2, 2016 at 7:24 AM, vishal wrote: > hi, > Im currently working on registering 2d x ray image with 3d CT volume (2d/3d > registration algorithm) and I have obtained pretty good results by using > euler 3d transform, siddon Raycast interpolator, powell optimizer and NCG > metric.. I read some post in the mailing list saying that using Versor 3d > transform for such application is feasible and I tried it unfortunately Im > not able to connect the Siddon ray cast interpolator to versor 3d > transform... this the piece of the code where im initializing the > interpolator > > const double dtr = ( atan(1.0) * 4.0 ) / 180.0; > interpolator1->SetProjectionAngle( dtr*projAngle1 ); > interpolator1->SetFocalPointToIsocenterDistance(scd); > interpolator1->SetThreshold(threshold); > interpolator1->SetTransform(transform); // this line the error occurs > interpolator1->Initialize(); > registration->SetInitialTransformParameters( transform->GetParameters() > ); > > the error is as follows.. > error C2664: > > 'itk::SiddonJacobsRayCastInterpolateImageFunction::SetTransform' > : cannot convert parameter 1 from 'itk::SmartPointer' to > 'itk::Euler3DTransform *' > D:\Project_realted_example\MyOwnCodeRegistratonWithVersor\versor.cxx 696 > > IntelliSense: no suitable conversion function from > "itk::SmartPointer>" to > "itk::Euler3DTransform *" exists > d:\Project_realted_example\MyOwnCodeRegistratonWithVersor\versor.cxx 696 > > > its seems as though it is impossible to connect siddon ray casting > interpolator to the versor 3d transform and IT ONLY WORKS with Euler3d > transform... > please give me some advice.. how can I solve this problem? > Regards > Vishal > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/problem-using-VersorRigid3DTransform-fo-2d-3d-registration-Please-advice-tp36714.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Tue Feb 2 15:37:26 2016 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 2 Feb 2016 20:37:26 +0000 Subject: [ITK] [ITK-users] Read a frame from a 3D image In-Reply-To: <38328D60-A911-4755-9375-AC3E96C8C83A@mail.nih.gov> References: , <38328D60-A911-4755-9375-AC3E96C8C83A@mail.nih.gov> Message-ID: Thanks Bradley. That sounds a bit beyond my C++ competence level. I'll go the page-splitting route. Cheers Gib ________________________________ From: Bradley Lowekamp [blowekamp at mail.nih.gov] Sent: Wednesday, 3 February 2016 3:30 a.m. To: Gib Bogle Cc: insight-users Subject: Re: [ITK] [ITK-users] Read a frame from a 3D image Gib, Currently the TIFFIO does not support streamed reading. Being able to just read a page is a straight forward first step. In fact when I refactored it I made sure it was clear how this could be done in the future [1]. The correct way to do it would be to upgrade TIFFImageIO with this feature. This would involve changing the parent class to StreamingImageIOBase, then overloading methods to disable streamed writing, and overloading the method ( GenerateStreamableReadRegionFromRequestedRegion ) to enable stream read such that the RequestedRegion is expanded to the whole slice, and verifying all the TIFF fields are valid for this operations. The tricky part would be to adapt existing tests, and test the new functionality. After that, the streaming would happen seamlessly with the ITK pipeline, giving there are stream compatible filters and all the features are configured correctly. Alternatively, there are utilities to split the pages of the TIFF in to separate files. HTH, Brad On Feb 2, 2016, at 12:25 AM, Gib Bogle > wrote: We want to work with a 3D TIFF that is much too big to fit in memory. It would be sufficient to be able to specify a 2D frame and read that. How can this be done? Thanks Gib _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From j.ascenso at campus.fct.unl.pt Tue Feb 2 16:01:47 2016 From: j.ascenso at campus.fct.unl.pt (Joao Ascenso) Date: Tue, 2 Feb 2016 21:01:47 +0000 Subject: [ITK] Canny edge detection filter results In-Reply-To: References: Message-ID: Hello again, For some reason this errors appear in itkSparceFieldLayer.hxx Error C2512 'itk::ListNode>': no appropriate default constructor available Error C2027 use of undefined type 'itk::ListNode>' Error C2227 left of '->Next' must point to class/struct/union/generic type Error C2027 use of undefined type 'itk::ListNode>' Error C2227 left of '->Previous' must point to class/struct/union/generic type They are related with the compilation of itk::CannyEdgeDetectionImageFilter. I've been using it so far with no problem. It started when I run the cmake file again and it complained about Platform Toolset v140 not being installed. I changed back to v120 to run it and those errors started. Generated project again in cmake to make sure it was with Visual Studio 12, same result. Any clues on this? Thanks On 19 January 2016 at 17:05, Joao Ascenso wrote: > Thank you D?enan. > > I did some oversampling between slices to solve the problem, with the > downside of making it much slower. > > > > On 18 January 2016 at 21:26, D?enan Zuki? wrote: > >> Hi Joao, >> >> if you are doing Canny filtering in 3D and then looking at 2D slices, the >> edges are usually not 1 pixel thick. This is because edge for 3D is a >> surface, and when you slice that surface along anatomical axes the surface >> will not be orthogonal to the slices in most places. Where surface is >> orthogonal, you get nice 1 pixel wide intersections. Where surface is >> parallel to the slice, you get a sizable intersection surface. >> >> Regards, >> D?enan >> >> On Mon, Jan 18, 2016 at 11:47 AM, Joao Ascenso < >> j.ascenso at campus.fct.unl.pt> wrote: >> >>> Hello, >>> I'm working on OCT images (DICOM volume) of the retina and trying to do >>> the segmentation of some layers. >>> >>> After doing some noise reduction I'm applying the >>> CannyEdgeDetectionImageFilter, but the result give me thicker edges than >>> should be expected from Canny. >>> >>> Changing thresholds influences the amount of edges detected but don't >>> improve this issue. >>> >>> Anyone have came across similar problem? Any suggestion is welcome. >>> >>> Thank you, >>> >>> Jo?o Ascenso >>> >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> >>> >> > > > -- > Jo?o Ascenso > Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias > Mestrado Integrado em Engenharia Electrot?cnica e de Computadores > > > -- Jo?o Ascenso Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias Mestrado Integrado em Engenharia Electrot?cnica e de Computadores -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Tue Feb 2 16:08:12 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 2 Feb 2016 16:08:12 -0500 Subject: [ITK] Canny edge detection filter results In-Reply-To: References: Message-ID: The safest cure for such things is to do a clean rebuild (create new build directory, do cmake and then open .sln file with VS and build). Let us know if you run into problems. HTH On Tue, Feb 2, 2016 at 4:01 PM, Joao Ascenso wrote: > Hello again, > > For some reason this errors appear in itkSparceFieldLayer.hxx > > Error C2512 'itk::ListNode>': no appropriate default > constructor available > Error C2027 use of undefined type 'itk::ListNode>' > Error C2227 left of '->Next' must point to class/struct/union/generic type > Error C2027 use of undefined type 'itk::ListNode>' > Error C2227 left of '->Previous' must point to class/struct/union/generic > type > > They are related with the compilation of > itk::CannyEdgeDetectionImageFilter. I've been using it so far with no > problem. It started when I run the cmake file again and it complained about > Platform Toolset v140 not being installed. I changed back to v120 to run it > and those errors started. > > Generated project again in cmake to make sure it was with Visual Studio > 12, same result. > Any clues on this? Thanks > > On 19 January 2016 at 17:05, Joao Ascenso > wrote: > >> Thank you D?enan. >> >> I did some oversampling between slices to solve the problem, with the >> downside of making it much slower. >> >> >> >> On 18 January 2016 at 21:26, D?enan Zuki? wrote: >> >>> Hi Joao, >>> >>> if you are doing Canny filtering in 3D and then looking at 2D slices, >>> the edges are usually not 1 pixel thick. This is because edge for 3D is a >>> surface, and when you slice that surface along anatomical axes the surface >>> will not be orthogonal to the slices in most places. Where surface is >>> orthogonal, you get nice 1 pixel wide intersections. Where surface is >>> parallel to the slice, you get a sizable intersection surface. >>> >>> Regards, >>> D?enan >>> >>> On Mon, Jan 18, 2016 at 11:47 AM, Joao Ascenso < >>> j.ascenso at campus.fct.unl.pt> wrote: >>> >>>> Hello, >>>> I'm working on OCT images (DICOM volume) of the retina and trying to do >>>> the segmentation of some layers. >>>> >>>> After doing some noise reduction I'm applying the >>>> CannyEdgeDetectionImageFilter, but the result give me thicker edges than >>>> should be expected from Canny. >>>> >>>> Changing thresholds influences the amount of edges detected but don't >>>> improve this issue. >>>> >>>> Anyone have came across similar problem? Any suggestion is welcome. >>>> >>>> Thank you, >>>> >>>> Jo?o Ascenso >>>> >>>> >>>> _______________________________________________ >>>> Community mailing list >>>> Community at itk.org >>>> http://public.kitware.com/mailman/listinfo/community >>>> >>>> >>> >> >> >> -- >> Jo?o Ascenso >> Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias >> Mestrado Integrado em Engenharia Electrot?cnica e de Computadores >> >> >> > > > -- > Jo?o Ascenso > Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias > Mestrado Integrado em Engenharia Electrot?cnica e de Computadores > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Tue Feb 2 16:10:55 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 2 Feb 2016 16:10:55 -0500 Subject: [ITK] [ITK-users] problem using VersorRigid3DTransform fo 2d/3d registration...Please advice?? In-Reply-To: References: <1454415864043-36714.post@n7.nabble.com> Message-ID: P.S. The up-to-date git repo is this: https://github.com/InsightSoftwareConsortium/ITKTwoProjectionRegistration and the corresponding source file: https://github.com/InsightSoftwareConsortium/ITKTwoProjectionRegistration/blob/master/include/itkSiddonJacobsRayCastInterpolateImageFunction.h Regards On Tue, Feb 2, 2016 at 3:36 PM, D?enan Zuki? wrote: > Hi Vishal, > > you probably need to change the line in > itkSiddonJacobsRayCastInterpolateImageFunction.h > > which says: > typedef Euler3DTransform TransformType; > > If you make improvements, would you mind making a pull request to the > repository so others > can benefit from your work? > > Regards > > On Tue, Feb 2, 2016 at 7:24 AM, vishal wrote: > >> hi, >> Im currently working on registering 2d x ray image with 3d CT volume >> (2d/3d >> registration algorithm) and I have obtained pretty good results by using >> euler 3d transform, siddon Raycast interpolator, powell optimizer and NCG >> metric.. I read some post in the mailing list saying that using Versor 3d >> transform for such application is feasible and I tried it unfortunately Im >> not able to connect the Siddon ray cast interpolator to versor 3d >> transform... this the piece of the code where im initializing the >> interpolator >> >> const double dtr = ( atan(1.0) * 4.0 ) / 180.0; >> interpolator1->SetProjectionAngle( dtr*projAngle1 ); >> interpolator1->SetFocalPointToIsocenterDistance(scd); >> interpolator1->SetThreshold(threshold); >> interpolator1->SetTransform(transform); // this line the error occurs >> interpolator1->Initialize(); >> registration->SetInitialTransformParameters( transform->GetParameters() >> ); >> >> the error is as follows.. >> error C2664: >> >> 'itk::SiddonJacobsRayCastInterpolateImageFunction::SetTransform' >> : cannot convert parameter 1 from 'itk::SmartPointer' to >> 'itk::Euler3DTransform *' >> D:\Project_realted_example\MyOwnCodeRegistratonWithVersor\versor.cxx >> 696 >> >> IntelliSense: no suitable conversion function from >> "itk::SmartPointer>" to >> "itk::Euler3DTransform *" exists >> d:\Project_realted_example\MyOwnCodeRegistratonWithVersor\versor.cxx >> 696 >> >> >> its seems as though it is impossible to connect siddon ray casting >> interpolator to the versor 3d transform and IT ONLY WORKS with Euler3d >> transform... >> please give me some advice.. how can I solve this problem? >> Regards >> Vishal >> >> >> >> -- >> View this message in context: >> http://itk-users.7.n7.nabble.com/problem-using-VersorRigid3DTransform-fo-2d-3d-registration-Please-advice-tp36714.html >> Sent from the ITK - Users mailing list archive at Nabble.com. >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From j.ascenso at campus.fct.unl.pt Tue Feb 2 16:24:26 2016 From: j.ascenso at campus.fct.unl.pt (Joao Ascenso) Date: Tue, 2 Feb 2016 21:24:26 +0000 Subject: [ITK] Canny edge detection filter results In-Reply-To: References: Message-ID: That's what have done. Started a new project, new directory and just using the canny filter gives me that, but no problems without it. Forget to mention I'm working with MITK. On 2 February 2016 at 21:08, D?enan Zuki? wrote: > The safest cure for such things is to do a clean rebuild (create new build > directory, do cmake and then open .sln file with VS and build). Let us know > if you run into problems. > > HTH > > On Tue, Feb 2, 2016 at 4:01 PM, Joao Ascenso > wrote: > >> Hello again, >> >> For some reason this errors appear in itkSparceFieldLayer.hxx >> >> Error C2512 'itk::ListNode>': no appropriate default >> constructor available >> Error C2027 use of undefined type 'itk::ListNode>' >> Error C2227 left of '->Next' must point to class/struct/union/generic >> type >> Error C2027 use of undefined type 'itk::ListNode>' >> Error C2227 left of '->Previous' must point to class/struct/union/generic >> type >> >> They are related with the compilation of >> itk::CannyEdgeDetectionImageFilter. I've been using it so far with no >> problem. It started when I run the cmake file again and it complained about >> Platform Toolset v140 not being installed. I changed back to v120 to run it >> and those errors started. >> >> Generated project again in cmake to make sure it was with Visual Studio >> 12, same result. >> Any clues on this? Thanks >> >> On 19 January 2016 at 17:05, Joao Ascenso >> wrote: >> >>> Thank you D?enan. >>> >>> I did some oversampling between slices to solve the problem, with the >>> downside of making it much slower. >>> >>> >>> >>> On 18 January 2016 at 21:26, D?enan Zuki? wrote: >>> >>>> Hi Joao, >>>> >>>> if you are doing Canny filtering in 3D and then looking at 2D slices, >>>> the edges are usually not 1 pixel thick. This is because edge for 3D is a >>>> surface, and when you slice that surface along anatomical axes the surface >>>> will not be orthogonal to the slices in most places. Where surface is >>>> orthogonal, you get nice 1 pixel wide intersections. Where surface is >>>> parallel to the slice, you get a sizable intersection surface. >>>> >>>> Regards, >>>> D?enan >>>> >>>> On Mon, Jan 18, 2016 at 11:47 AM, Joao Ascenso < >>>> j.ascenso at campus.fct.unl.pt> wrote: >>>> >>>>> Hello, >>>>> I'm working on OCT images (DICOM volume) of the retina and trying to >>>>> do the segmentation of some layers. >>>>> >>>>> After doing some noise reduction I'm applying the >>>>> CannyEdgeDetectionImageFilter, but the result give me thicker edges than >>>>> should be expected from Canny. >>>>> >>>>> Changing thresholds influences the amount of edges detected but don't >>>>> improve this issue. >>>>> >>>>> Anyone have came across similar problem? Any suggestion is welcome. >>>>> >>>>> Thank you, >>>>> >>>>> Jo?o Ascenso >>>>> >>>>> >>>>> _______________________________________________ >>>>> Community mailing list >>>>> Community at itk.org >>>>> http://public.kitware.com/mailman/listinfo/community >>>>> >>>>> >>>> >>> >>> >>> -- >>> Jo?o Ascenso >>> Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias >>> Mestrado Integrado em Engenharia Electrot?cnica e de Computadores >>> >>> >>> >> >> >> -- >> Jo?o Ascenso >> Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias >> Mestrado Integrado em Engenharia Electrot?cnica e de Computadores >> >> >> > -- Jo?o Ascenso Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias Mestrado Integrado em Engenharia Electrot?cnica e de Computadores -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Tue Feb 2 16:25:28 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 2 Feb 2016 16:25:28 -0500 Subject: [ITK] Canny edge detection filter results In-Reply-To: References: Message-ID: Can you share the source code of the example which uses the Canny filter? On Tue, Feb 2, 2016 at 4:24 PM, Joao Ascenso wrote: > That's what have done. Started a new project, new directory and just using > the canny filter gives me that, but no problems without it. > Forget to mention I'm working with MITK. > > > On 2 February 2016 at 21:08, D?enan Zuki? wrote: > >> The safest cure for such things is to do a clean rebuild (create new >> build directory, do cmake and then open .sln file with VS and build). Let >> us know if you run into problems. >> >> HTH >> >> On Tue, Feb 2, 2016 at 4:01 PM, Joao Ascenso > > wrote: >> >>> Hello again, >>> >>> For some reason this errors appear in itkSparceFieldLayer.hxx >>> >>> Error C2512 'itk::ListNode>': no appropriate default >>> constructor available >>> Error C2027 use of undefined type 'itk::ListNode>' >>> Error C2227 left of '->Next' must point to class/struct/union/generic >>> type >>> Error C2027 use of undefined type 'itk::ListNode>' >>> Error C2227 left of '->Previous' must point to >>> class/struct/union/generic type >>> >>> They are related with the compilation of >>> itk::CannyEdgeDetectionImageFilter. I've been using it so far with no >>> problem. It started when I run the cmake file again and it complained about >>> Platform Toolset v140 not being installed. I changed back to v120 to run it >>> and those errors started. >>> >>> Generated project again in cmake to make sure it was with Visual Studio >>> 12, same result. >>> Any clues on this? Thanks >>> >>> On 19 January 2016 at 17:05, Joao Ascenso >>> wrote: >>> >>>> Thank you D?enan. >>>> >>>> I did some oversampling between slices to solve the problem, with the >>>> downside of making it much slower. >>>> >>>> >>>> >>>> On 18 January 2016 at 21:26, D?enan Zuki? wrote: >>>> >>>>> Hi Joao, >>>>> >>>>> if you are doing Canny filtering in 3D and then looking at 2D slices, >>>>> the edges are usually not 1 pixel thick. This is because edge for 3D is a >>>>> surface, and when you slice that surface along anatomical axes the surface >>>>> will not be orthogonal to the slices in most places. Where surface is >>>>> orthogonal, you get nice 1 pixel wide intersections. Where surface is >>>>> parallel to the slice, you get a sizable intersection surface. >>>>> >>>>> Regards, >>>>> D?enan >>>>> >>>>> On Mon, Jan 18, 2016 at 11:47 AM, Joao Ascenso < >>>>> j.ascenso at campus.fct.unl.pt> wrote: >>>>> >>>>>> Hello, >>>>>> I'm working on OCT images (DICOM volume) of the retina and trying to >>>>>> do the segmentation of some layers. >>>>>> >>>>>> After doing some noise reduction I'm applying the >>>>>> CannyEdgeDetectionImageFilter, but the result give me thicker edges than >>>>>> should be expected from Canny. >>>>>> >>>>>> Changing thresholds influences the amount of edges detected but don't >>>>>> improve this issue. >>>>>> >>>>>> Anyone have came across similar problem? Any suggestion is welcome. >>>>>> >>>>>> Thank you, >>>>>> >>>>>> Jo?o Ascenso >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Community mailing list >>>>>> Community at itk.org >>>>>> http://public.kitware.com/mailman/listinfo/community >>>>>> >>>>>> >>>>> >>>> >>>> >>>> -- >>>> Jo?o Ascenso >>>> Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias >>>> Mestrado Integrado em Engenharia Electrot?cnica e de Computadores >>>> >>>> >>>> >>> >>> >>> -- >>> Jo?o Ascenso >>> Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias >>> Mestrado Integrado em Engenharia Electrot?cnica e de Computadores >>> >>> >>> >> > > > -- > Jo?o Ascenso > Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias > Mestrado Integrado em Engenharia Electrot?cnica e de Computadores > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zivrafael.yaniv at nih.gov Tue Feb 2 16:26:20 2016 From: zivrafael.yaniv at nih.gov (Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]) Date: Tue, 2 Feb 2016 21:26:20 +0000 Subject: [ITK] [ITK-users] SimpleITK, Python, Local User, Anaconda -- how to install without messing up shared libraries? Message-ID: Hello Robert, We understand our documentation was not sufficiently clear, so we have updated our installation instructions page (http://www.itk.org/Wiki/SimpleITK/GettingStarted). Hopefully the instructions are clearer now. Instructions for anaconda: 0. See which virtual environments already exist: $ conda info -e 1. Assuming sitkpy doesn't exist, create it and install SimpleITK there: $ conda create -n sitkpy -c https://conda.binstar.org/simpleitk python=3.4 anaconda SimpleITK 2. Activate the environment and start working: $ source activate sitkpy If there is no binary distribution for your operating system, step 1 fails, then you will have to build from source using our conda-recipe: $ git clone https://github.com/conda/conda-recipes.git $ cd conda-recipes $ conda build simpleitk This will take a while as it will download the source and compile everything. We assume you have git and a supported compiler installed. For more information on conda recipes see the conda documentation http://conda.pydata.org/docs/building/recipe.html. Ziv On 2/2/16, 6:58 AM, "Robert.Atwood at diamond.ac.uk" wrote: > >Hi, ITK people! > > >I don't maintain the Python installation at work so I know little about >all the intricacies of python modules and distributions and path >searching and so on. >What I do know is that if I follow the instructions for including >SimpleITK as on the web page for Anacoda installation, everyone gets very >angry. >That is because it automatically resolves some dependencies in a way that >breaks other people's applications, and it does this within the shared >Python Anaconda installation on the cluster shared file system. > >It was suggested (strongly) that I "use the --user option of pip" . >However I cannot get this to do anything by following the pip instruction >on the SimpleITK web site, I know nothing of eggs and wheels nor pipit >nor "more complicated commands. " > >Does anyone know the magic incantation to do what I want? Is there an >Anaconda command that does it? > > >Instructions from website with questions annotated: > >Wheels [ Recommended ] >You need a recent version of pip ( >= 6.0, newer is better) to install >wheels. Please go to pip homepage for more information about installation. >Once you have pip, the package can be installed: >$ pip install --allow-external SimpleITK --trusted-host www.simpleitk.org >SimpleITK --timeout 30 SimpleITK >Note: We do have window wheels hosted on pypi, but due to size and Linux >binary restrictions neither OS X nor Linux are hosted on pipit, so the >more complicated command is needed(1). >However, you may need to manually download the file(2) from SourceForge. >And specify it (3) on the command line if the automatic search does not >work. > >(1) What is the 'more complicated command' ??? >(2) Which file? An egg? Wheel? Huh? >(3) Specify what? How (what is the syntax for specifying 'it' )? > > >Output of session trying to follow the instructions. > >$ pip install --user --allow-external SimpleITK --trusted-host >www.simpleitk.org SimpleITK --timeout 30 SimpleITK >Double requirement given: SimpleITK (already in SimpleITK, >name='SimpleITK') >You are using pip version 7.1.2, however version 8.0.2 is available. >You should consider upgrading via the 'pip install --upgrade pip' command. >[kny48981 at i12-ws011 6137]$ pip install --user --allow-external SimpleITK >--trusted-host www.simpleitk.org --timeout 30 SimpleITK >Collecting SimpleITK > Could not find a version that satisfies the requirement SimpleITK (from >versions: ) >No matching distribution found for SimpleITK >You are using pip version 7.1.2, however version 8.0.2 is available. >You should consider upgrading via the 'pip install --upgrade pip' command. >[kny48981 at i12-ws011 6137]$ pip install --user --allow-external SimpleITK >--trusted-host www.simpleitk.org SimpleITK >Collecting SimpleITK > Could not find a version that satisfies the requirement SimpleITK (from >versions: ) >No matching distribution found for SimpleITK >You are using pip version 7.1.2, however version 8.0.2 is available. >You should consider upgrading via the 'pip install --upgrade pip' command. >[kny48981 at i12-ws011 6137]$ pip install --user --allow-external >--trusted-host www.simpleitk.org SimpleITK >Collecting www.simpleitk.org > Could not find a version that satisfies the requirement >www.simpleitk.org (from versions: ) >No matching distribution found for www.simpleitk.org >You are using pip version 7.1.2, however version 8.0.2 is available. >You should consider upgrading via the 'pip install --upgrade pip' command. > > > > > > > > > >-- >This e-mail and any attachments may contain confidential, copyright and >or privileged material, and are for the use of the intended addressee >only. If you are not the intended addressee or an authorised recipient of >the addressee please notify us of receipt by returning the e-mail and do >not use, copy, retain, distribute or disclose the information in or >attached to the e-mail. >Any opinions expressed within this e-mail are those of the individual and >not necessarily of Diamond Light Source Ltd. >Diamond Light Source Ltd. cannot guarantee that this e-mail or any >attachments are free from viruses and we cannot accept liability for any >damage which you may sustain as a result of software viruses which may be >transmitted in or with the message. >Diamond Light Source Limited (company no. 4375679). Registered in England >and Wales with its registered office at Diamond House, Harwell Science >and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > >_____________________________________ >Powered by www.kitware.com > >Visit other Kitware open-source projects at >http://www.kitware.com/opensource/opensource.html > >Kitware offers ITK Training Courses, for more information visit: >http://www.kitware.com/products/protraining.php > >Please keep messages on-topic and check the ITK FAQ at: >http://www.itk.org/Wiki/ITK_FAQ > >Follow this link to subscribe/unsubscribe: >http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From j.ascenso at campus.fct.unl.pt Tue Feb 2 16:59:17 2016 From: j.ascenso at campus.fct.unl.pt (Joao Ascenso) Date: Tue, 2 Feb 2016 21:59:17 +0000 Subject: [ITK] Canny edge detection filter results In-Reply-To: References: Message-ID: A simple test I made. Just getting this example http://docs.mitk.org/nightly/Step01Page.html with no use of the filters Added #include #include and in the end void canny(){ typedef itk::Image ImageType; typedef itk::CannyEdgeDetectionImageFilter CannyFilter; CannyFilter::Pointer filter = CannyFilter::New(); } void derivative(){ typedef itk::Image ImageType; typedef itk::DerivativeImageFilter DerivativeFilter; DerivativeFilter::Pointer filter = DerivativeFilter::New(); } Only with derivative() builds successful and shows image added canny() gets the errors On 2 February 2016 at 21:25, D?enan Zuki? wrote: > Can you share the source code of the example which uses the Canny filter? > > On Tue, Feb 2, 2016 at 4:24 PM, Joao Ascenso > wrote: > >> That's what have done. Started a new project, new directory and just using >> the canny filter gives me that, but no problems without it. >> Forget to mention I'm working with MITK. >> >> >> On 2 February 2016 at 21:08, D?enan Zuki? wrote: >> >>> The safest cure for such things is to do a clean rebuild (create new >>> build directory, do cmake and then open .sln file with VS and build). Let >>> us know if you run into problems. >>> >>> HTH >>> >>> On Tue, Feb 2, 2016 at 4:01 PM, Joao Ascenso < >>> j.ascenso at campus.fct.unl.pt> wrote: >>> >>>> Hello again, >>>> >>>> For some reason this errors appear in itkSparceFieldLayer.hxx >>>> >>>> Error C2512 'itk::ListNode>': no appropriate default >>>> constructor available >>>> Error C2027 use of undefined type 'itk::ListNode>' >>>> Error C2227 left of '->Next' must point to class/struct/union/generic >>>> type >>>> Error C2027 use of undefined type 'itk::ListNode>' >>>> Error C2227 left of '->Previous' must point to >>>> class/struct/union/generic type >>>> >>>> They are related with the compilation of >>>> itk::CannyEdgeDetectionImageFilter. I've been using it so far with no >>>> problem. It started when I run the cmake file again and it complained about >>>> Platform Toolset v140 not being installed. I changed back to v120 to run it >>>> and those errors started. >>>> >>>> Generated project again in cmake to make sure it was with Visual Studio >>>> 12, same result. >>>> Any clues on this? Thanks >>>> >>>> On 19 January 2016 at 17:05, Joao Ascenso >>>> wrote: >>>> >>>>> Thank you D?enan. >>>>> >>>>> I did some oversampling between slices to solve the problem, with the >>>>> downside of making it much slower. >>>>> >>>>> >>>>> >>>>> On 18 January 2016 at 21:26, D?enan Zuki? wrote: >>>>> >>>>>> Hi Joao, >>>>>> >>>>>> if you are doing Canny filtering in 3D and then looking at 2D slices, >>>>>> the edges are usually not 1 pixel thick. This is because edge for 3D is a >>>>>> surface, and when you slice that surface along anatomical axes the surface >>>>>> will not be orthogonal to the slices in most places. Where surface is >>>>>> orthogonal, you get nice 1 pixel wide intersections. Where surface is >>>>>> parallel to the slice, you get a sizable intersection surface. >>>>>> >>>>>> Regards, >>>>>> D?enan >>>>>> >>>>>> On Mon, Jan 18, 2016 at 11:47 AM, Joao Ascenso < >>>>>> j.ascenso at campus.fct.unl.pt> wrote: >>>>>> >>>>>>> Hello, >>>>>>> I'm working on OCT images (DICOM volume) of the retina and trying to >>>>>>> do the segmentation of some layers. >>>>>>> >>>>>>> After doing some noise reduction I'm applying the >>>>>>> CannyEdgeDetectionImageFilter, but the result give me thicker edges than >>>>>>> should be expected from Canny. >>>>>>> >>>>>>> Changing thresholds influences the amount of edges detected but >>>>>>> don't improve this issue. >>>>>>> >>>>>>> Anyone have came across similar problem? Any suggestion is welcome. >>>>>>> >>>>>>> Thank you, >>>>>>> >>>>>>> Jo?o Ascenso >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Community mailing list >>>>>>> Community at itk.org >>>>>>> http://public.kitware.com/mailman/listinfo/community >>>>>>> >>>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Jo?o Ascenso >>>>> Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias >>>>> Mestrado Integrado em Engenharia Electrot?cnica e de Computadores >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Jo?o Ascenso >>>> Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias >>>> Mestrado Integrado em Engenharia Electrot?cnica e de Computadores >>>> >>>> >>>> >>> >> >> >> -- >> Jo?o Ascenso >> Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias >> Mestrado Integrado em Engenharia Electrot?cnica e de Computadores >> >> >> > -- Jo?o Ascenso Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias Mestrado Integrado em Engenharia Electrot?cnica e de Computadores -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Tue Feb 2 17:13:30 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 2 Feb 2016 17:13:30 -0500 Subject: [ITK] Canny edge detection filter results In-Reply-To: References: Message-ID: The following example compiles for me. I guess the trick is in MITK, so you should ask them for help. #include #include void canny(){ typedef itk::Image ImageType; typedef itk::CannyEdgeDetectionImageFilter CannyFilter; CannyFilter::Pointer filter = CannyFilter::New(); } void derivative(){ typedef itk::Image ImageType; typedef itk::DerivativeImageFilter DerivativeFilter; DerivativeFilter::Pointer filter = DerivativeFilter::New(); } int main(){} On Tue, Feb 2, 2016 at 4:59 PM, Joao Ascenso wrote: > A simple test I made. Just getting this example > http://docs.mitk.org/nightly/Step01Page.html with no use of the filters > > Added #include > #include > > > and in the end > > void canny(){ > typedef itk::Image ImageType; > typedef itk::CannyEdgeDetectionImageFilter > CannyFilter; > > CannyFilter::Pointer filter = CannyFilter::New(); > } > > void derivative(){ > typedef itk::Image ImageType; > typedef itk::DerivativeImageFilter DerivativeFilter; > > DerivativeFilter::Pointer filter = DerivativeFilter::New(); > } > > > Only with derivative() builds successful and shows image > > added canny() gets the errors > > > On 2 February 2016 at 21:25, D?enan Zuki? wrote: > >> Can you share the source code of the example which uses the Canny filter? >> >> On Tue, Feb 2, 2016 at 4:24 PM, Joao Ascenso > > wrote: >> >>> That's what have done. Started a new project, new directory and just >>> using the canny filter gives me that, but no problems without it. >>> Forget to mention I'm working with MITK. >>> >>> >>> On 2 February 2016 at 21:08, D?enan Zuki? wrote: >>> >>>> The safest cure for such things is to do a clean rebuild (create new >>>> build directory, do cmake and then open .sln file with VS and build). Let >>>> us know if you run into problems. >>>> >>>> HTH >>>> >>>> On Tue, Feb 2, 2016 at 4:01 PM, Joao Ascenso < >>>> j.ascenso at campus.fct.unl.pt> wrote: >>>> >>>>> Hello again, >>>>> >>>>> For some reason this errors appear in itkSparceFieldLayer.hxx >>>>> >>>>> Error C2512 'itk::ListNode>': no appropriate default >>>>> constructor available >>>>> Error C2027 use of undefined type 'itk::ListNode>' >>>>> Error C2227 left of '->Next' must point to class/struct/union/generic >>>>> type >>>>> Error C2027 use of undefined type 'itk::ListNode>' >>>>> Error C2227 left of '->Previous' must point to >>>>> class/struct/union/generic type >>>>> >>>>> They are related with the compilation of >>>>> itk::CannyEdgeDetectionImageFilter. I've been using it so far with no >>>>> problem. It started when I run the cmake file again and it complained about >>>>> Platform Toolset v140 not being installed. I changed back to v120 to run it >>>>> and those errors started. >>>>> >>>>> Generated project again in cmake to make sure it was with Visual >>>>> Studio 12, same result. >>>>> Any clues on this? Thanks >>>>> >>>>> On 19 January 2016 at 17:05, Joao Ascenso >>>> > wrote: >>>>> >>>>>> Thank you D?enan. >>>>>> >>>>>> I did some oversampling between slices to solve the problem, with the >>>>>> downside of making it much slower. >>>>>> >>>>>> >>>>>> >>>>>> On 18 January 2016 at 21:26, D?enan Zuki? wrote: >>>>>> >>>>>>> Hi Joao, >>>>>>> >>>>>>> if you are doing Canny filtering in 3D and then looking at 2D >>>>>>> slices, the edges are usually not 1 pixel thick. This is because edge for >>>>>>> 3D is a surface, and when you slice that surface along anatomical axes the >>>>>>> surface will not be orthogonal to the slices in most places. Where surface >>>>>>> is orthogonal, you get nice 1 pixel wide intersections. Where surface is >>>>>>> parallel to the slice, you get a sizable intersection surface. >>>>>>> >>>>>>> Regards, >>>>>>> D?enan >>>>>>> >>>>>>> On Mon, Jan 18, 2016 at 11:47 AM, Joao Ascenso < >>>>>>> j.ascenso at campus.fct.unl.pt> wrote: >>>>>>> >>>>>>>> Hello, >>>>>>>> I'm working on OCT images (DICOM volume) of the retina and trying >>>>>>>> to do the segmentation of some layers. >>>>>>>> >>>>>>>> After doing some noise reduction I'm applying the >>>>>>>> CannyEdgeDetectionImageFilter, but the result give me thicker edges than >>>>>>>> should be expected from Canny. >>>>>>>> >>>>>>>> Changing thresholds influences the amount of edges detected but >>>>>>>> don't improve this issue. >>>>>>>> >>>>>>>> Anyone have came across similar problem? Any suggestion is welcome. >>>>>>>> >>>>>>>> Thank you, >>>>>>>> >>>>>>>> Jo?o Ascenso >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Community mailing list >>>>>>>> Community at itk.org >>>>>>>> http://public.kitware.com/mailman/listinfo/community >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Jo?o Ascenso >>>>>> Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias >>>>>> Mestrado Integrado em Engenharia Electrot?cnica e de Computadores >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Jo?o Ascenso >>>>> Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias >>>>> Mestrado Integrado em Engenharia Electrot?cnica e de Computadores >>>>> >>>>> >>>>> >>>> >>> >>> >>> -- >>> Jo?o Ascenso >>> Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias >>> Mestrado Integrado em Engenharia Electrot?cnica e de Computadores >>> >>> >>> >> > > > -- > Jo?o Ascenso > Universidade Nova de Lisboa - Faculdade de Ci?ncias e Tecnologias > Mestrado Integrado em Engenharia Electrot?cnica e de Computadores > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.bogle at auckland.ac.nz Tue Feb 2 18:48:46 2016 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 2 Feb 2016 23:48:46 +0000 Subject: [ITK] [ITK-users] Using ImageFileReader iteratively Message-ID: I am reading a set of 2D image files, like this: typedef itk::Image ImageType2; // 2D image ImageType2::Pointer im2; unsigned char *p2; typedef itk::ImageFileReader FileReaderType; FileReaderType::Pointer reader = FileReaderType::New(); for (z=0; zSetFileName(frame_file); try { reader->Update(); printf("did reader->update\n"); } catch (itk::ExceptionObject &e) { std::cout << e << std::endl; return 2; } im2 = reader->GetOutput(); printf("got im2\n"); ... } This reads the first 2D file, but the next time through the loop it crashes while executing reader->Update(). What am I doing wrong? Thanks Gib -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Feb 2 21:17:04 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 2 Feb 2016 21:17:04 -0500 Subject: [ITK] [ITK-users] Using ImageFileReader iteratively In-Reply-To: References: Message-ID: Hi Gib, It may be related to what is happening in "...". Try im2->DisconnectPipeline(); after im2 = reader->GetOutput(); This will disassociate the output image from the reader object, and the reader will create a new output image in the next iteration of the loop. HTH, Matt On Tue, Feb 2, 2016 at 6:48 PM, Gib Bogle wrote: > I am reading a set of 2D image files, like this: > > typedef itk::Image ImageType2; // 2D image > ImageType2::Pointer im2; > unsigned char *p2; > > typedef itk::ImageFileReader FileReaderType; > FileReaderType::Pointer reader = FileReaderType::New(); > > for (z=0; z ... // make frame_file > printf("frame_file: %s\n",frame_file); > reader->SetFileName(frame_file); > try > { > reader->Update(); > printf("did reader->update\n"); > } > catch (itk::ExceptionObject &e) > { > std::cout << e << std::endl; > return 2; > } > > im2 = reader->GetOutput(); > printf("got im2\n"); > ... > } > > This reads the first 2D file, but the next time through the loop it crashes > while executing reader->Update(). > What am I doing wrong? > > Thanks > Gib > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Tue Feb 2 21:48:34 2016 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 3 Feb 2016 02:48:34 +0000 Subject: [ITK] [ITK-users] Using ImageFileReader iteratively In-Reply-To: References: , Message-ID: Hi Matt, Indeed it was! Just a careless oversight. It's all working now. Cheers, Gib ________________________________________ From: Matt McCormick [matt.mccormick at kitware.com] Sent: Wednesday, 3 February 2016 3:17 p.m. To: Gib Bogle Cc: insight-users Subject: Re: [ITK-users] Using ImageFileReader iteratively Hi Gib, It may be related to what is happening in "...". Try im2->DisconnectPipeline(); after im2 = reader->GetOutput(); This will disassociate the output image from the reader object, and the reader will create a new output image in the next iteration of the loop. HTH, Matt On Tue, Feb 2, 2016 at 6:48 PM, Gib Bogle wrote: > I am reading a set of 2D image files, like this: > > typedef itk::Image ImageType2; // 2D image > ImageType2::Pointer im2; > unsigned char *p2; > > typedef itk::ImageFileReader FileReaderType; > FileReaderType::Pointer reader = FileReaderType::New(); > > for (z=0; z ... // make frame_file > printf("frame_file: %s\n",frame_file); > reader->SetFileName(frame_file); > try > { > reader->Update(); > printf("did reader->update\n"); > } > catch (itk::ExceptionObject &e) > { > std::cout << e << std::endl; > return 2; > } > > im2 = reader->GetOutput(); > printf("got im2\n"); > ... > } > > This reads the first 2D file, but the next time through the loop it crashes > while executing reader->Update(). > What am I doing wrong? > > Thanks > Gib > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From itkhelpacc at gmail.com Tue Feb 2 23:46:18 2016 From: itkhelpacc at gmail.com (vishal) Date: Tue, 2 Feb 2016 21:46:18 -0700 (MST) Subject: [ITK] [ITK-users] problem using VersorRigid3DTransform fo 2d/3d registration...Please advice?? In-Reply-To: References: <1454415864043-36714.post@n7.nabble.com> Message-ID: <1454474778171-36725.post@n7.nabble.com> hi D?enan, thank you for advice.. il post the result after i have made the changes.. Regards Vishal -- View this message in context: http://itk-users.7.n7.nabble.com/problem-using-VersorRigid3DTransform-fo-2d-3d-registration-Please-advice-tp36714p36725.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From cyril.mory at uclouvain.be Wed Feb 3 04:22:42 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Wed, 3 Feb 2016 10:22:42 +0100 Subject: [ITK] [ITK-users] Reading 4d image using SimpleITK Message-ID: <56B1C6E2.9000304@uclouvain.be> Hi ITK users, I have more or less the same goal as Andriy had five years ago: I need to read a 4D image, and extract 2D slices from it to serve as figures in a paper. I was wondering if there was a quick way to break my 4D image down into 3D images using SimpleITK. Cyril On Wed, Dec 14, 2011 at 5:06 PM, Bradley Lowekamp > wrote: >/There is nothing really in the architecture that is specific to 2D and 3D. However, there are numerous compile assertions and other methods to ensure that we are only instantiating filters and objects as we expect to. So there is no quick way of enabling 4D images in simpleITK. />// Ok, makes sense. >/You just indicate that you want to read the image. What do you plan on doing with it after that? />// At this point, I just want to do some plotting of time course curves. I will break it down into individual time frames, and load frame-by-frame, no big deal. Thank you. >/Brad />//>>//>>/AF />>//>>//>>//>>/On Wed, Dec 14, 2011 at 4:39 PM, Bradley Lowekamp />>/> wrote: />>>/Hello Andriy, />>>//>>>/SimpleITK only supports 2D and 3D sitk::Images. />>>//>>>/Could you please share a little more about the image you are trying to read? />>>/What type is it and what is the meta data that ITK's ImageIO sees when it />>>/reads the header (ie Number of Dimensions, Size of the dimensions, etc...)? />>>/I would like to be able to reproduce your problem. />>>//>>>/When ITK's ImageFileReader is instantiated over a dimension that is less />>>/than that the file is reporting it will generally, just read that first />>>/hyper-slice. We could do similar behavior is SimpleITK. Always try to read, />>>/and print a warning if the dimensions is higher. />>>//>>>/Another feature that is planned, is the support for reading ROI's. I had not />>>/previously thought about the possibility of this feature enabling support />>>/for reading higher dimension images into 3D images, but is may be possible. />>>//>>>/Brad />>>//>>>/======================================================== />>>//>>>/Bradley Lowekamp />>>//>>>/Medical Science and Computing for />>>//>>>/Office of High Performance Computing and Communications />>>//>>>/National Library of Medicine />>>//>>>/blowekamp at mail.nih.gov />>>//>>>//>>>/On Dec 14, 2011, at 4:29 PM, Andriy Fedorov wrote: />>>//>>>/Hi, />>>//>>>/I would like to be able to read a 4d image using SimpleITK. />>>//>>>/Currently, this is not allowed />>>/(https://github.com/SimpleITK/SimpleITK/blob/master/Code/IO/src/sitkImageFileReader.cxx#L44). />>>//>>>/Can someone give me an idea what it takes to enable this feature? />>>//>>>/Thanks />>>//>>>/AF />>>/_____________________________________ />>>/Powered by www.kitware.com />>>//>>>/Visit other Kitware open-source projects at />>>/http://www.kitware.com/opensource/opensource.html />>>//>>>/Kitware offers ITK Training Courses, for more information visit: />>>/http://www.kitware.com/products/protraining.html />>>//>>>/Please keep messages on-topic and check the ITK FAQ at: />>>/http://www.itk.org/Wiki/ITK_FAQ />>>//>>>/Follow this link to subscribe/unsubscribe: />>>/http://www.itk.org/mailman/listinfo/insight-users />>>//>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From tevain at telecom-paristech.fr Wed Feb 3 07:04:41 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Wed, 3 Feb 2016 13:04:41 +0100 (CET) Subject: [ITK] [ITK-users] Reading 4d image using SimpleITK In-Reply-To: <56B1C6E2.9000304@uclouvain.be> References: <56B1C6E2.9000304@uclouvain.be> Message-ID: <1077484351.12010208.1454501081539.JavaMail.zimbra@enst.fr> Hello, I'm not an user of SimpleITK, but it seems that you can now build the library with an cmake option to support 4D images (since release ~0.9?). If you are able to do so, you can then use the ExtractImageFilter to get your 3D/2D data : http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ExtractImageFilter.html HTH, Tim ----- Mail original ----- De: "Cyril Mory" ?: insight-users at itk.org Envoy?: Mercredi 3 F?vrier 2016 10:22:42 Objet: [ITK] [ITK-users] Reading 4d image using SimpleITK Hi ITK users, I have more or less the same goal as Andriy had five years ago: I need to read a 4D image, and extract 2D slices from it to serve as figures in a paper. I was wondering if there was a quick way to break my 4D image down into 3D images using SimpleITK. Cyril On Wed, Dec 14, 2011 at 5:06 PM, Bradley Lowekamp < blowekamp at mail.nih.gov > wrote: > There is nothing really in the architecture that is specific to 2D and 3D. However, there are numerous compile assertions and other methods to ensure that we are only instantiating filters and objects as we expect to. So there is no quick way of enabling 4D images in simpleITK. > Ok, makes sense. > You just indicate that you want to read the image. What do you plan on doing with it after that? > At this point, I just want to do some plotting of time course curves. I will break it down into individual time frames, and load frame-by-frame, no big deal. Thank you. > Brad > >> >> AF >> >> >> >> On Wed, Dec 14, 2011 at 4:39 PM, Bradley Lowekamp >> < blowekamp at mail.nih.gov > wrote: >>> Hello Andriy, >>> >>> SimpleITK only supports 2D and 3D sitk::Images. >>> >>> Could you please share a little more about the image you are trying to read? >>> What type is it and what is the meta data that ITK's ImageIO sees when it >>> reads the header (ie Number of Dimensions, Size of the dimensions, etc...)? >>> I would like to be able to reproduce your problem. >>> >>> When ITK's ImageFileReader is instantiated over a dimension that is less >>> than that the file is reporting it will generally, just read that first >>> hyper-slice. We could do similar behavior is SimpleITK. Always try to read, >>> and print a warning if the dimensions is higher. >>> >>> Another feature that is planned, is the support for reading ROI's. I had not >>> previously thought about the possibility of this feature enabling support >>> for reading higher dimension images into 3D images, but is may be possible. >>> >>> Brad >>> >>> ======================================================== >>> >>> Bradley Lowekamp >>> >>> Medical Science and Computing for >>> >>> Office of High Performance Computing and Communications >>> >>> National Library of Medicine >>> >>> blowekamp at mail.nih.gov >>> >>> >>> On Dec 14, 2011, at 4:29 PM, Andriy Fedorov wrote: >>> >>> Hi, >>> >>> I would like to be able to read a 4d image using SimpleITK. >>> >>> Currently, this is not allowed >>> ( https://github.com/SimpleITK/SimpleITK/blob/master/Code/IO/src/sitkImageFileReader.cxx#L44 ). >>> >>> Can someone give me an idea what it takes to enable this feature? >>> >>> Thanks >>> >>> AF >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.html >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://www.itk.org/mailman/listinfo/insight-users >>> >>> _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From Robert.Atwood at diamond.ac.uk Wed Feb 3 05:42:29 2016 From: Robert.Atwood at diamond.ac.uk (Robert.Atwood at diamond.ac.uk) Date: Wed, 3 Feb 2016 10:42:29 +0000 Subject: [ITK] [ITK-users] SimpleITK, Python, Local User, Anaconda -- how to install without messing up shared libraries? In-Reply-To: References: Message-ID: <6CCDD8FC6578314C902BBF87D511D9D8EA6743D2@EXCHMBX01.fed.cclrc.ac.uk> Thank you very much! The detailed instruction is greatly appreciated (and especially by the other users of the shared installation of Python) So far I used the following command: pip install --user SimpleITK-0.9.1-cp26-none-linux_x86_64.whl I would make the instruction for such installation: a) Download the appropriate .whl file from Sourceforge(link) The file name scheme is as follows: SimpleITK-version-PYTHON-????-os-platform.whl, where 'version' is the SimpleITK version, 'PYTHON' (I don't completely understand this version , what are the letters 'cp' for?) is the Python version, ???? is ???? (I don't see what this 'none' is for?), 'os' is the operating system (Linux, win ..) and 'platform' is the hardware platform. (x86-64, i386, etc) b) Run the pip command with --user flag and with the target as the downloaded .whl file , e.g. pip install --user SimpleITK-version-PYTHON-????-os-platform.whl This will install the Python library in the user's local file ~/.local/lib/python.X.x/site-packages Thanks Robert ____________________ Dr. Robert C. Atwood Senior Support Scientist Beamline I12-JEEP The Joint Engineering and Environmental Processing Beamline Diamond Light Source The Harwell Science and Innovation Campus Didcot,OXON OX11 0DE +44 (0) 1235 778 670 > -----Original Message----- > From: Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] [mailto:zivrafael.yaniv at nih.gov] > Sent: 02 February 2016 21:26 > To: Atwood, Robert (DLSLtd,RAL,SCI); insight-users at itk.org > Subject: Re: [ITK-users] SimpleITK, Python, Local User, Anaconda -- how to > install without messing up shared libraries? > > Hello Robert, > > We understand our documentation was not sufficiently clear, so we have > updated our installation instructions page > (http://www.itk.org/Wiki/SimpleITK/GettingStarted). Hopefully the > instructions are clearer now. > > Instructions for anaconda: > 0. See which virtual environments already exist: > $ conda info -e > 1. Assuming sitkpy doesn't exist, create it and install SimpleITK there: > $ conda create -n sitkpy -c https://conda.binstar.org/simpleitk > python=3.4 anaconda SimpleITK > 2. Activate the environment and start working: > $ source activate sitkpy > > > If there is no binary distribution for your operating system, step 1 fails, then > you will have to build from source using our conda-recipe: > > $ git clone https://github.com/conda/conda-recipes.git > $ cd conda-recipes > $ conda build simpleitk > > This will take a while as it will download the source and compile everything. > We assume you have git and a supported compiler installed. For more > information on conda recipes see the conda documentation > http://conda.pydata.org/docs/building/recipe.html. > > Ziv > > > > > > > > On 2/2/16, 6:58 AM, "Robert.Atwood at diamond.ac.uk" > wrote: > > > > >Hi, ITK people! > > > > > >I don't maintain the Python installation at work so I know little about > >all the intricacies of python modules and distributions and path > >searching and so on. > >What I do know is that if I follow the instructions for including > >SimpleITK as on the web page for Anacoda installation, everyone gets > >very angry. > >That is because it automatically resolves some dependencies in a way > >that breaks other people's applications, and it does this within the > >shared Python Anaconda installation on the cluster shared file system. > > > >It was suggested (strongly) that I "use the --user option of pip" . > >However I cannot get this to do anything by following the pip > >instruction on the SimpleITK web site, I know nothing of eggs and > >wheels nor pipit nor "more complicated commands. " > > > >Does anyone know the magic incantation to do what I want? Is there an > >Anaconda command that does it? > > > > > >Instructions from website with questions annotated: > > > >Wheels [ Recommended ] > >You need a recent version of pip ( >= 6.0, newer is better) to install > >wheels. Please go to pip homepage for more information about installation. > >Once you have pip, the package can be installed: > >$ pip install --allow-external SimpleITK --trusted-host > >www.simpleitk.org SimpleITK --timeout 30 SimpleITK > >Note: We do have window wheels hosted on pypi, but due to size and > >Linux binary restrictions neither OS X nor Linux are hosted on pipit, > >so the more complicated command is needed(1). > >However, you may need to manually download the file(2) from SourceForge. > >And specify it (3) on the command line if the automatic search does not > >work. > > > >(1) What is the 'more complicated command' ??? > >(2) Which file? An egg? Wheel? Huh? > >(3) Specify what? How (what is the syntax for specifying 'it' )? > > > > > >Output of session trying to follow the instructions. > > > >$ pip install --user --allow-external SimpleITK --trusted-host > >www.simpleitk.org SimpleITK --timeout 30 SimpleITK Double requirement > >given: SimpleITK (already in SimpleITK, > >name='SimpleITK') > >You are using pip version 7.1.2, however version 8.0.2 is available. > >You should consider upgrading via the 'pip install --upgrade pip' command. > >[kny48981 at i12-ws011 6137]$ pip install --user --allow-external SimpleITK > >--trusted-host www.simpleitk.org --timeout 30 SimpleITK > >Collecting SimpleITK > > Could not find a version that satisfies the requirement SimpleITK > >(from > >versions: ) > >No matching distribution found for SimpleITK You are using pip version > >7.1.2, however version 8.0.2 is available. > >You should consider upgrading via the 'pip install --upgrade pip' command. > >[kny48981 at i12-ws011 6137]$ pip install --user --allow-external > >SimpleITK --trusted-host www.simpleitk.org SimpleITK Collecting > >SimpleITK > > Could not find a version that satisfies the requirement SimpleITK > >(from > >versions: ) > >No matching distribution found for SimpleITK You are using pip version > >7.1.2, however version 8.0.2 is available. > >You should consider upgrading via the 'pip install --upgrade pip' command. > >[kny48981 at i12-ws011 6137]$ pip install --user --allow-external > >--trusted-host www.simpleitk.org SimpleITK Collecting www.simpleitk.org > > Could not find a version that satisfies the requirement > >www.simpleitk.org (from versions: ) No matching distribution found for > >www.simpleitk.org You are using pip version 7.1.2, however version > >8.0.2 is available. > >You should consider upgrading via the 'pip install --upgrade pip' command. > > > > > > > > > > > > > > > > > > > >-- > >This e-mail and any attachments may contain confidential, copyright and > >or privileged material, and are for the use of the intended addressee > >only. If you are not the intended addressee or an authorised recipient > >of the addressee please notify us of receipt by returning the e-mail > >and do not use, copy, retain, distribute or disclose the information in > >or attached to the e-mail. > >Any opinions expressed within this e-mail are those of the individual > >and not necessarily of Diamond Light Source Ltd. > >Diamond Light Source Ltd. cannot guarantee that this e-mail or any > >attachments are free from viruses and we cannot accept liability for > >any damage which you may sustain as a result of software viruses which > >may be transmitted in or with the message. > >Diamond Light Source Limited (company no. 4375679). Registered in > >England and Wales with its registered office at Diamond House, Harwell > >Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United > >Kingdom > > > >_____________________________________ > >Powered by www.kitware.com > > > >Visit other Kitware open-source projects at > >http://www.kitware.com/opensource/opensource.html > > > >Kitware offers ITK Training Courses, for more information visit: > >http://www.kitware.com/products/protraining.php > > > >Please keep messages on-topic and check the ITK FAQ at: > >http://www.itk.org/Wiki/ITK_FAQ > > > >Follow this link to subscribe/unsubscribe: > >http://public.kitware.com/mailman/listinfo/insight-users -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From cyril.mory at uclouvain.be Wed Feb 3 08:14:28 2016 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Wed, 3 Feb 2016 14:14:28 +0100 Subject: [ITK] [ITK-users] Reading 4d image using SimpleITK In-Reply-To: <1077484351.12010208.1454501081539.JavaMail.zimbra@enst.fr> References: <56B1C6E2.9000304@uclouvain.be> <1077484351.12010208.1454501081539.JavaMail.zimbra@enst.fr> Message-ID: <56B1FD34.1070609@uclouvain.be> Oh, yes, there is indeed. Thanks a lot, Timothee On 02/03/2016 01:04 PM, Timothee Evain wrote: > Hello, > > I'm not an user of SimpleITK, but it seems that you can now build the library with an cmake option to support 4D images (since release ~0.9?). > If you are able to do so, you can then use the ExtractImageFilter to get your 3D/2D data : http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ExtractImageFilter.html > > HTH, > > Tim > > > ----- Mail original ----- > De: "Cyril Mory" > ?: insight-users at itk.org > Envoy?: Mercredi 3 F?vrier 2016 10:22:42 > Objet: [ITK] [ITK-users] Reading 4d image using SimpleITK > > Hi ITK users, > > I have more or less the same goal as Andriy had five years ago: I need to read a 4D image, and extract 2D slices from it to serve as figures in a paper. I was wondering if there was a quick way to break my 4D image down into 3D images using SimpleITK. > > Cyril > > > > On Wed, Dec 14, 2011 at 5:06 PM, Bradley Lowekamp > < blowekamp at mail.nih.gov > wrote: >> There is nothing really in the architecture that is specific to 2D and 3D. However, there are numerous compile assertions and other methods to ensure that we are only instantiating filters and objects as we expect to. So there is no quick way of enabling 4D images in simpleITK. > Ok, makes sense. >> You just indicate that you want to read the image. What do you plan on doing with it after that? > At this point, I just want to do some plotting of time course curves. > I will break it down into individual time frames, and load > frame-by-frame, no big deal. > > Thank you. > >> Brad > >> >> AF >> >> >> >> On Wed, Dec 14, 2011 at 4:39 PM, Bradley Lowekamp >> < blowekamp at mail.nih.gov > wrote: >>> Hello Andriy, >>> >>> SimpleITK only supports 2D and 3D sitk::Images. >>> >>> Could you please share a little more about the image you are trying to read? >>> What type is it and what is the meta data that ITK's ImageIO sees when it >>> reads the header (ie Number of Dimensions, Size of the dimensions, etc...)? >>> I would like to be able to reproduce your problem. >>> >>> When ITK's ImageFileReader is instantiated over a dimension that is less >>> than that the file is reporting it will generally, just read that first >>> hyper-slice. We could do similar behavior is SimpleITK. Always try to read, >>> and print a warning if the dimensions is higher. >>> >>> Another feature that is planned, is the support for reading ROI's. I had not >>> previously thought about the possibility of this feature enabling support >>> for reading higher dimension images into 3D images, but is may be possible. >>> >>> Brad >>> >>> ======================================================== >>> >>> Bradley Lowekamp >>> >>> Medical Science and Computing for >>> >>> Office of High Performance Computing and Communications >>> >>> National Library of Medicine >>> >>> blowekamp at mail.nih.gov >>> >>> >>> On Dec 14, 2011, at 4:29 PM, Andriy Fedorov wrote: >>> >>> Hi, >>> >>> I would like to be able to read a 4d image using SimpleITK. >>> >>> Currently, this is not allowed >>> ( https://github.com/SimpleITK/SimpleITK/blob/master/Code/IO/src/sitkImageFileReader.cxx#L44 ). >>> >>> Can someone give me an idea what it takes to enable this feature? >>> >>> Thanks >>> >>> AF >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.html >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://www.itk.org/mailman/listinfo/insight-users >>> >>> > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From eduardo.ecamargo at gmail.com Wed Feb 3 09:03:52 2016 From: eduardo.ecamargo at gmail.com (Eduardo - Gmail) Date: Wed, 3 Feb 2016 12:03:52 -0200 Subject: [ITK] [ITK-users] OFF TOPIC Message-ID: Hi , my friends!! First of all, sorry for this off topic message but I have to ask for help. Well, I will move from Brazil to Canada (Vancouver) in next March and I was wondering if there is someone, or some company, that is using VTK. I have a lot of experience in software development using VTK/ITK and I want to work with it in Vancouver, if someone could help me I will apreciate. This is my LinkedIn profile https://ca.linkedin.com/in/camargoeduardo Atenciosamente, Eduardo Camargo, M.Sc. Analista de Sistemas Instituto Nacional de Ci?ncia e Tecnologia em Medicina Assistida por Computa??o Cient?fica INCT-MACC http://macc.lncc.br Laborat?rio Nacional de Computa??o Cient?fica LNCC - http://www.lncc.br Skype: camargo_rh "Work hard toward your goals, no matter what obstacles get in your way. Even if you think you can?t do it, just be disciplined, put your mind to it, and then do your best." - Jean Chiar - SETI Institute -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Feb 3 10:04:29 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 3 Feb 2016 10:04:29 -0500 Subject: [ITK] =?utf-8?b?77u/W0FOTl0gSVRLIDQuOS4wIGhhcyBiZWVuIHJlbGVhc2Vk?= =?utf-8?q?!?= Message-ID: ?The Insight Segmentation and Registration Toolkit (ITK), is an open-source, cross-platform library for multidimensional image analysis. On behalf of the Insight Toolkit community, we are proud to announce that ITK 4.9.0 has been released! Links to the Sourceforge.net tarballs can be found on the download page: http://www.itk.org/ITK/resources/software.html Outline ------- 1. Introduction 2. New Features 3. ITK Changelog 4. ITK Sphinx Examples Changelog 5. ITK Software Guide Changelog Introduction ----------------- Developed by an international community, ITK collects best-of-breed algorithms for registering, segmenting, analyzing, and quantifying n-dimensional imaging data. The high-quality library facilitates reproducible research, provides a software resource for teaching image analysis, and is a platform for commercial product development. A few selected highlights for the 4.9 release include the following: * new remote modules, such as the Cuberille module for smooth generation of meshes from binary segmentation images, and enhancements, such as advanced edge-preserving smoothing for the AnisotropicDiffusionLBR module; * the ability to build Python wrapping, including Python 3, faster with a more standard installation; * improved performance of itk::Image::GetPixel and operations on itk::VariableLengthVector; * the ability to generate a FlatStructuringElement from an image * the ability to perform point-set registration with time-varying B-splines * the ability to specify module dependencies as public / private / compile / test Congratulations and well done to the 48 contributors to this release. We would especially like to recognize new contributors: Mikhail Isakov, Sreekanth Arikatla, Tobias Wood, Ricardo Ortiz, Junjie Bai, Alexander Leinoff, Eugene Prilepin, Seun Odutola, Martin Michlmayr, Betsy McPhail, Luc Hermitte, Abhishek Tiwari, Sumedha Singla, Lucas Gandel, Alexis Girault, Max Smolens, Shawn Waldon, Hyun Jae Kang, Adam Snyder, Isaiah Norton, Pablo Hernandez-Cerdan, Zach Williamson, Laurentiu Nicola, and Floris Berendsen. New in the ITK Software Guide is a chapter on how to create an ITK module. Since a module can now be configured as a separate CMake project outside of the ITK build tree, external module development is faster and amenable to continuous integration testing. With an external module, Python wrapping can easily be added to algorithms implemented in C++. For example External modules, see the InsightSoftwareConsortium GitHub organization. Since the Insight Applications (ITKApps) are no longer actively being developed, and they are a considerable maintenance burden, ITKApps will no longer be released. There are a number of other projects that provide this functionality, like 3D Slicer and ITK-SNAP. Archived versions of some ITKApps executables will be made available in Docker images in the future. This release also brings support, including Python wrapping support, to the latest compilers including Visual Studio 2015 and the soon-to-be released GCC 6. New Features ------------ Wrapping improvements ^^^^^^^^^^^^^^^^^^^^^ * Python 3 supported * Visual Studio 2015 supported * C++14 standard supported * GCC 6 supported * Wrapping builds much faster due to CastXML binaries * LandmarkBasedTransformInitializer now wrapped * NumPy bridge with VisualStudio * Wrapping for the MinimalPathExtraction module * Wrapping is now installed into Python?s site-packages directory in the ?itk? package * Wrapping package size is decreased * Better package portability on Mac OSX New Remote Modules ^^^^^^^^^^^^^^^^^^ * Cuberille * Insight Journal Article: http://hdl.handle.net/10380/3186 * AnisotropicDiffusionLBR * Insight Journal Article: http://hdl.handle.net/10380/3505 * Web browser reproducibility: http://www.kitware.com/blog/home/post/942 Core Improvements ^^^^^^^^^^^^^^^^^ * External Modules can now be developed outside of the ITK source tree and on GitHub * Details: http://www.kitware.com/blog/home/post/997 * New utilities in itk::Math: * AlmostEquals * NotAlmostEquals * ExactlyEquals * NotExactlyEquals * New itk::NumericTraits * IsInteger * IsSigned * Improved C++11 support * New ITK_DELETE_FUNCTION macro for ?=delete? * New ITK_NOEXCEPT macro for the ?noexcept? keyword * Improved capabilities of itk::ResourceProbe and itk::ResourceProbesCollectorBase * Improve numerical stability in VNL eigen system estimation * itksys_ios:: and itksys_stl:: have been remove (use std::) * ImageIO and TransformIO classes only get registered once in the object factory * The use of dynamic_cast with itk::TransformTemplate pointers should be avoided. It can fail on Mac OSX and older Linux systems. Filtering Improvements ^^^^^^^^^^^^^^^^^^^^^^ * Generate a FlatStructuringElement from an image * WarpImageFilter support VectorImage?s * ConvertLabelMap supports different LabelMap types * ImageToPathFilter moved from the ITKReview to the ITKPath module * itk::MovingHistogramImageFilter moved to the ITKImageFilterBase module Registration Improvements ^^^^^^^^^^^^^^^^^^^^^^^^^ * Point-set registration with time-varying B-splines Build Improvements ^^^^^^^^^^^^^^^^^^ * Module dependencies can now be specified as public / private / compile / test * BUILD_EXAMPLES CMake option is now OFF by default * Option to export all library symbols on Windows: * Details: http://www.kitware.com/blog/home/post/939 * Expat third party library is now name mangled * Many more modules can be built as shared libraries * KWStyle is automatically built and configured when tests are built Performance Improvements ^^^^^^^^^^^^^^^^^^^^^^^^ * New MetaProgrammingLibrary namespace (itk::mpl) holds members for metaprogramming for compile-time determination of optimal code paths * itk::mpl::{TrueType,FalseType} * itk::mpl::{If,Not,And,Or,Xor} * itk::mpl::EnableIf * itk::mpl::IsBaseOf * itk::mpl::IsConvertible * itk::mpl::IsNumber * itk::mpl::IsSame * itk::mpl::PromoteType * Image::GetPixel performance improvements * Many itk::VariableLengthVector performance improvements * AdaptiveHistogramEqualization uses a moving histogram * WarpImageFilter performance improvements Documentation Improvements ^^^^^^^^^^^^^^^^^^^^^^^^^^ * Updates to the Software Guide, Doxygen, Wiki and Sphinx Examples * ITK Software Guide improvements * How to use Python wrapping * How to create an ITK module * Improvements to segmentation examples * Expanded Canny edge detection example * Expanded tree container example * ITK Sphinx Examples improvements * Python wrapping in the ITK superbuild * Bootstrap-based HTML rendering * Python versions of examples * New examples Third Party Library Updates ^^^^^^^^^^^^^^^^^^^^^^^^^^^ * FFTW updated to latest upstream * Build with recent OpenCV 2 and 3 * Build with the latest VTK * PNG update to the latest upstream * KWSys updated to the latest upstream * MINC updated to the latest upstream * SWIG updated to the latest upstream * Third party PNG and MINC are now Git subtrees Style improvements -- ITK gets more stylish with every release! ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Private copy constructors and operator= use ITK_DELETE_FUNCTION * Improved code coverage -- we are at 84.9%! *Lots* of important bug fixes ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Histogram-related outputs may change due to a fix to Histogram interval computation (Change-Id: I2063912edee79422d88125ffd5f7513c31a9e98c) * And much more! See details in the log below. Changes from v4.9rc03..v4.9.0 ----------------------------- Bill Hoffman (3): COMP: fix 64 bit build warnings with windows auto-export on. COMP: work around for VS 2015 optimizer bug causing test failures. COMP: work around for VS 2015 optimizer bug causing test failures. Bradley Lowekamp (1): BUG: Fix precision with accumulation and scaling in AdaptiveHistogram Davis Vigneault (1): COMP: Include itkMacro.h in itkTestingMacros.h Dzenan Zukic (1): COMP: fix itkStaticAssert warnings with clang++ Hans Johnson (6): COMP: BSD command lines do not have --version COMP: Respect CMAKE_CXX_STANDARD during config COMP: Clang Override warnings removed BUG: Download URL was wrong for macosx COMP: The ComputeUpdate function is needed COMP: Incomplete solution for operators corrected Hyun Jae Kang (12): COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6 BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6 BUG: Fixed the runtime crash of itkTimeProbeTest2 BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6 BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6 BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's tests on OSX 10.6 COMP: Fixed the data conversion warning messages of itkResourceProbe BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6 BUG: Fixed the runtime crash of itkBinaryShapeOpeningImageFilterTest1 BUG: Fixed the runtime crash of test_pow_log on OSX 10.6 BUG: Fixed the runtime crash of vnl_test_numeric_traits BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6 Isaiah Norton (1): COMP: fix build with -std=c++11 when ITK/VXL initially configured without Jon Haitz Legarreta (1): BUG: Fix OpenCVBridge bug for two-byte images. Lucas Gandel (2): BUG: Change CMAKE_SOURCE_DIR to CMAKE_CURRENT_SOURCE_DIR BUG: Fix multiple external modules wrapping Martin Michlmayr (1): COMP: fixed error "Dunno about this gcc" for gcc 6 Matthew McCormick (22): BUG: Do not perform dynamic_cast in CompositeIOTransformIOHelper. COMP: Do not set property on itkhdf5 with ITK_USE_SYSTEM_HDF5. DOC: Update the location of the GNUPlot Software Guide scripts. DOC: Update the Software Guide repo location in Examples/README.txt. COMP: Add export specification for itk::ResourceProbe. COMP: Require NO_MODULE with DCMTK find_package. COMP: Update CastXML revision for C++14 VS 2015. BUG: Fix PythonTransformCoverage test for Python 3.4. BUG: Fix PythonExtras test with Python 3. BUG: Fix PythonTypemaps tests with Python 3. ENH: Do not force shared libraries when wrapping. DOC: Update WikiExamples to 2016-10-20 BUG: BUILD_TESTING should be not advanced. COMP: Use enum in itkStaticConstMacro for old GCC. BUG: Correct FlatStructuringElement wrapping location. BUG: Correct itkStaticConstMacro GCC version comparison operator. BUG: Improve GCC detection in itkStaticAssert.h preprocessor macro. BUG: Fix OpenCV version check. DOC: Update the SphinxExamples Remote Module. COMP: Wrap FlatStructuringElement before other classes. COMP: Workaround inconsistent OpenCV pre-processor variables. COMP: Update CastXML to support wrapping with GCC 6. Michka Popoff (3): ENH: Allow Python 3 wrapping for Glue and Review Modules with VTK 7 COMP: Re-enable review module for python 3 and older VTK's ENH: Use importlib for python 3.4 instead of imp Nick Tustison (1): ENH: Accommodate epsilon error on left side. Sean McBride (1): DOC: Update some woefully out-of-date GDCM comments, and typos Seun Odutola (1): BUG: Improved itkAnalyzeImageIO to handle case insensitive extensions Sumedha Singla (3): ENH: Fixed the numeric traits for datatypes DOC: Added a comment to support the changes in numeric traits datatypes. BUG: Invalid memory access of itk::NotAlmostEquals Bug#ITK-3403 Changes from v4.9rc02..v4.9rc03 ------------------------------------------------ Alexis Girault (1): BUG: Implement SetAutoMinimumMaximum in itkScalarImageToHistogramGenerator Bill Lorensen (1): BUG: nifti_read_subregion_image was leaking file pointers Brad King (7): ENH: Teach ITK module macros to support independent header-only modules ENH: Add script to import KWIML library source code ENH: Add `ITKKWIML` module to provide external KWIML library ENH: Port TIFF integer types from KWSys to KWIML ENH: Port LSM integer types from KWSys to KWIML ENH: Port itkIntTypes.h from KWSys to KWIML ENH: Drop KWSys FundamentalType component Bradley Lowekamp (1): ENH: Add option to choose scheme for git download Davis Vigneault (1): STYLE: Use cstdlib return macros in ITK examples D?enan Zuki? (3): BUG: do not pass 0,0,0 to Versor.Set() STYLE: Removing the unused NeighborhoodRadius property ENH: Write out transform in DeformableRegistration15 Gert Wollny (1): BUG: Remove double-conversion from public interface, use system. Hyun Jae Kang (8): ENH: Create a test for the SpawnThread function ( ITK-3317) STYLE: Remove an unnecessary file (-w) from source code BUG: Fixed the failed case of itkStdStreamStateSaveTest on OS X 10.8 BUG: Fixed the failed test case of itkThreadPoolTest on OS X 10.8 BUG: Fixed a failed test of ITKDistanceMapTestDriver BUG: Fixed the failed test VideoSourceTest PERF: Improve the performance of a test of ITKRegistrationMethodsv4TestDriver COMP: Fixed the compiler error of itkDisplacementFieldToBSplineImageFilterTest Jean-Christophe Fillion-Robin (25): BUG: Build ITKIOTransformHDF5 as shared library. See #3393 BUG: Build ITKIOTransformMINC as shared library. See #3393 BUG: Build ITKIOTransformMatlab as shared library. See #3393 BUG: Build ITKIOTransformInsightLegacy as shared library. See #3393 STYLE: TransformIOFactory: Remove obsolete declaration. See #3393 COMP: TransformIOFactory: Add missing ctor/dtor from hxx file. See #3393 COMP: TransformFileWriter: Remove method "OpenStream()" without definition COMP: TransformFileReaderTemplate: Remove undefined method "CreateTransform()" ENH: Update ITKIOPhilipsREC to allow static initialization. See #3393 ENH: Update ITKIOTransformMINC to allow static initialization. See #3393 COMP: MINC: Fix VS2008 "unknown round" build error. See #3393 COMP: MINC: Fix VS2008 "unknown arpa/inet.h" build error. See #3393 COMP: Configure ENABLE_SHARED into .cmake file. See #3393 COMP: Fix configuration of IOFactory header. See #3393 STYLE: UseITK: Removed redundant code setting ImageIO factory name. See #3393 STYLE: UseITK: Re-factor introducing _configure_IOFactoryRegisterManager STYLE: UseITK: Set TransformIO factory and module name using convention. BUG: Ensure Image IO factories are registered once. See #3393 BUG: Ensure Transform IO factories are registered once. COMP: ITKIOXML: Fix VS11 "already defined std::string" link error. See #3393 BUG: TransformIO: Implement explicit template instantiation using "extern". COMP: TransformIO: Fix VS build errors removing extra EXPORT COMP: TransformIO: Handle compiler not supporting "pragma diagnostic". COMP: TransformIO: TransformFile(Reader|Writer) still need to be exported. COMP: TransformIO: Fix explicit instantiation approach Johan Andruejol (1): ENH: Add ITK_RUNTIME_LIBRARY_DIRS for external projects KWIML Upstream (1): KWIML 2015-12-09 (43f9f8d0) Lucas Gandel (1): BUG: PhysicsBasedNonRigidRegistrationMethod test failure on Debian 32bit Matthew McCormick (16): COMP: Fix PointDimension reference in AzimuthElevationToCartesian test. STYLE: Improve scoping in AzimuthElevationToCartesian test. STYLE: Explicitly mark the ProcessObject methods virtual in SignedMaurer. BUG: Do not try to install targets that do not exist when building externally. BUG: ITKIOMeta needs a public dependency on ITKMetaIO. COMP: Update LesionSizingToolkit for external build and style test failures. BUG: Add CMake OpenCV export code to ITKVideoBridgeOpenCV. COMP: Improve compatibility with OpenCV 3. DOC: Fix class references in StatisticsLabelMapFilter. STYLE: Improved readability of itkStatisticsUniqueLabelMapFilterTest1. DOC: Correct ReverseOrdering description in ShapeUniqueLabelMapFilter. STYLE: Add own copy of GenerateExportHeader COMP: Create _TEMPLATE_EXPORT macros. COMP: TransformIOBaseTemplate must be explicitly instantiated. BUG: Do not use dynamic_cast for DisplacementFieldType in HDF5 test. COMP: Do not use string(MAKE_C_IDENTIFIER with CMake < 2.8.12 Max Smolens (1): BUG: VoronoiSegmentationRGBImageFilter: add pixel dimension check Mikhail Isakov (1): DOC: correction in DiffusionTensor3D Reconstruction Ricardo Ortiz (1): BUG: Set itkBinaryImageTo*LabelMapFilter foreground/background values Seun Odutola (1): BUG: absolute value of tolerance taken to cater for negative spacing Shawn Waldon (1): COMP: OSX set deployment target when building fftw Simon Alexander (4): STYLE: Change to make git bash on windows happy with the function name COMP: fixes for visual studio 2015update1 x86 in release mode COMP: fixes for visual studio 2015update1 x86 in release mode COMP: fixes for visual studio 2015update1 x86 in release mode Sreekanth Arikatla (2): BUG: Resolved const correctness in itkMatrix.h ENH: Fixes the symmetry of AzimuthElevationToCartesianTransform and adds tests Changes from v4.9rc01..v4.9rc02 ------------------------------------------------ Bill Lorensen (1): BUG: Valgrind detected an invalid read Davis Vigneault (1): STYLE: Address some warnings when running cppcheck Hyun Jae Kang (2): COMP: Fixed a warning message of data-conversion on VS14 COMP: Update KWStyle to remove format-string warning message Matthew McCormick (3): DOC: Remove invalid wrapping example. BUG: Wrap AdaptiveEqualizationHistogram. COMP: Ignore Doxygen endcond warning in itkIsConvertible.h. Seun Odutola (1): COMP: Corrected minc2.h path installation from libsrc2/minc2.h to minc2.h Ziv Yaniv (2): BUG: Affine transformation was estimated without sufficient number of points. BUG: fixed BSpline initializer crash when reference image not set. Changes from v4.8.0..v4.9rc01 -------------------------------------------- Abhishek Tiwari (1): BUG: "tmpImageIndex" not initialized to 0. Adam Snyder (1): PERF: Reworked MMI Threading using a per-thread buffer Alexander Leinoff (6): ENH: Adds IsInteger and IsSigned to NumericTraits. COMP: Doxygen itkMath.h 'OneValue()' could not be resolved. ENH: Adds ExactlyEquals and NotExactlyEquals functions to itkMath.h COMP: Removes floating-point equality checks ENH: COMP: Adds support for complex values to Math::AlmostEquals ENH: Updates fftw dependency Arnaud Gelas (5): COMP: fix warning (unused local typedef) COMP: simplify ITKVideoBridgeOpenCV dependency DOC: add doxgen documentation for BinaryImageToLevelSetImageAdaptor ENH: add tests to exercise itk::ThreadedIteratorRangePartitioner COMP: fix compilation error with OpenCV2 and OpenCV3 Betsy McPhail (1): BUG: Improve buffer alignment in OctreeNode . Bill Hoffman (2): ENH: Use new CMake Windows export symbol dll feature. COMP: Put vnl_export.h in the list of sources so it gets installed. Bill Lorensen (4): COMP: VTkGlue linker errors BUG: Inappropriate use of AlmostEquals ENH: Bump tag for wiki examples ENH: Better layout strategy Brad King (3): ENH: Remove use of include and itksys_ios::* ENH: Remove use of include and itksys_stl::* ENH: Update CMake Policy settings in Testing/TestExternal project Bradley Lowekamp (31): BUG: Avoid null deference in PrintSelf with default construction ENH: Enable base classes for templates of landmark initializer STYLE: Use "Swap" for ITK member name BUG: Demonstrate Eigen analysis failure BUG: Fix computation of Eigen analysis ENH: Update DiscreteHessianGaussian Test baseline ENH: Correctly demonstrate float point Eigen failure ENH: compile vnl_math_hypot, and use at least double ENH: Adding initial update script from used libpng version. ENH: removing non-subtree files for itkpng ENH: Ported ITK changes for building to subtree merged code ENH: Update libpng update script for v1.6.9 BUG: Use ParameterValueType for computation of landmark affine ENH: Wrap LandmarkBasedTransformInitializer BUG: Avoid potential exception in itk::Object::UnRegister ENH: Update itkpng zlib, configuration, and rename ENH: Update itkpng name mangling BUG: Use const pointer in Set method for constant ReferenceImage ivar BUG: Increase tolerance for PhysicsBasedNonRigidRegistrationMethod BUG: Demonstrate side effect on registration due to BSplineScatter change ENH: Move MovingHistogramImageFilter base classes to ImageFilterBase BUG: Avoid potential exception in itk::Object::UnRegister BUG: Avoid null deference in PrintSelf with default construction BUG: Use const pointer in Set method for constant ReferenceImage ivar ENH: Optimize AdaptiveHistogramEqualization with MovingHistogram base COMP: address sign unsigned comparison warning COMP: Address signed unsigned comparison warning COMP: Address unused member variable and methods in anonymous ns BUG: Fix segfault when with empty IsolatedWatershed Threshold range BUG: Adjust intensity tolerance for PhysicsBasedNonRigid test BUG: Reduce number of targets with MSVC Davis Vigneault (7): DOC: Minor improvements to segmentation examples. DOC: Expanded Canny Edge Detection Example DOC: Expanded TreeContainer Example COMP: Warnings in itkVTKImageExport when compiling with c++11 COMP: Warnings in FFTW Classes when compiling with c++11 COMP: Update Git Tag for Subdivision Module COMP: Warnings in FFTW Classes when compiling with c++11 D?enan Zuki? (1): STYLE: better formatting of the "usage" message Eugene Prilepin (1): BUG: Fix a template name formation in python wrappings Floris Berendsen (1): STYLE: Improve naming conventions in comments. Hans Johnson (29): STYLE: Instrument for FixedParameters typedef BUG: Demonstrate DisplacementTransformFailure BUG: FixedParameters should be double precision STYLE: Minor code style issues for MGHIO COMP: Update to version for WikiExamples ENH: Update Sphinx for ITK 4.8.0 ENH: Update MGHIO to be shared lib ENH: Provide consistent floating point comparisons BUG: Fix MGHIO to fix write failures PERF: Remove floating point as sentinal value COMP: Const correctness needs to be maintained BUG: Preserve backwards compatibility DOC: Provide consistent naming in comments ENH: Conversion between transform type tolerance STYLE: Prefer initialization to assignment ENH: Missing ITK_OVERRIDE COMP: Need to propagate ITKGDCM COMP: Need to propagate ITKGDCM COMP: Add missing ITK_OVERRIDE STYLE: Minor code style issues for MGHIO COMP: Update to version for WikiExamples ENH: Update Sphinx for ITK 4.8.0 ENH: Update MGHIO to be shared lib BUG: Fix MGHIO to fix write failures ENH: C++11 allows for rigorous =delete COMP: Remove unnecessary failing assert test ENH: Ignore internal files for the Clion editor COMP: Fix VNL compilation for wider C++11 support BUG: In configuration test need to mirror code Hyun Jae Kang (27): BUG: Remove std::cout calls from class BUG: Avoid an unexpected output of static_cast BUG: Update python example codes for ImageRegistration BUG: Retrieve the missed wrap file BUG: itkVTKImageIO class does not handle blank lines in VTK file header. BUG: Fix HDF5 CMake configuration with VS2015 BUG: Fix a compilation issue on ITK4 with FFTW and shared libraries BUG: Fixed older XCode linking error ENH: Use CastXML binaries when building with x86_64 Mac OS X BUG: Remove std::cout calls from class BUG: itkVTKImageIO class does not handle blank lines in VTK file header. BUG: Fixed older XCode linking error ENH: Add automatic KWStyle build and configuration setup COMP: KWStyle shadow, format-nonliteral and autological-compare warning. COMP: Fixed the warning messages from itkGPU Module COMP: Fixed a warning message of unused-private-field COMP: Apply latest version of KWStyle COMP: Update KWStyle to fix its additional warning messages COMP: Update KWStyle to fix its additional warning messages COMP: Fix data-conversion warning messages on Windows ENH: Update itkResourceProbe to calculate statistical data COMP: Fix data-conversion warning messages on VS14 COMP: Fixed 'std::sqrt' : ambiguous call to overloaded function ENH: Update the Report() function of itkResourceProbesCollectorBase COMP: Fix data-conversion warning message on itkResourceProbe COMP: Fix additional warning messages of KWStyle COMP: Fix data-conversion warning messages Jon Haitz Legarreta (6): ENH: Add test for itkStatisticsUniqueLabelMapFilter BUG: Fix compilation issues for StatisticsUniqueLabelMapFilterTest BUG: Fix comparison issues for itkStatisticsUniqueLabelMapFilter BUG: Test for StatisticsUniqueLabelMapFilter stability ENH: Add test for itkParametricStpaceToImageSpaceFilter ENH: Improve code coverage for itkParametricSpaceToImageSpaceMeshFilter Julien Michel (1): ENH: Support of VectorImage as template parameters for WarpImageFilter Junjie Bai (2): BUG: ConvertLabelMap with different LabelMapTypes BUG: LabelObject CopyAttribute support different LabelObject type KWSys Robot (4): KWSys 2015-07-10 (c9336bcf) KWSys 2015-07-30 (f63febb7) KWSys 2015-08-24 (cdaf522c) KWSys 2015-08-28 (dc3fdd7f) LIBPNG Upstream (2): PNG 2009-04-06 (e68f5a36) PNG 2014-02-05 (3e753eb8) Laurentiu Nicola (2): PERF: Avoid temporary smartptr in ProcessObject::GetInput PERF: Optimize WarpImageFilter by avoiding refcount bouncing Luc Hermitte (8): PERF: itk::Image::GetPixel() performance improvment. PERF: Performance enhancements on VariableLengthVectors 1/... ENH: Dependencies on itkVariableLengthVector.h reduced BUG: Error in VariableLengthVector Unit Tests PERF: Performance enhancements on VLV 2/... PERF: Performances enhancements on VLV 3/... COMP: Fix signed/unsigned warnings BUG: std::copy/fill on empty VLV Lucas Gandel (4): ENH: Move ImageToPathFilter from ITKReview to ITKPath module. BUG: Fixing ImageToPathFilter wrapping call from Review Module STYLE: Fix KWStyle dashboard errors BUG: Fix external module BUILD_SHARED_LIBS status Mathieu Malaterre (1): BUG: Name mangle the included expat third party library. Matthew McCormick (94): ENH: Change itkSystemInformationTest to itkCMakeConfigurationTest. ENH: Add AnisotropicDiffusionLBR Remote Module. ENH: Bump ITK version to 4.9.0. BUG: Remove std::cout calls from classes. COMP: Remove unused argument in ConditionVariableNoThreads. BUG: Implement UpdateLargestPossibleRegion for ImageToVTKImageFilter. COMP: Add link interface specification for wrapping target_link_libraries. STYLE: Fix indentation in itkMINCTransformIOFactory.cxx. COMP: Fix MINCTransformIO factory registration. COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with Emscripten-1. COMP: Remove unknown doxygen command in AnisotropicDiffusionLBR. BUG: Initialize mutex for 32 bit AtomicInt. ENH: Use CastXML binaries when building with x86_64 Linux. STYLE: Rename gccxml -> castxml in {idx,igenerator}.py. COMP: Disable the gold linker for static builds on Ubuntu 14.04. ENH: Use Windows binaries for CastXML. ENH: Add better scoping in igenerator.py. BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja + MSVC. BUG: LevelSetsv4 used signed char instead of char. ENH: Add better scoping to idx.py. COMP: Define newSize and oldSize in VariableLengthVector. STYLE: Use prefix increment operator in ImageBase. DOC: Correct spelling of Continuous. ENH: Add more progress information to IterativeClosestPoint2. BUG: Build BridgeNumPy with Visual Studio. ENH: Add ITKModuleExternal.cmake COMP: Wrap Image< bool, D > for FlatStructuringElement. BUG: Use CastXML binary built in Release. BUG: ContinuousIndex should not be templated over TCoordRep. COMP: Set CMP0054 to new. COMP: Address line length too long for Software Guide. COMP: Fix CannyEdgeDetectionImageFilter.cxx types. BUG: Support Python 3 wrapping module initialization. BUG: Update itkTemplate.py for Python 3. BUG: Update itkExtras.py for Python 3. BUG: Prevent Python callback addition recursion. BUG: Fix test scripts for Python 3. BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. ENH: Allow projects to build against an external module. ENH: Replace CABLE_CONFIGURATION with ITK_WRAPPING_PARSER. ENH: Rename _cable_ to _wrappers_. BUG: Replace __GCCXML__ with CABLE_CONFIGURATION. BUG: Define ITK_WRAPPING_PARSER when wrapping. COMP: Do not use C++11 alignas in itkAlignedTypedef. ENH: Bump CMakeLists.txt version to 4.8.1. BUG: Pass the CMAKE_CXX_FLAGS to castxml. ENH: Bump CastXML version to 2015-30-29. ENH: Bump LLVM / Clang to 3.7.0. COMP: Avoid itklibminc linking with ITK_USE_SYSTEM_HDF5. COMP: Add missing ITKIOImageBase dependency for ITKTransformMINC. COMP: Use itkSimpleNewMacro in ThreadedIteratorRangePartitionerTest. ENH: Add wrapping support for building modules externally. BUG: Fix KWStyle test paths when building a module externally. ENH: Add Cuberille Remote module. COMP: Remove carriage returns from Cuberille remote. COMP: Remove unused argument in ConditionVariableNoThreads. DOC: Correct spelling of Continuous. ENH: Bump the MinimalPathExtraction Remote to 2015-10-20. COMP: Fix KernelTransform SetFixedParameters argument type. STYLE: Use prefix increment operator in ImageBase. COMP: Use ITK's pygccxml by correctly setting up the sys.path Revert "COMP: Put vnl_export.h in the list of sources so it gets installed." BUG: Revert "BUG: ConvertLabelMap with different LabelMapTypes" ENH: Marking wrapping CMake configuration variables as advanced. STYLE: Rename CASTXML to CASTXML_EXECUTABLE. COMP: Non-virtual copy attribute members in LabelMap cannot have override. COMP: Add wrapping for AdaptiveHistogramEqualizationImageFilter. COMP: Add itkMacro.h to itkPromoteType.h for ITK_EXCEPT. ENH: Remove CMake version check in ITKModuleHeaderTest.cmake BUG: Improve KWStyle ExternalProject utilization. ENH: Remove old KWStyle build script. COMP: Address VariableLengthVector Doxygen rhs @param not found. ENH: Rename WRAPPING_LIBRARY_GROUPS to WRAPPING_SUBMODULE_ORDER. ENH: Install Python bindings into site-packages. ENH: Improve readability of Python site-packages path detection. COMP: DiscreteGaussianDerivativeImageFilter unsigned expression warning. BUG: ITKCommon publically depends on ITKDoubleConversion. COMP: Improve scoping in CovariantVectorGeometryTest. ENH: Improves names and export of module dependencies. STYLE: Improve namespace bracket style in itkIsConvertible. COMP: Set CMP0054 to new. BUG: Remove unused wrapping files. BUG: Do install install wrapping development files. ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER. BUG: Remove duplicate inclusion of wrapping submodules. COMP: Do not use C++ style comments for Doxygen cond. BUG: Fix detection of the gold linker. BUG: Update Python package installation locations. ENH: Bump CMakeLists.txt version to 4.8.2. ENH: Change BUILD_EXAMPLES default to OFF. BUG: Use 'from itk import ITKCommon' in module2module test. COMP: Link to VTK Python when built with Kits support. BUG: Install itk_minc2.h header. COMP: ITKIOMINC has a public dependency on ITKIOImageBase. Michka Popoff (9): ENH: Update to swig 3.0.7 ENH: Do not link against specific Python library on OS X COMP: Fix wrapping warnings when building with ITK_WRAP_IMAGE_DIMS=2 COMP: Add missing wrapping for TransformBase COMP: Use ITK's pygccxml by correctly setting up the sys.path COMP: Disable incompatible modules when using Python 3 wrapping COMP: Move MovingHistogramImageFilterBase wrapping to ImageFilterBase module COMP: Disable incompatible modules when using Python 3 wrapping ENH: Allow operations on Indexes and Offsets in Python Mikhail Isakov (1): BUG: DiffusionTensor3DReconstruction segfault if no baseline image Nick Tustison (5): BUG: Set a default b-spline epsilon. ENH: Adding testing for closed loop. BUG: Updating B-spline classes with the same epsilon strategy. PERF: Switch vnl_vectors for fixed arrays. ENH: Point-set registration with time-varying B-spline. Olivier Commowick (3): BUG: Correct discrepancy in tridiagonal reduction wrt VNL eigen system BUG: Correct under/overflows in vnl_math_hypot (taken from pythag from V3P) BUG: Switch eigenvalues computation to double Pablo Hernandez-Cerdan (2): ENH: Help class for itkFlatStructuringElement with constructor from images. COMP: Fix test errors and warnings in FlatStructuringElement. Seun Odutola (1): COMP: Fixed name clash with Apple header (check Macro), renamed check to Check Shawn Waldon (1): COMP: Set target OS X version in environment for tools using compiler Simon Alexander (1): BUG: incorrect closest point computation Tobias Wood (2): BUG: LBFGSB was printing messages even with debug switched off. BUG: Removed an unguarded print statement. Vladimir S. FONOV (9): BUG: Missing ITKIOMINC_EXPORT on __Private() COMP: Changing the order of HDF5 library components COMP: Splitting up IOMINC module into two parts: MINC and Transform STYLE: updated comments to properly reference LIBMINC ENH: Add script to merge upstream MINC as a subtree MINC 2015-07-23 (c033d431) COMP: Update MINC CMake code MINC 2015-08-18 (6d7e3ba8) MINC 2015-09-13 (95cd5374) Xiaoxiao Liu (1): DOC: update email address for xiaoxiao. Zach Williamson (10): BUG: Use correct libraries for ImageFusion tests ENH: Consolidate Library Dependencies COMP: Add a missing link to Review module COMP: Use correct linking macro in DCMTK BUG: Use correct libraries for TestKernel tests COMP: Fix inconsistant naming of GPUPDEDeformableRegistration ENH: Use new linking system macros PERF: Avoid searching private dependencies for include directories COMP: Recover missing dependencies ENH: use new linking macros in Filtering module ITK Sphinx Examples Changelog --------------------------------------------- Brad King (1): ENH: Remove use of itksys_ios::* D?enan Zuki? (1): ENH: Avoid warning window when the directory does not contain any DICOM series Hans Johnson (1): BUG: FixedParameters different from Parameters Matt McCormick (38): ENH: Bump ITK ExternalProject to v4.8.0. COMP: Do not try to add html files twice to the tarballs. BUG: Turn off ITK modules when superbuild options are disabled. DOC: Consistently refer to source directory in length warning. BUG: Use os.path.sep for CreateNewExample.py on both Unix and Windows. ENH: Use a StringIO for the headers content in CreateNewExample. ENH: Make CreateNewExample compatible with Python 3. ENH: Enable BridgeNumPy in the Superbuild when NumPy available. ENH: Silence gitstats execution. ENH: Add sphinx-bootstrap-theme submodule. ENH: Update ITK ExternalProject to 4.9rc02. COMP: Support OpenCV 3.0.0. BUG: Pass the Sphinx output components in the superbuild. BUG: Work around epub output filename irregularity. ENH: Use side-by-side images in Binary Mathematical Morphology. ENH: Use all caps in Binary Mathematical Morphology examples. ENH: Move the Download button location. BUG: Rename CreateAnApplyCustomColormap -> CreateACustomColorMap. ENH: Use note directive in CreateACustomColorMap. ENH: Move ITkExampleMacros.cmake into the CMake/ directory. STYLE: Use more standard spacing in ITKExamplesMacros.cmake. DOC: Improve TryCatchException result rendering and synopsis. DOC: Update the Download page image for the bootstrap layout. ENH: Use presence of Code.py to create Python baseline comparison tests. DOC: Fix ComputeTimeBetweenPoints output rendering. ENH: Add Python version of ComputeTimeBetweenPoints. ENH: Demonstrate Report() in ComputeTimeBetweenPoints. ENH: Add Python superbuild. COMP: Fix type of Sphinx output variables. BUG: Ensure that the JavaScript files get copied to HTML output. COMP: Fix ConceptCheckingIsFloatingPoint index entry. BUG: Avoid system installation without superbuild Python. COMP: Find ITKExamplesMacros.cmake when build as a Remote Module. COMP: Support OpenCV 3 in ConvertAnITKGrayScaleImageToCVMat. COMP: Support double typed FixedParameters in ITK 4.9.0 BUG: Do not run Python comparison tests without ITK_WRAP_PYTHON. BUG: Correct CreateACustomColorMapTestPython test name. ENH: Bump ITK ExternalProject to 4.9.0. Michka Popoff (4): ENH: Add ImageRegistration1 example COMP: Fix images in 2D Translation Registration ENH: Add AddOffsetToIndex Python example ENH: Add missing licence headers and hide headers in doc ITK Software Guide Changelog --------------------------------------------- Matt McCormick (9): COMP: Address missing bracket and backslash escapes. BUG: Fix backslash specification in Windows PATH. DOC: Recommend the Release build configuration when wrapping. DOC: Document .GetTypes and Python type conversion. DOC: Add chapter on how to create a module. COMP: Do not set PYTHONCXXPARSER with find_program. ENH: Update ITK ExternalProject to v4.9rc01. DOC: Corrections to formatting of wrapping content. ENH: Bump ITK ExternalProject version to v4.9.0. From bakkari.abdelkhalek at hotmail.fr Wed Feb 3 13:31:43 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Wed, 3 Feb 2016 19:31:43 +0100 Subject: [ITK] [ITK-users] Save VTK 3D result image as .mha Message-ID: Dear Insight Users, I would like to create a new button which saves the results providing by VTK (3D images) as .mha file.Any suggestion about this matter ? Thank you in advance. Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Wed Feb 3 13:39:46 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 3 Feb 2016 13:39:46 -0500 Subject: [ITK] [ITK-users] Save VTK 3D result image as .mha In-Reply-To: References: Message-ID: You should look into itkVtkGlue and its examples. HTH On Wed, Feb 3, 2016 at 1:31 PM, Abdelkhalek Bakkari < bakkari.abdelkhalek at hotmail.fr> wrote: > > Dear Insight Users, > > I would like to create a new button which saves the results providing by > VTK (3D images) as .mha file. > Any suggestion about this matter ? > > Thank you in advance. > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From itkhelpacc at gmail.com Thu Feb 4 00:08:30 2016 From: itkhelpacc at gmail.com (vishal) Date: Wed, 3 Feb 2016 22:08:30 -0700 (MST) Subject: [ITK] [ITK-users] Problem building jounal paper->cannot open input file 'ITKAlgorithms.lib' Message-ID: <1454562510446-36734.post@n7.nabble.com> hi, I came across this paper An ITK-Based Framework for 2D-3D Registration with Multiple Fixed Images by Alvaro Bertelsen and Diego Borro... first had to replace ::itk::OStringStream diffName; by std::ostringstream diffName; which solved some errors and now upon building the project again Im getting the error saying *cannot open input file 'ITKAlgorithms.lib'*.. I searched for ITKAlgorithms in my ITK 4.8.2 build folder but i *couldnt* find it... i build the project in debug mode.. Please advice Regards vishal -- View this message in context: http://itk-users.7.n7.nabble.com/Problem-building-jounal-paper-cannot-open-input-file-ITKAlgorithms-lib-tp36734.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Thu Feb 4 13:41:16 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 4 Feb 2016 13:41:16 -0500 Subject: [ITK] [ITK-users] Problem building jounal paper->cannot open input file 'ITKAlgorithms.lib' In-Reply-To: <1454562510446-36734.post@n7.nabble.com> References: <1454562510446-36734.post@n7.nabble.com> Message-ID: Hi Vishal, the most likely reason is listing libraries by name in CMakeLists.txt file. You should replace line set(Libraries ITKAlgorithms ITKBasicFilters ITKCommon ITKIO) by line: set(Libraries ${ITK_LIBRARIES}) If it doesn't work, let us know. HTH On Thu, Feb 4, 2016 at 12:08 AM, vishal wrote: > hi, > I came across this paper An ITK-Based Framework for 2D-3D Registration with > Multiple Fixed Images by Alvaro Bertelsen and Diego Borro... first had to > replace ::itk::OStringStream diffName; by std::ostringstream diffName; > which solved some errors and now upon building the project again Im getting > the error saying *cannot open input file 'ITKAlgorithms.lib'*.. I searched > for ITKAlgorithms in my ITK 4.8.2 build folder but i *couldnt* find it... > i > build the project in debug mode.. Please advice > Regards > vishal > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/Problem-building-jounal-paper-cannot-open-input-file-ITKAlgorithms-lib-tp36734.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From olivier.commowick at inria.fr Thu Feb 4 14:07:27 2016 From: olivier.commowick at inria.fr (Olivier Commowick) Date: Thu, 4 Feb 2016 20:07:27 +0100 Subject: [ITK] [ITK-users] Multi-threader and thread pool Message-ID: <919FD08C-D1FF-42B2-8806-CA70DE593E77@inria.fr> Hi everyone, I have recently discovered the existence of a thread pool class in ITK (http://itk.org/Doxygen/html/classitk_1_1ThreadPool.html ), closely linked to the multi threader. From the doxygen, I am not really able to understand how it can be used and I do not see any example for it. I have been looking for some time for a multi-threader, working on all OSes, that can have more jobs in queue than the number of threads and execute them when threads gets free, and this would seem like a good start. So I was wondering how this thread pool actually behaves when used by the multi-threader, what its goal is in ITK and all this sort of things. If anyone had some idea about this or may be an example on how it could be used, that would be great. Thanks Olivier -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From hyunjae.kang at kitware.com Thu Feb 4 14:36:20 2016 From: hyunjae.kang at kitware.com (Hyun Jae Kang) Date: Thu, 4 Feb 2016 14:36:20 -0500 Subject: [ITK] [ITK-dev] [SimpleITK] Data Bridge for SimpleITK Message-ID: Hi all, To support data transparency between the functions of SimpleITK and NumPy, SimpleITK provides functional integration with NumPy-based script and a method of data-conversion between SimpleITK?s image data and the N-dimensional array object of NumPy. But, there is a significant performance bottleneck in the data-conversion which is based on the operation of data copy. The performance bottleneck can be increased with the size of handling image data and the number of data-conversion. The performance bottle can be removed by allowing SimpleITK?s image and the arrays of NumPy to share pointers to the same memory symmetrically with copy-on-write semantics. That is, reduce data-copy operations in the data conversion. This approach can be accomplished by developing and/or improving existing data handling methods in ITK and SimpleITK to enable copy-on-write sharing of data between SimpleITK?s image data and other common data object of Python libraries used for scientific computing and image processing. For more detail information, please check the following website: http://www.itk.org/Wiki/SimpleITK/Design_And_Proposals/SIP_002 Any your valuable comments are welcome. Thanks, Hyun Jae -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Thu Feb 4 15:04:11 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 4 Feb 2016 15:04:11 -0500 Subject: [ITK] [ITK-users] Multi-threader and thread pool In-Reply-To: <919FD08C-D1FF-42B2-8806-CA70DE593E77@inria.fr> References: <919FD08C-D1FF-42B2-8806-CA70DE593E77@inria.fr> Message-ID: Hi Olivier, The itk::ThreadPool is an experimental thread-pool feature. It is considered experimental, and it maybe majorly modified in its API or removed in the future. Our preliminary experiences is that ITK runs slower when it is enabled. To enable it, call itk::MultiThreader::SetGlobalDefaultUseThreadPool( true ); In the future, we will be moving towards other thread pool backends by adopting interfaces similar to vtkSMPTools and VTK-m. Thanks, Matt On Thu, Feb 4, 2016 at 2:07 PM, Olivier Commowick wrote: > Hi everyone, > > I have recently discovered the existence of a thread pool class in ITK > (http://itk.org/Doxygen/html/classitk_1_1ThreadPool.html), closely linked to > the multi threader. From the doxygen, I am not really able to understand how > it can be used and I do not see any example for it. > > I have been looking for some time for a multi-threader, working on all OSes, > that can have more jobs in queue than the number of threads and execute them > when threads gets free, and this would seem like a good start. So I was > wondering how this thread pool actually behaves when used by the > multi-threader, what its goal is in ITK and all this sort of things. If > anyone had some idea about this or may be an example on how it could be > used, that would be great. > > Thanks > Olivier > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From david.mo.burns at gmail.com Thu Feb 4 18:03:08 2016 From: david.mo.burns at gmail.com (David Burns) Date: Thu, 4 Feb 2016 18:03:08 -0500 Subject: [ITK] [ITK-dev] [SimpleITK] Data Bridge for SimpleITK In-Reply-To: References: Message-ID: <56B3D8AC.9090606@gmail.com> I just finished creating an interface between numpy/slicer and my ITK C++ project module using SWIG. I use pointers to avoid copying and it works well. Happy to share what I have. - David On 02/04/2016 02:36 PM, Hyun Jae Kang wrote: > Hi all, > > To support data transparency between the functions of SimpleITK and > NumPy, SimpleITK provides functional integration with NumPy-based > script and a method of data-conversion between SimpleITK?s image data > and the N-dimensional array object of NumPy. But, there is a > significant performance bottleneck in the data-conversion which is > based on the operation of data copy. The performance bottleneck can be > increased with the size of handling image data and the number of > data-conversion. > > The performance bottle can be removed by allowing SimpleITK?s image > and the arrays of NumPy to share pointers to the same memory > symmetrically with copy-on-write semantics. That is, reduce data-copy > operations in the data conversion. This approach can be accomplished > by developing and/or improving existing data handling methods in ITK > and SimpleITK to enable copy-on-write sharing of data between > SimpleITK?s image data and other common data object of Python > libraries used for scientific computing and image processing. > > For more detail information, please check the following website: > http://www.itk.org/Wiki/SimpleITK/Design_And_Proposals/SIP_002 > > Any your valuable comments are welcome. > > Thanks, > > Hyun Jae > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From hyunjae.kang at kitware.com Thu Feb 4 19:08:55 2016 From: hyunjae.kang at kitware.com (Hyun Jae Kang) Date: Thu, 4 Feb 2016 19:08:55 -0500 Subject: [ITK] [ITK-dev] [SimpleITK] Data Bridge for SimpleITK Message-ID: Hi David, Thanks for your prompt response! That is great news. It would be very helpful for us if you could share your interface for the data conversion between numpy/slicer and ITK with us. So, we do not need to start from scratch. Thanks, Hyun Jae On Thu, Feb 4, 2016 at 6:03 PM, wrote: > Send Community mailing list submissions to > community at itk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/community > or, via email, send a message with subject or body 'help' to > community-request at itk.org > > You can reach the person managing the list at > community-owner at itk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Community digest..." > > > Today's Topics: > > 1. Re: [ITK-users] Problem building jounal paper->cannot open > input file 'ITKAlgorithms.lib' (D?enan Zuki?) > 2. [ITK-users] Multi-threader and thread pool (Olivier Commowick) > 3. [ITK-dev] [SimpleITK] Data Bridge for SimpleITK (Hyun Jae Kang) > 4. Re: [ITK-users] Multi-threader and thread pool (Matt McCormick) > 5. Re: [ITK-dev] [SimpleITK] Data Bridge for SimpleITK (David Burns) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 4 Feb 2016 13:41:16 -0500 > From: D?enan Zuki? > To: vishal > Cc: Insight-users > Subject: Re: [ITK] [ITK-users] Problem building jounal paper->cannot > open input file 'ITKAlgorithms.lib' > Message-ID: > < > CAPf2UMRevWFVsNmOrfF4AFjjjpmRXJLkjCtXbyqF+nO7eutBeQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Vishal, > > the most likely reason is listing libraries by name in CMakeLists.txt file. > You should replace line > set(Libraries ITKAlgorithms ITKBasicFilters ITKCommon ITKIO) > by line: > set(Libraries ${ITK_LIBRARIES}) > > If it doesn't work, let us know. > > HTH > > On Thu, Feb 4, 2016 at 12:08 AM, vishal wrote: > > > hi, > > I came across this paper An ITK-Based Framework for 2D-3D Registration > with > > Multiple Fixed Images by Alvaro Bertelsen and Diego Borro... first had to > > replace ::itk::OStringStream diffName; by std::ostringstream diffName; > > which solved some errors and now upon building the project again Im > getting > > the error saying *cannot open input file 'ITKAlgorithms.lib'*.. I > searched > > for ITKAlgorithms in my ITK 4.8.2 build folder but i *couldnt* find > it... > > i > > build the project in debug mode.. Please advice > > Regards > > vishal > > > > > > > > -- > > View this message in context: > > > http://itk-users.7.n7.nabble.com/Problem-building-jounal-paper-cannot-open-input-file-ITKAlgorithms-lib-tp36734.html > > Sent from the ITK - Users mailing list archive at Nabble.com. > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/community/attachments/20160204/a7f37d1e/attachment-0001.html > > > -------------- next part -------------- > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > ------------------------------ > > Message: 2 > Date: Thu, 4 Feb 2016 20:07:27 +0100 > From: Olivier Commowick > To: Insight-users > Subject: [ITK] [ITK-users] Multi-threader and thread pool > Message-ID: <919FD08C-D1FF-42B2-8806-CA70DE593E77 at inria.fr> > Content-Type: text/plain; charset="us-ascii" > > Hi everyone, > > I have recently discovered the existence of a thread pool class in ITK ( > http://itk.org/Doxygen/html/classitk_1_1ThreadPool.html < > http://itk.org/Doxygen/html/classitk_1_1ThreadPool.html>), closely linked > to the multi threader. From the doxygen, I am not really able to understand > how it can be used and I do not see any example for it. > > I have been looking for some time for a multi-threader, working on all > OSes, that can have more jobs in queue than the number of threads and > execute them when threads gets free, and this would seem like a good start. > So I was wondering how this thread pool actually behaves when used by the > multi-threader, what its goal is in ITK and all this sort of things. If > anyone had some idea about this or may be an example on how it could be > used, that would be great. > > Thanks > Olivier > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/community/attachments/20160204/e0352c21/attachment-0001.html > > > -------------- next part -------------- > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > ------------------------------ > > Message: 3 > Date: Thu, 4 Feb 2016 14:36:20 -0500 > From: Hyun Jae Kang > To: insight-developers at itk.org, Patrick Reynolds > > Subject: [ITK] [ITK-dev] [SimpleITK] Data Bridge for SimpleITK > Message-ID: > < > CAAsPJLowri4GCUDUnVUu858BVFMNYcsEhiuTxRvQz-9Otb4VHw at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > To support data transparency between the functions of SimpleITK and NumPy, > SimpleITK provides functional integration with NumPy-based script and a > method of data-conversion between SimpleITK?s image data and the > N-dimensional array object of NumPy. But, there is a significant > performance bottleneck in the data-conversion which is based on the > operation of data copy. The performance bottleneck can be increased with > the size of handling image data and the number of data-conversion. > > The performance bottle can be removed by allowing SimpleITK?s image and the > arrays of NumPy to share pointers to the same memory symmetrically with > copy-on-write semantics. That is, reduce data-copy operations in the data > conversion. This approach can be accomplished by developing and/or > improving existing data handling methods in ITK and SimpleITK to enable > copy-on-write sharing of data between SimpleITK?s image data and other > common data object of Python libraries used for scientific computing and > image processing. > > For more detail information, please check the following website: > http://www.itk.org/Wiki/SimpleITK/Design_And_Proposals/SIP_002 > > Any your valuable comments are welcome. > > Thanks, > > Hyun Jae > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/community/attachments/20160204/839f8f51/attachment-0001.html > > > -------------- next part -------------- > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > ------------------------------ > > Message: 4 > Date: Thu, 4 Feb 2016 15:04:11 -0500 > From: Matt McCormick > To: Olivier Commowick > Cc: Insight-users > Subject: Re: [ITK] [ITK-users] Multi-threader and thread pool > Message-ID: > BSA at mail.gmail.com> > Content-Type: text/plain; charset="us-ascii" > > Hi Olivier, > > The itk::ThreadPool is an experimental thread-pool feature. It is > considered experimental, and it maybe majorly modified in its API or > removed in the future. Our preliminary experiences is that ITK runs > slower when it is enabled. > > To enable it, call > > itk::MultiThreader::SetGlobalDefaultUseThreadPool( true ); > > In the future, we will be moving towards other thread pool backends by > adopting interfaces similar to vtkSMPTools and VTK-m. > > Thanks, > Matt > > On Thu, Feb 4, 2016 at 2:07 PM, Olivier Commowick > wrote: > > Hi everyone, > > > > I have recently discovered the existence of a thread pool class in ITK > > (http://itk.org/Doxygen/html/classitk_1_1ThreadPool.html), closely > linked to > > the multi threader. From the doxygen, I am not really able to understand > how > > it can be used and I do not see any example for it. > > > > I have been looking for some time for a multi-threader, working on all > OSes, > > that can have more jobs in queue than the number of threads and execute > them > > when threads gets free, and this would seem like a good start. So I was > > wondering how this thread pool actually behaves when used by the > > multi-threader, what its goal is in ITK and all this sort of things. If > > anyone had some idea about this or may be an example on how it could be > > used, that would be great. > > > > Thanks > > Olivier > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > > Message: 5 > Date: Thu, 4 Feb 2016 18:03:08 -0500 > From: David Burns > To: insight-developers at itk.org > Subject: Re: [ITK] [ITK-dev] [SimpleITK] Data Bridge for SimpleITK > Message-ID: <56B3D8AC.9090606 at gmail.com> > Content-Type: text/plain; charset="windows-1252"; Format="flowed" > > I just finished creating an interface between numpy/slicer and my ITK > C++ project module using SWIG. I use pointers to avoid copying and it > works well. Happy to share what I have. > > - David > > On 02/04/2016 02:36 PM, Hyun Jae Kang wrote: > > Hi all, > > > > To support data transparency between the functions of SimpleITK and > > NumPy, SimpleITK provides functional integration with NumPy-based > > script and a method of data-conversion between SimpleITK?s image data > > and the N-dimensional array object of NumPy. But, there is a > > significant performance bottleneck in the data-conversion which is > > based on the operation of data copy. The performance bottleneck can be > > increased with the size of handling image data and the number of > > data-conversion. > > > > The performance bottle can be removed by allowing SimpleITK?s image > > and the arrays of NumPy to share pointers to the same memory > > symmetrically with copy-on-write semantics. That is, reduce data-copy > > operations in the data conversion. This approach can be accomplished > > by developing and/or improving existing data handling methods in ITK > > and SimpleITK to enable copy-on-write sharing of data between > > SimpleITK?s image data and other common data object of Python > > libraries used for scientific computing and image processing. > > > > For more detail information, please check the following website: > > http://www.itk.org/Wiki/SimpleITK/Design_And_Proposals/SIP_002 > > > > Any your valuable comments are welcome. > > > > Thanks, > > > > Hyun Jae > > > > > > > > _______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-developers > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/community/attachments/20160204/19640093/attachment.html > > > -------------- next part -------------- > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > ------------------------------ > > End of Community Digest, Vol 29, Issue 15 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From itkhelpacc at gmail.com Fri Feb 5 05:48:37 2016 From: itkhelpacc at gmail.com (vishal) Date: Fri, 5 Feb 2016 03:48:37 -0700 (MST) Subject: [ITK] [ITK-users] Problem building jounal paper->cannot open input file 'ITKAlgorithms.lib' In-Reply-To: References: <1454562510446-36734.post@n7.nabble.com> Message-ID: <1454669317139-36738.post@n7.nabble.com> hi D?enan, thanks for the help it worked.. Regards Vishal -- View this message in context: http://itk-users.7.n7.nabble.com/Problem-building-jounal-paper-cannot-open-input-file-ITKAlgorithms-lib-tp36734p36738.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From itkhelpacc at gmail.com Fri Feb 5 06:04:48 2016 From: itkhelpacc at gmail.com (vishal) Date: Fri, 5 Feb 2016 04:04:48 -0700 (MST) Subject: [ITK] [ITK-users] Multiresolution Registration error while trying to improve a journal paper Message-ID: <1454670288825-36739.post@n7.nabble.com> hi, Im trying to improve upon the code presenting the website below https://github.com/InsightSoftwareConsortium/ITKTwoProjectionRegistration This is code that performs 2d/3d registration using two input 2D Xray image and one input 3D CT volume... it uses Euler3DTransform for registration...Im trying to do the following improvements to the code 1) Im trying to reduce the number in Xray input (to one since it is better for patient). this i have successfully achieve but the accuraccy is a little issue 2) inorder to improve the accuracy im trying write a MultiResolution version of the code. 3) use of Affine (or versor transform) to see if it improve the quality of registration. im having problems with 2 and 3... now for (2) im following An ITK-Based Framework for 2D-3D Registration with Multiple Fixed Images by Alvaro Bertelsen and Diego Borro paper AS WELL AS a out dated code "IntensityBased2D3DRegistration.cxx" as reference....im getting the following error:- *"Vector subscript out of range"* Can anyone please help me out? Regards Vishal -- View this message in context: http://itk-users.7.n7.nabble.com/Multiresolution-Registration-error-while-trying-to-improve-a-journal-paper-tp36739.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From davis.vigneault at gmail.com Fri Feb 5 07:12:56 2016 From: davis.vigneault at gmail.com (Davis Vigneault) Date: Fri, 5 Feb 2016 12:12:56 +0000 Subject: [ITK] [ITK-users] External Modules: Passing data to unit tests? In-Reply-To: References: <1453734722405-7588384.post@n2.nabble.com> <1453739768868-7588385.post@n2.nabble.com> Message-ID: Matt-- Sorry for the late reply--this looks like a valuable resource. I've just registered. Since this is phase data, it is best for it to be floating point. Does ITK have a preference for FP file type? I use .vtk out of habit but don't mind switching. Best, --Davis On Mon, Jan 25, 2016 at 6:23 PM, Matt McCormick wrote: > Hi Davis, > > ITKPhase looks like a very interesting module. > > It sounds like you have a handle on the ExternalData. Another > approach for ExternalData is to upload it to the "ITK" community on > midas3.kitware.com: > > http://midas3.kitware.com/midas/folder/10126 > > If you sign up for the community, please send me an email, and I will > give you upload permissions. Then, there is an icon for each file to > download the .md5 file. This process is illustrated here: > > > http://itk.org/ITKExamples/Documentation/Contribute/UploadBinaryData.html#upload-via-the-web-interface > > HTH, > Matt > > On Mon, Jan 25, 2016 at 11:36 AM, DVigneault > wrote: > > All-- > > > > I have it working now--here's what I didn't understand: > > > > 1. The hash replacement happens in the source tree only (not the bin). > > 2. The data files can be referenced as usual, e.g. > > DATA{Input//swi_wrapped.vtk} > > 3. The data files should be copied into > > bin/ExternalData/Modules/External/ITKPhase/text/Input, but if they are > not, > > copying them in manually may fix this (as it did in my case). > > > > Best, > > > > --Davis > > > > > > > > -- > > View this message in context: > http://itk-insight-users.2283740.n2.nabble.com/External-Modules-Passing-data-to-unit-tests-tp7588384p7588385.html > > Sent from the ITK Insight Users mailing list archive at Nabble.com. > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From steve at sumost.ca Fri Feb 5 08:49:37 2016 From: steve at sumost.ca (Steve M. Robbins) Date: Fri, 05 Feb 2016 07:49:37 -0600 Subject: [ITK] [ITK-dev] Nightly dashboard name changes Message-ID: <1700402.5GriD2y9rb@riemann> Hi, Last weekend, I realized that my nightly dashboard submissions were misnamed -- they had "gcc4" in the name, dating from the time that Debian's default gcc was switching to 4. In reality, the configuration uses the Debian default gcc which is now 5.x. So, please change the expected builds from: Debian-sid-gcc4-64bit Debian-sid-gcc4-32bit to: Debian-sid-default-64bit Debian-sid-default-32bit I also took the opportunity to update the configuration -- in terms of modules and external libs -- to match the current Debian package configuration. And now the 32-bit build is showing segfaults with FFTW. I believe we have seen this for a while; e.g. Debian's ITK 4.9 packages disabled FFTW on 32-bit for this reason. Thanks! -Steve -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 819 bytes Desc: This is a digitally signed message part. URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From sean at rogue-research.com Fri Feb 5 15:12:10 2016 From: sean at rogue-research.com (Sean McBride) Date: Fri, 5 Feb 2016 15:12:10 -0500 Subject: [ITK] [ITK-dev] Possible to build ITK libs without version number in filename? Message-ID: <20160205201210.521704264@mail.rogue-research.com> Hi all, Is it possible to build ITK such that the resulting library names do not have version numbers in them? ie instead of "libITKCommon-4.9.a" could it be just "libITKCommon.a"? VTK has a build option VTK_CUSTOM_LIBRARY_SUFFIX that you can set to an empty string to get this. Does ITK have something analogous? (The version numbers are annoying for me because my Xcode projects reference the ITK libs by filename, and every time the version is bumped it's a pain to switch back and forth.) Thanks, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From marcus.hanwell at kitware.com Fri Feb 5 18:44:13 2016 From: marcus.hanwell at kitware.com (Marcus D. Hanwell) Date: Fri, 5 Feb 2016 18:44:13 -0500 Subject: [ITK] [ITK-dev] Possible to build ITK libs without version number in filename? In-Reply-To: <20160205201210.521704264@mail.rogue-research.com> References: <20160205201210.521704264@mail.rogue-research.com> Message-ID: On Fri, Feb 5, 2016 at 3:12 PM, Sean McBride wrote: > Hi all, > > Is it possible to build ITK such that the resulting library names do not have version numbers in them? ie instead of "libITKCommon-4.9.a" could it be just "libITKCommon.a"? > > VTK has a build option VTK_CUSTOM_LIBRARY_SUFFIX that you can set to an empty string to get this. Does ITK have something analogous? > > (The version numbers are annoying for me because my Xcode projects reference the ITK libs by filename, and every time the version is bumped it's a pain to switch back and forth.) > This is something I would love to see, and I have been looking at this for VTK/ParaView too. You can set variables as you point out there to remove the version numbers, but there is not currently a simple option to turn it off. When creating binary packages the version numbers add to path lengths (can be an issue on Windows), and offer another point of failure. I can see why they are useful, but it would be good to make it simpler to turn them off in projects offering versioned install libraries/directories. Best, Marcus _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Fri Feb 5 21:36:10 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 5 Feb 2016 21:36:10 -0500 Subject: [ITK] [ITK-users] External Modules: Passing data to unit tests? In-Reply-To: References: <1453734722405-7588384.post@n2.nabble.com> <1453739768868-7588385.post@n2.nabble.com> Message-ID: Hi Davis, > Sorry for the late reply--this looks like a valuable resource. I've just > registered. Great! Your account now has upload permissions. > Since this is phase data, it is best for it to be floating point. Does ITK > have a preference for FP file type? I use .vtk out of habit but don't mind > switching. There is not a preferred format -- .vtk will be fine. I personally prefer MetaImage with .mha. ITK has the best support for this format (streaming read and write, compression, read/write of the MetaDataDictionary, all pixel types supported). Thanks, Matt _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Fri Feb 5 23:17:03 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 5 Feb 2016 23:17:03 -0500 Subject: [ITK] [ITK-dev] Nightly dashboard name changes In-Reply-To: <1700402.5GriD2y9rb@riemann> References: <1700402.5GriD2y9rb@riemann> Message-ID: Hi Steve, Thanks for the updates! The builds have been move out / in of the Expected Nightly section on the dashboard. Thanks, Matt On Fri, Feb 5, 2016 at 8:49 AM, Steve M. Robbins wrote: > Hi, > > Last weekend, I realized that my nightly dashboard submissions were misnamed > -- they had "gcc4" in the name, dating from the time that Debian's default gcc > was switching to 4. In reality, the configuration uses the Debian default gcc > which is now 5.x. > > So, please change the expected builds from: > Debian-sid-gcc4-64bit > Debian-sid-gcc4-32bit > > to: > Debian-sid-default-64bit > Debian-sid-default-32bit > > I also took the opportunity to update the configuration -- in terms of modules > and external libs -- to match the current Debian package configuration. And > now the 32-bit build is showing segfaults with FFTW. I believe we have seen > this for a while; e.g. Debian's ITK 4.9 packages disabled FFTW on 32-bit for > this reason. > > Thanks! > -Steve > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From bakkari.abdelkhalek at hotmail.fr Sat Feb 6 06:31:20 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Sat, 6 Feb 2016 12:31:20 +0100 Subject: [ITK] [ITK-users] Failed to allocate memory for image Message-ID: Hi, I am using ITK for loading 361 CT images. But, When I tried to process it, an error appears : Exception caught ! itk::MemoryAllocationError (01CDCE98)Location: "unknown"File: c:\itk 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxxLine: 199Description: Failed to allocate memory for image. Exception caught ! itk::MemoryAllocationError (01CDCE5C)Location: "unknown"File: c:\itk 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxxLine: 199Description: Failed to allocate memory for image. Exception thrown while writing the series itk::MemoryAllocationError (01CDCD90)Location: "unknown"File: c:\itk 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxxLine: 199Description: Failed to allocate memory for image. Best regards, Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Sat Feb 6 08:29:10 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Sat, 6 Feb 2016 08:29:10 -0500 Subject: [ITK] [ITK-users] Failed to allocate memory for image In-Reply-To: References: Message-ID: Isn't it self explanatory? If you have compiled ITK in 32 bits, or have little available memory would trigger such an exception. Regards On Sat, Feb 6, 2016 at 6:31 AM, Abdelkhalek Bakkari < bakkari.abdelkhalek at hotmail.fr> wrote: > > Hi, > > I am using ITK for loading 361 CT images. But, When I tried to process it, > an error appears : > > > Exception caught ! > > itk::MemoryAllocationError (01CDCE98) > Location: "unknown" > File: c:\itk > 4.8.1\source\modules\core\common\include\itkImportImageContainer.hx > x > Line: 199 > Description: Failed to allocate memory for image. > > > Exception caught ! > > itk::MemoryAllocationError (01CDCE5C) > Location: "unknown" > File: c:\itk > 4.8.1\source\modules\core\common\include\itkImportImageContainer.hx > x > Line: 199 > Description: Failed to allocate memory for image. > > > Exception thrown while writing the series > > itk::MemoryAllocationError (01CDCD90) > Location: "unknown" > File: c:\itk > 4.8.1\source\modules\core\common\include\itkImportImageContainer.hx > x > Line: 199 > Description: Failed to allocate memory for image. > > > Best regards, > > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From millerjv at gmail.com Sat Feb 6 09:27:52 2016 From: millerjv at gmail.com (Jim Miller) Date: Sat, 6 Feb 2016 09:27:52 -0500 Subject: [ITK] [ITK-users] Failed to allocate memory for image In-Reply-To: <20160206140303.GA32042@jerng.de> References: <20160206140303.GA32042@jerng.de> Message-ID: <5E7F8A68-C4A9-4CA0-9825-D769D4497E90@gmail.com> Each of Abdelkhalek's volumes are 180 MB if kept as shorts. How much memory is needed depends on the types and sequences of filters. If a filter switches to processing floats (diffusion) or vectors (gradients), then the memory will needs escalate. Most filters needs two buffers - an input and output. Some need intermediate and temporary buffers. Filters like Watershed can need a lot of internal storage. If you have a long pipeline of filters, you should investigate the methods to release memory after a filter executes, such as ReleaseDataFlagOn(). You can also use scoping and DIsconnectPipeline() to force individual filters to release resources. Jim > On Feb 6, 2016, at 9:03 AM, JE via Insight-users wrote: > > How large is one CT image (file size on disk)? > >> On 06.02.16, 12:31, Abdelkhalek Bakkari wrote: >> Hi, >> I am using ITK for loading 361 CT images. But, When I tried to process it, an error appears : >> >> Exception caught ! >> itk::MemoryAllocationError (01CDCE98)Location: "unknown"File: c:\itk 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxxLine: 199Description: Failed to allocate memory for image. >> >> Exception caught ! >> itk::MemoryAllocationError (01CDCE5C)Location: "unknown"File: c:\itk 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxxLine: 199Description: Failed to allocate memory for image. >> >> Exception thrown while writing the series >> itk::MemoryAllocationError (01CDCD90)Location: "unknown"File: c:\itk 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxxLine: 199Description: Failed to allocate memory for image. >> >> Best regards, >> >> Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland >> > >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From bakkari.abdelkhalek at hotmail.fr Sat Feb 6 09:51:39 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Sat, 6 Feb 2016 15:51:39 +0100 Subject: [ITK] [ITK-users] Failed to allocate memory for image In-Reply-To: <20160206140303.GA32042@jerng.de> References: , <20160206140303.GA32042@jerng.de> Message-ID: 512*512 Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland > Date: Sat, 6 Feb 2016 15:03:03 +0100 > From: wer.wie.was.wiso.weshalb.warum at googlemail.com > To: bakkari.abdelkhalek at hotmail.fr > CC: insight-users at itk.org > Subject: Re: [ITK-users] Failed to allocate memory for image > > How large is one CT image (file size on disk)? > > On 06.02.16, 12:31, Abdelkhalek Bakkari wrote: > > Hi, > > I am using ITK for loading 361 CT images. But, When I tried to process it, an error appears : > > > > Exception caught ! > > itk::MemoryAllocationError (01CDCE98)Location: "unknown"File: c:\itk 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxxLine: 199Description: Failed to allocate memory for image. > > > > Exception caught ! > > itk::MemoryAllocationError (01CDCE5C)Location: "unknown"File: c:\itk 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxxLine: 199Description: Failed to allocate memory for image. > > > > Exception thrown while writing the series > > itk::MemoryAllocationError (01CDCD90)Location: "unknown"File: c:\itk 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxxLine: 199Description: Failed to allocate memory for image. > > > > Best regards, > > > > Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland > > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Sat Feb 6 12:51:58 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Sat, 6 Feb 2016 12:51:58 -0500 Subject: [ITK] [ITK-dev] Possible to build ITK libs without version number in filename? In-Reply-To: <20160205201210.521704264@mail.rogue-research.com> References: <20160205201210.521704264@mail.rogue-research.com> Message-ID: Hi Sean, version numbers shouldn't be an issue if you configure your project using CMake (which automatically takes care of all library paths). I forgot how much of a pain in the ass it is to set those paths without CMake - something one project reminded me of this week. HTH, D?enan On Fri, Feb 5, 2016 at 3:12 PM, Sean McBride wrote: > Hi all, > > Is it possible to build ITK such that the resulting library names do not > have version numbers in them? ie instead of "libITKCommon-4.9.a" could it > be just "libITKCommon.a"? > > VTK has a build option VTK_CUSTOM_LIBRARY_SUFFIX that you can set to an > empty string to get this. Does ITK have something analogous? > > (The version numbers are annoying for me because my Xcode projects > reference the ITK libs by filename, and every time the version is bumped > it's a pain to switch back and forth.) > > Thanks, > > -- > ____________________________________________________________ > Sean McBride, B. Eng sean at rogue-research.com > Rogue Research www.rogue-research.com > Mac Software Developer Montr?al, Qu?bec, Canada > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From dzenanz at gmail.com Sat Feb 6 12:56:07 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Sat, 6 Feb 2016 12:56:07 -0500 Subject: [ITK] [ITK-users] Multiresolution Registration error while trying to improve a journal paper In-Reply-To: <1454670288825-36739.post@n7.nabble.com> References: <1454670288825-36739.post@n7.nabble.com> Message-ID: Hi Vishal, if compiler or OS says that vector subscript is out of range, you better believe it :) Joking aside, we will need more information (source code, preferably MWE) to help you. Index out of bounds is way too general. Regards, D?enan On Fri, Feb 5, 2016 at 6:04 AM, vishal wrote: > hi, > Im trying to improve upon the code presenting the website below > https://github.com/InsightSoftwareConsortium/ITKTwoProjectionRegistration > This is code that performs 2d/3d registration using two input 2D Xray image > and one input 3D CT volume... it uses Euler3DTransform for > registration...Im > trying to do the following improvements to the code > 1) Im trying to reduce the number in Xray input (to one since it is better > for patient). this i have successfully achieve but the accuraccy is a > little > issue > 2) inorder to improve the accuracy im trying write a MultiResolution > version > of the code. > > 3) use of Affine (or versor transform) to see if it improve the quality of > registration. > > im having problems with 2 and 3... now for (2) im following An ITK-Based > Framework for 2D-3D Registration with Multiple Fixed Images by Alvaro > Bertelsen and Diego Borro paper AS WELL AS a out dated code > "IntensityBased2D3DRegistration.cxx" as reference....im getting the > following error:- > *"Vector subscript out of range"* > > Can anyone please help me out? > Regards > Vishal > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/Multiresolution-Registration-error-while-trying-to-improve-a-journal-paper-tp36739.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From sean at rogue-research.com Sat Feb 6 13:55:57 2016 From: sean at rogue-research.com (Sean McBride) Date: Sat, 6 Feb 2016 13:55:57 -0500 Subject: [ITK] [ITK-dev] Possible to build ITK libs without version number in filename? In-Reply-To: References: <20160205201210.521704264@mail.rogue-research.com> Message-ID: <20160206185557.1429073654@mail.rogue-research.com> On Sat, 6 Feb 2016 12:51:58 -0500, D?enan Zuki? said: >version numbers shouldn't be an issue if you configure your project using >CMake (which automatically takes care of all library paths). I know, but as I said in my post, I don't use CMake. I use CMake to build ITK of course, but my main app, which links to ITK, uses Xcode, and that can't/won't change. ITK is a library, it's common to link to libraries in a variety of ways. Do you know how your libc was built? Do you care? Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From bakkari.abdelkhalek at hotmail.fr Sat Feb 6 14:48:31 2016 From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari) Date: Sat, 6 Feb 2016 20:48:31 +0100 Subject: [ITK] [ITK-users] FW: Failed to allocate memory for image In-Reply-To: References: , , Message-ID: Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland Fuzzy image processing is the collection of all approaches that understand, represent and process the images, their segments and features as fuzzy sets. The representation and processing depend on selected fuzzy technique and on the problem to be solved. From: bakkari.abdelkhalek at hotmail.fr To: dzenanz at gmail.com Subject: RE: Failed to allocate memory for image Date: Sat, 6 Feb 2016 20:47:54 +0100 Yes, it is self explanatory.I have compiled ITK in 32 bits. The RAM of my laptop is 16 Go. How can I solve this problem, please? Best regards, Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland From: dzenanz at gmail.com Date: Sat, 6 Feb 2016 08:29:10 -0500 Subject: Re: Failed to allocate memory for image To: bakkari.abdelkhalek at hotmail.fr CC: insight-users at itk.org Isn't it self explanatory? If you have compiled ITK in 32 bits, or have little available memory would trigger such an exception. Regards On Sat, Feb 6, 2016 at 6:31 AM, Abdelkhalek Bakkari wrote: Hi, I am using ITK for loading 361 CT images. But, When I tried to process it, an error appears : Exception caught ! itk::MemoryAllocationError (01CDCE98)Location: "unknown"File: c:\itk 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxxLine: 199Description: Failed to allocate memory for image. Exception caught ! itk::MemoryAllocationError (01CDCE5C)Location: "unknown"File: c:\itk 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxxLine: 199Description: Failed to allocate memory for image. Exception thrown while writing the series itk::MemoryAllocationError (01CDCD90)Location: "unknown"File: c:\itk 4.8.1\source\modules\core\common\include\itkImportImageContainer.hxxLine: 199Description: Failed to allocate memory for image. Best regards, Abdelkhalek BakkariPh.D candidate in Computer ScienceInstitute of Applied Computer ScienceLodz University of Technology, Poland -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Sat Feb 6 14:54:29 2016 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Sat, 6 Feb 2016 19:54:29 +0000 Subject: [ITK] [ITK-users] FW: Failed to allocate memory for image In-Reply-To: References: , , , Message-ID: Build the 64-bit libraries. ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Abdelkhalek Bakkari [bakkari.abdelkhalek at hotmail.fr] Sent: Sunday, 7 February 2016 8:48 a.m. To: dzenanz at gmail.com Cc: insight-users Subject: [ITK-users] FW: Failed to allocate memory for image Abdelkhalek Bakkari Ph.D candidate in Computer Science Institute of Applied Computer Science Lodz University of Technology, Poland Fuzzy image processing is the collection of all approaches that understand, represent and process the images, their segments and features as fuzzy sets. The representation and processing depend on selected fuzzy technique and on the problem to be solved. ________________________________ From: bakkari.abdelkhalek at hotmail.fr To: dzenanz at gmail.com Subject: RE: Failed to allocate memory for image Date: Sat, 6 Feb 2016 20:47:54 +0100 Yes, it is self explanatory. I have compiled ITK in 32 bits. The RAM of my laptop is 16 Go. How can I solve this problem, please? Best regards, Abdelkhalek Bakkari Ph.D candidate in Computer Science Institute of Applied Computer Science Lodz University of Technology, Poland ________________________________ From: dzenanz at gmail.com Date: Sat, 6 Feb 2016 08:29:10 -0500 Subject: Re: Failed to allocate memory for image To: bakkari.abdelkhalek at hotmail.fr CC: insight-users at itk.org Isn't it self explanatory? If you have compiled ITK in 32 bits, or have little available memory would trigger such an exception. Regards On Sat, Feb 6, 2016 at 6:31 AM, Abdelkhalek Bakkari > wrote: Hi, I am using ITK for loading 361 CT images. But, When I tried to process it, an error appears : Exception caught ! itk::MemoryAllocationError (01CDCE98) Location: "unknown" File: c:\itk 4.8.1\source\modules\core\common\include\itkImportImageContainer.hx x Line: 199 Description: Failed to allocate memory for image. Exception caught ! itk::MemoryAllocationError (01CDCE5C) Location: "unknown" File: c:\itk 4.8.1\source\modules\core\common\include\itkImportImageContainer.hx x Line: 199 Description: Failed to allocate memory for image. Exception thrown while writing the series itk::MemoryAllocationError (01CDCD90) Location: "unknown" File: c:\itk 4.8.1\source\modules\core\common\include\itkImportImageContainer.hx x Line: 199 Description: Failed to allocate memory for image. Best regards, Abdelkhalek Bakkari Ph.D candidate in Computer Science Institute of Applied Computer Science Lodz University of Technology, Poland -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Sat Feb 6 14:57:23 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sat, 6 Feb 2016 14:57:23 -0500 Subject: [ITK] [ITK-users] FW: Failed to allocate memory for image In-Reply-To: References: Message-ID: Hi, Depending on classes involved, streaming can reduce memory consumption. See [1] [2] [3]. HTH, Matt [1] http://itk.org/ITKExamples/src/Core/Common/StreamAPipeline/Documentation.html [2] http://www.kitware.com/media/html/IOStreamingInITK.html [3] http://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch8.html#x49-1300008.3 On Sat, Feb 6, 2016 at 2:54 PM, Gib Bogle wrote: > Build the 64-bit libraries. > ________________________________ > From: Insight-users [insight-users-bounces at itk.org] on behalf of Abdelkhalek > Bakkari [bakkari.abdelkhalek at hotmail.fr] > Sent: Sunday, 7 February 2016 8:48 a.m. > To: dzenanz at gmail.com > Cc: insight-users > Subject: [ITK-users] FW: Failed to allocate memory for image > > > > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > Fuzzy image processing is the collection of all approaches that understand, > represent and process the images, their segments and features as fuzzy sets. > The representation and processing depend on selected fuzzy technique and on > the problem to be solved. > > > ________________________________ > From: bakkari.abdelkhalek at hotmail.fr > To: dzenanz at gmail.com > Subject: RE: Failed to allocate memory for image > Date: Sat, 6 Feb 2016 20:47:54 +0100 > > > Yes, it is self explanatory. > I have compiled ITK in 32 bits. The RAM of my laptop is 16 Go. > > How can I solve this problem, please? > > Best regards, > > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > > ________________________________ > From: dzenanz at gmail.com > Date: Sat, 6 Feb 2016 08:29:10 -0500 > Subject: Re: Failed to allocate memory for image > To: bakkari.abdelkhalek at hotmail.fr > CC: insight-users at itk.org > > Isn't it self explanatory? If you have compiled ITK in 32 bits, or have > little available memory would trigger such an exception. > > Regards > > On Sat, Feb 6, 2016 at 6:31 AM, Abdelkhalek Bakkari > wrote: > > > Hi, > > I am using ITK for loading 361 CT images. But, When I tried to process it, > an error appears : > > > Exception caught ! > > itk::MemoryAllocationError (01CDCE98) > Location: "unknown" > File: c:\itk > 4.8.1\source\modules\core\common\include\itkImportImageContainer.hx > x > Line: 199 > Description: Failed to allocate memory for image. > > > Exception caught ! > > itk::MemoryAllocationError (01CDCE5C) > Location: "unknown" > File: c:\itk > 4.8.1\source\modules\core\common\include\itkImportImageContainer.hx > x > Line: 199 > Description: Failed to allocate memory for image. > > > Exception thrown while writing the series > > itk::MemoryAllocationError (01CDCD90) > Location: "unknown" > File: c:\itk > 4.8.1\source\modules\core\common\include\itkImportImageContainer.hx > x > Line: 199 > Description: Failed to allocate memory for image. > > > Best regards, > > > Abdelkhalek Bakkari > Ph.D candidate in Computer Science > Institute of Applied Computer Science > Lodz University of Technology, Poland > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Sat Feb 6 16:03:21 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sat, 6 Feb 2016 16:03:21 -0500 Subject: [ITK] [ITK-dev] Possible to build ITK libs without version number in filename? In-Reply-To: <20160206185557.1429073654@mail.rogue-research.com> References: <20160205201210.521704264@mail.rogue-research.com> <20160206185557.1429073654@mail.rogue-research.com> Message-ID: Hi, Please review this patch, which adds an ITK_CUSTOM_LIBRARY_SUFFIX variable similar to VTK. HTH, Matt On Sat, Feb 6, 2016 at 1:55 PM, Sean McBride wrote: > On Sat, 6 Feb 2016 12:51:58 -0500, D?enan Zuki? said: > >>version numbers shouldn't be an issue if you configure your project using >>CMake (which automatically takes care of all library paths). > > I know, but as I said in my post, I don't use CMake. I use CMake to build ITK of course, but my main app, which links to ITK, uses Xcode, and that can't/won't change. ITK is a library, it's common to link to libraries in a variety of ways. Do you know how your libc was built? Do you care? > > Cheers, > > -- > ____________________________________________________________ > Sean McBride, B. Eng sean at rogue-research.com > Rogue Research www.rogue-research.com > Mac Software Developer Montr?al, Qu?bec, Canada > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From goretzki.imre at gmail.com Sun Feb 7 15:27:54 2016 From: goretzki.imre at gmail.com (Imre Goretzki) Date: Sun, 7 Feb 2016 21:27:54 +0100 Subject: [ITK] Image Quartiles Message-ID: <56B7A8CA.4070706@gmail.com> Hey guys, I'd like to ask, if there already is a filter, that calculates the lower and upper quartile of an (3D) image. I know there is the StatisticsImageFilter http://itk.org/Wiki/ITK/Examples/Statistics/StatisticsImageFilter but this filter only returns the mean, min, max and the standard deviation. Thanks in advance. Imre From matt.mccormick at kitware.com Sun Feb 7 17:21:45 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 7 Feb 2016 17:21:45 -0500 Subject: [ITK] Image Quartiles In-Reply-To: <56B7A8CA.4070706@gmail.com> References: <56B7A8CA.4070706@gmail.com> Message-ID: Hi Imre, ITK has a a fast quick select algorithm that can be used to find quartiles. The Software Guide describes its application [1]. HTH, Matt [1] http://itk.org/ITKSoftwareGuide/html/Book2/ITKSoftwareGuide-Book2ch5.html#x38-2000005 On Sun, Feb 7, 2016 at 3:27 PM, Imre Goretzki wrote: > Hey guys, > > I'd like to ask, if there already is a filter, that calculates the lower and > upper quartile of an (3D) image. > I know there is the StatisticsImageFilter > > http://itk.org/Wiki/ITK/Examples/Statistics/StatisticsImageFilter > > but this filter only returns the mean, min, max and the standard deviation. > > Thanks in advance. > Imre > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From goretzki.imre at gmail.com Mon Feb 8 02:03:55 2016 From: goretzki.imre at gmail.com (Imre Goretzki) Date: Sun, 7 Feb 2016 23:03:55 -0800 Subject: [ITK] Image Quartiles In-Reply-To: References: <56B7A8CA.4070706@gmail.com> Message-ID: Thank you Matt Am 07.02.2016 23:22 schrieb "Matt McCormick" : > Hi Imre, > > ITK has a a fast quick select algorithm that can be used to find > quartiles. The Software Guide describes its application [1]. > > HTH, > Matt > > [1] > http://itk.org/ITKSoftwareGuide/html/Book2/ITKSoftwareGuide-Book2ch5.html#x38-2000005 > > On Sun, Feb 7, 2016 at 3:27 PM, Imre Goretzki > wrote: > > Hey guys, > > > > I'd like to ask, if there already is a filter, that calculates the lower > and > > upper quartile of an (3D) image. > > I know there is the StatisticsImageFilter > > > > http://itk.org/Wiki/ITK/Examples/Statistics/StatisticsImageFilter > > > > but this filter only returns the mean, min, max and the standard > deviation. > > > > Thanks in advance. > > Imre > > _______________________________________________ > > Community mailing list > > Community at itk.org > > http://public.kitware.com/mailman/listinfo/community > -------------- next part -------------- An HTML attachment was scrubbed... URL: From itkhelpacc at gmail.com Mon Feb 8 03:03:23 2016 From: itkhelpacc at gmail.com (vishal) Date: Mon, 8 Feb 2016 01:03:23 -0700 (MST) Subject: [ITK] [ITK-users] Multiresolution Registration error while trying to improve a journal paper In-Reply-To: References: <1454670288825-36739.post@n7.nabble.com> Message-ID: <1454918603453-36751.post@n7.nabble.com> hey D?enan, this is the code below is a multiresolution version of the registration code in this https://github.com/InsightSoftwareConsortium/ITKTwoProjectionRegistration project... first when i tried to build and execute the code it shows the error "vector subscript is out of range".. then i tried to modified the github code keeping IntensityBased2D3DRegistration(the code below) as a reference it still shows another error called "access violation location...." ... kindly help me out... PLS NOTE:- i modified the code to take only one 2d image and one 3d volume inorder to perform registration. to run this code u will have to build the GetSiddonRayCastTracing.cxx code and obtain a projection. then build the code below and give the following arguments: Something.exe -v theProjectionFromtheStepAbove.dcm 0 3Dvolume.dcm where 0 is the projection angle. regards Vishal /*========================================================================= * * Copyright Insight Software Consortium * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0.txt * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * *=========================================================================*/ /*========================================================================= This program implements an intensity based 2D-3D registration algorithm using the SiddonJacobsRayCastInterpolateImageFunction and NormalizedCorrelationTwoImageToOneImageMetric similarity measure PowellOptimizer is used as the optimization method to avoid gradient calculation. Euler3DTransform instead of CenteredEuler3DTransform is used to avoid the shift of the center. When generating DRRs, the program attempts to simulate a 2D imaging system attached to a linac for radiation therapy. The program registers two 2D portal images with their corresponding DRR images generated from the 3D dataset. The portal images may be acquired at any arbitrary projection angles. The similarity measure is the summation of the measures calculated each projection. Multiresolution strategy was not implemented. This program was modified from the ITK application--IntensityBased2D3DRegistration.cxx =========================================================================*/ //#include "itkTwoProjectionImageRegistrationMethod.h" // The transformation used is a rigid 3D Euler transform with the // provision of a center of rotation which defaults to the center of // the 3D volume. In practice the center of the particular feature of // interest in the 3D volume should be used. #include //WRITTEN USING IntesityBased2D3dRegistration.cxx & MultiResImageRegistration3.cxx #include "itkEuler3DTransform.h" // We have chosen to implement the registration using the normalized coorelation // similarity measure. //#include "itkGradientDifferenceTwoImageToOneImageMetric.h" //#include "itkNormalizedCorrelationTwoImageToOneImageMetric.h" // This is an intensity based registration algorithm so ray casting is // used to project the 3D volume onto pixels in the target 2D image. #include "itkSiddonJacobsRayCastInterpolateImageFunction.h" #include "itkMultiResolutionImageRegistrationMethod.h" // Finally the Powell optimizer is used to avoid requiring gradient information. //#include "itkPowellOptimizer.h" #include "itkRegularStepGradientDescentOptimizer.h" #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkResampleImageFilter.h" #include "itkCastImageFilter.h" #include "itkRescaleIntensityImageFilter.h" #include "itkFlipImageFilter.h" #include "itkCommand.h" #include "itkTimeProbesCollectorBase.h" //MODIFIED HEADERS //#include "itkImageRegistrationMethodv4.h" //#include #include //#include "itkMattesMutualInformationImageToImageMetric.h" //#include //#include "itkEuler3DTransform.h" //#include "itkPowellOptimizer.h" // //#include "itkImageFileReader.h" //#include "itkImageFileWriter.h" // //#include "itkResampleImageFilter.h" //#include "itkCastImageFilter.h" //#include "itkRescaleIntensityImageFilter.h" //#include "itkFlipImageFilter.h" // //#include "itkCommand.h" //#include "itkTimeProbesCollectorBase.h" //#include "itkSiddonJacobsRayCastInterpolateImageFunction.h" // First we define the command class to allow us to monitor the registration. class CommandIterationUpdate : public itk::Command { public: typedef CommandIterationUpdate Self; typedef itk::Command Superclass; typedef itk::SmartPointer Pointer; itkNewMacro( Self ); protected: CommandIterationUpdate() {}; public: typedef itk::RegularStepGradientDescentOptimizer OptimizerType; typedef const OptimizerType * OptimizerPointer; void Execute(itk::Object *caller, const itk::EventObject & event) { Execute( (const itk::Object *)caller, event); } void Execute(const itk::Object *object, const itk::EventObject & event) { OptimizerPointer optimizer = dynamic_cast< OptimizerPointer >( object ); if( typeid( event ) != typeid( itk::IterationEvent ) ) { return; } std::cout << "Iteration: " << optimizer->GetCurrentIteration() << std::endl; std::cout << "Similarity: " << optimizer->GetValue() << std::endl; std::cout << "Position: " << optimizer->GetCurrentPosition() << std::endl; //std::cout<<"GETCURRENT LINE VALUE "<GetCurrentLineIteration()<< std::endl; } }; // Software Guide : BeginLatex // // A second \emph{Command/Observer} is used to reduce the minimum // registration step length on each occasion that the resolution of // the multi-scale registration is increased (see // \doxygen{MultiResImageRegistration1} for more info). // // Software Guide : EndLatex // Software Guide : BeginCodeSnippet template class RegistrationInterfaceCommand : public itk::Command { public: typedef RegistrationInterfaceCommand Self; typedef itk::Command Superclass; typedef itk::SmartPointer Pointer; itkNewMacro( Self ); protected: RegistrationInterfaceCommand() {}; public: typedef TRegistration RegistrationType; typedef RegistrationType * RegistrationPointer; typedef itk::RegularStepGradientDescentOptimizer OptimizerType; typedef OptimizerType * OptimizerPointer; void Execute(itk::Object * object, const itk::EventObject & event) ITK_OVERRIDE { /* if( typeid( event ) != typeid( itk::IterationEvent ) ) { return; }*/ //old if( !(itk::IterationEvent().CheckEvent( &event )) ) { return; } // RegistrationPointer registration = // dynamic_cast( object ); RegistrationPointer registration = static_cast( object ); // If this is the first resolution level we assume that the // maximum step length (representing the first step size) and the // minimum step length (representing the convergence criterion) // have already been set. At each subsequent resolution level, we // will reduce the minimum step length by a factor of four in order // to allow the optimizer to focus on progressively smaller // regions. The maximum step length is set to the current step // length. In this way, when the optimizer is reinitialized at the // beginning of the registration process for the next level, the // step length will simply start with the last value used for the // previous level. This will guarantee the continuity of the path // taken by the optimizer through the parameter space. if(registration == ITK_NULLPTR) { return; } /*OptimizerPointer optimizer = dynamic_cast< OptimizerPointer >( registration->GetOptimizer() );*/ OptimizerPointer optimizer = static_cast< OptimizerPointer >(registration->GetModifiableOptimizer() ); std::cout << "-------------------------------------" << std::endl; std::cout << "MultiResolution Level : " << registration->GetCurrentLevel() << std::endl; std::cout << std::endl; //if ( registration->GetCurrentLevel() != 0 ) //old // { // optimizer->SetMaximumStepLength( optimizer->GetCurrentStepLength() ); // optimizer->SetMinimumStepLength( optimizer->GetMinimumStepLength() / 4.0 ); // } if ( registration->GetCurrentLevel() == 0 ) { optimizer->SetMaximumStepLength( 16.00 ); optimizer->SetMinimumStepLength( 0.01 ); } else { optimizer->SetMaximumStepLength( optimizer->GetMaximumStepLength() / 4.0 ); optimizer->SetMinimumStepLength( optimizer->GetMinimumStepLength() / 10.0 ); } //mulit3 optimizer->Print( std::cout ); } /* void Execute(const itk::Object * , const itk::EventObject & ) { return; }*/ //old void Execute(const itk::Object * , const itk::EventObject & ) ITK_OVERRIDE { return; } //multi3 }; // Software Guide : EndCodeSnippet void exe_usage() { std::cerr << "\n"; std::cerr << "Usage: TwoProjection2D3DRegistration Image2D1 ProjAngle1 Image2D2 ProjAngle2 Volume3D\n"; std::cerr << " Registers two 2D images to a 3D volume. \n\n"; std::cerr << " where is one or more of the following:\n\n"; std::cerr << " <-h> Display (this) usage information\n"; std::cerr << " <-v> Verbose output [default: no]\n"; std::cerr << " <-dbg> Debugging output [default: no]\n"; // old std::cerr << " <-n int> The number of scales to apply [default: 2]\n"; std::cerr << " <-maxScale int> The scale factor corresponding to max resolution [default: 1]\n"; std::cerr << " <-step float float> Maximum and minimum step sizes [default: 4 and 0.01]\n"; //end old std::cerr << " <-scd float> Source to isocenter distance [default: 1000mm]\n"; std::cerr << " <-t float float float> CT volume translation in x, y, and z direction in mm \n"; std::cerr << " <-rx float> CT volume rotation about x axis in degrees \n"; std::cerr << " <-ry float> CT volume rotation about y axis in degrees \n"; std::cerr << " <-rz float> CT volume rotation about z axis in degrees \n"; std::cerr << " <-2dcx float float float float> Central axis positions of the 2D images in continuous indices \n"; std::cerr << " <-res float float float float> Pixel spacing of projection images in the isocenter plane [default: 1x1 mm] \n"; std::cerr << " <-iso float float float> Isocenter location in voxel in indices (center of rotation and projection center)\n"; std::cerr << " <-threshold float> Intensity threshold below which are ignore [default: 0]\n"; std::cerr << " <-o file> Output image filename\n\n"; std::cerr << " by Jian Wu\n"; std::cerr << " eewujian at hotmail.com\n"; std::cerr << " (Univeristy of Florida)\n\n"; exit(EXIT_FAILURE); } int main( int argc, char *argv[] ) { char *fileImage2D1 = NULL; double projAngle1 = -999; /* char *fileImage2D2 = NULL; double projAngle2 = -999;*/ char *fileVolume3D = NULL; // Default output file names const char *fileOutput1 = "Image2D1_Registered.tif"; //const char *fileOutput2 = "Image2D2_Registered.tif"; bool ok; bool verbose = false; bool debug = false; bool customized_iso = false; bool customized_2DCX = false; // Flag for customized 2D image central axis positions bool customized_2DRES = false; // Flag for customized 2D image pixel spacing unsigned int nScales = 2; //OLD PROG int maxScale = 1; //OLD PROG double rx = 0.; double ry = 0.; double rz = 0.; double tx = 0.; double ty = 0.; double tz = 0.; double cx = 0.; double cy = 0.; double cz = 0.; double scd = 1000.; // Source to isocenter distance double maxStepSize = 4.; //OLD PROG double minStepSize = 1.; //OLD PROG double image1centerX = 0.0; double image1centerY = 0.0; double image2centerX = 0.0; double image2centerY = 0.0; double image1resX = 1.0; double image1resY = 1.0; double image2resX = 1.0; double image2resY = 1.0; double threshold = 0.0; // Parse command line parameters //if (argc <= 5) //ORIGINAL if (argc <= 4) exe_usage(); while (argc > 1) { ok = false; if ((ok == false) && (strcmp(argv[1], "-h") == 0)) { argc--; argv++; ok = true; exe_usage(); } if ((ok == false) && (strcmp(argv[1], "-v") == 0)) { argc--; argv++; ok = true; verbose = true; std::cout<<"INSIDE -v"< ImageType3D; typedef unsigned char OutputPixelType; typedef itk::Image< OutputPixelType, Dimension > OutputImageType; // The following lines define each of the components used in the // registration: The transform, optimizer, metric, interpolator and // the registration method itself. typedef itk::Image< InternalPixelType, Dimension > InternalImageType; typedef itk::Euler3DTransform< double > TransformType; typedef itk::RegularStepGradientDescentOptimizer OptimizerType; //typedef itk::GradientDifferenceTwoImageToOneImageMetric< /* typedef itk::NormalizedCorrelationTwoImageToOneImageMetric< InternalImageType, InternalImageType > MetricType;*/ typedef itk::NormalizedCorrelationImageToImageMetric< InternalImageType, InternalImageType > MetricType; typedef itk::SiddonJacobsRayCastInterpolateImageFunction< InternalImageType, double > InterpolatorType; /* typedef itk::TwoProjectionImageRegistrationMethod< InternalImageType, InternalImageType > RegistrationType;*/ typedef itk::MultiResolutionImageRegistrationMethod< InternalImageType, InternalImageType > RegistrationType; // Software Guide : BeginCodeSnippet //THESE ARE THE CHANGES MADE typedef itk::MultiResolutionPyramidImageFilter< InternalImageType, InternalImageType > ImagePyramidType2D; typedef itk::MultiResolutionPyramidImageFilter< InternalImageType, InternalImageType > ImagePyramidType3D; // Software Guide : EndCodeSnippet // Each of the registration components are instantiated in the // usual way... ImagePyramidType2D::Pointer imagePyramid2D = ImagePyramidType2D::New(); ImagePyramidType3D::Pointer imagePyramid3D = ImagePyramidType3D::New(); std::cout<<"TYPES INTIALIZED"<ComputeGradientOff(); //ORIGINAL metric->ComputeGradientOn(); metric->SetSubtractMean( true ); // and passed to the registration method: registration->SetMetric( metric ); registration->SetOptimizer( optimizer ); registration->SetTransform( transform ); registration->SetInterpolator( interpolator1 ); // registration->SetInterpolator2( interpolator2 ); registration->SetFixedImagePyramid( imagePyramid2D ); registration->SetMovingImagePyramid( imagePyramid3D ); //changes made from 2d/3d std::cout<<"REGISTRATION METHODS SET"<DebugOn(); //transform->DebugOn(); //optimizer->DebugOn(); interpolator1->DebugOn(); // interpolator2->DebugOn(); //registration->DebugOn(); } // The 2- and 3-D images are read from files, typedef itk::ImageFileReader< InternalImageType > ImageReaderType2D; typedef itk::ImageFileReader< ImageType3D > ImageReaderType3D; ImageReaderType2D::Pointer imageReader2D1 = ImageReaderType2D::New(); // ImageReaderType2D::Pointer imageReader2D2 = ImageReaderType2D::New(); ImageReaderType3D::Pointer imageReader3D = ImageReaderType3D::New(); imageReader2D1->SetFileName( fileImage2D1 ); //imageReader2D2->SetFileName( fileImage2D2 ); imageReader3D->SetFileName( fileVolume3D ); imageReader3D->Update(); std::cout<<"2d 3d volume filename SET"<GetOutput(); // To simply Siddon-Jacob's fast ray-tracing algorithm, we force the origin of the CT image // to be (0,0,0). Because we align the CT isocenter with the central axis, the projection // geometry is fully defined. The origin of the CT image becomes irrelavent. ImageType3D::PointType image3DOrigin; image3DOrigin[0] = 0.0; image3DOrigin[1] = 0.0; image3DOrigin[2] = 0.0; image3DIn->SetOrigin(image3DOrigin); std::cout<<"VOLUME ORIGIN SET"<GetOutput(); //InternalImageType::Pointer image_tmp2 = imageReader2D2->GetOutput(); imageReader2D1->Update(); // imageReader2D2->Update(); if (customized_2DRES) { InternalImageType::SpacingType spacing; spacing[0] = image1resX; spacing[1] = image1resY; spacing[2] = 1.0; image_tmp1->SetSpacing( spacing ); // spacing[0] = image2resX; // spacing[1] = image2resY; // image_tmp2->SetSpacing( spacing ); } // The input 2D images were loaded as 3D images. They were considered // as a single slice from a 3D volume. By default, images stored on the // disk are treated as if they have RAI orientation. After view point // transformation, the order of 2D image pixel reading is equivalent to // from inferior to superior. This is contradictory to the traditional // 2D x-ray image storage, in which a typical 2D image reader reads and // writes images from superior to inferior. Thus the loaded 2D DICOM // images should be flipped in y-direction. This was done by using a. // FilpImageFilter. typedef itk::FlipImageFilter< InternalImageType > FlipFilterType; FlipFilterType::Pointer flipFilter1 = FlipFilterType::New(); // FlipFilterType::Pointer flipFilter2 = FlipFilterType::New(); typedef FlipFilterType::FlipAxesArrayType FlipAxesArrayType; FlipAxesArrayType flipArray; flipArray[0] = 0; flipArray[1] = 1; flipArray[2] = 0; flipFilter1->SetFlipAxes( flipArray ); // flipFilter2->SetFlipAxes( flipArray ); flipFilter1->SetInput( imageReader2D1->GetOutput() ); //flipFilter2->SetInput( imageReader2D2->GetOutput() ); // The input 2D images may have 16 bits. We rescale the pixel value to between 0-255. typedef itk::RescaleIntensityImageFilter< InternalImageType, InternalImageType > Input2DRescaleFilterType; Input2DRescaleFilterType::Pointer rescaler2D1 = Input2DRescaleFilterType::New(); rescaler2D1->SetOutputMinimum( 0 ); rescaler2D1->SetOutputMaximum( 255 ); rescaler2D1->SetInput( flipFilter1->GetOutput() ); std::cout<<"flipFilter1->GetOutput() SET"<SetOutputMinimum( 0 ); rescaler2D2->SetOutputMaximum( 255 ); rescaler2D2->SetInput( flipFilter2->GetOutput() );*/ // The 3D CT dataset is casted to the internal image type using // {CastImageFilters}. typedef itk::CastImageFilter< ImageType3D, InternalImageType > CastFilterType3D; CastFilterType3D::Pointer caster3D = CastFilterType3D::New(); caster3D->SetInput( image3DIn ); rescaler2D1->Update(); //rescaler2D2->Update(); caster3D->Update(); std::cout<<"caster3D->GetOutput() SET"<SetFixedImage( rescaler2D1->GetOutput() ); //registration->SetFixedImage2( rescaler2D2->GetOutput() ); registration->SetMovingImage( caster3D->GetOutput() ); registration->SetFixedImageRegion( rescaler2D1->GetOutput()->GetBufferedRegion() ); //changes made from 2d/3d // Initialise the transform // ~~~~~~~~~~~~~~~~~~~~~~~~ // Set the order of the computation. Default ZXY transform->SetComputeZYX(true); // The transform is initialised with the translation [tx,ty,tz] and // rotation [rx,ry,rz] specified on the command line TransformType::OutputVectorType translation; translation[0] = tx; translation[1] = ty; translation[2] = tz; transform->SetTranslation(translation); std::cout<<"transform->SetTranslation(translation); SET"<SetRotation(dtr*rx, dtr*ry, dtr*rz); std::cout<<"transform->SetRotation(dtr*rx, dtr*ry, dtr*rz) SET"<GetOrigin(); const itk::Vector resolution3D = image3DIn->GetSpacing(); typedef ImageType3D::RegionType ImageRegionType3D; typedef ImageRegionType3D::SizeType SizeType3D; ImageRegionType3D region3D = caster3D->GetOutput()->GetBufferedRegion(); SizeType3D size3D = region3D.GetSize(); TransformType::InputPointType isocenter; if (customized_iso) { // Isocenter location given by the user. isocenter[0] = origin3D[0] + resolution3D[0] * cx; isocenter[1] = origin3D[1] + resolution3D[1] * cy; isocenter[2] = origin3D[2] + resolution3D[2] * cz; } else { // Set the center of the image as the isocenter. isocenter[0] = origin3D[0] + resolution3D[0] * static_cast( size3D[0] ) / 2.0; isocenter[1] = origin3D[1] + resolution3D[1] * static_cast( size3D[1] ) / 2.0; isocenter[2] = origin3D[2] + resolution3D[2] * static_cast( size3D[2] ) / 2.0; } transform->SetCenter(isocenter); if (verbose) { std::cout << "3D image size: " << size3D[0] << ", " << size3D[1] << ", " << size3D[2] << std::endl << " resolution: " << resolution3D[0] << ", " << resolution3D[1] << ", " << resolution3D[2] << std::endl << "Transform: " << transform << std::endl; } // Set the origin of the 2D image // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // For correct (perspective) projection of the 3D volume, the 2D // image needs to be placed at a certain distance (the source-to- // isocenter distance {scd} ) from the focal point, and the normal // from the imaging plane to the focal point needs to be specified. // // By default, the imaging plane normal is set by default to the // center of the 2D image but may be modified from this using the // command line parameters [image1centerX, image1centerY, // image2centerX, image2centerY]. double origin2D1[ Dimension ]; // double origin2D2[ Dimension ]; // Note: Two 2D images may have different image sizes and pixel dimensions, although // scd are the same. const itk::Vector resolution2D1 = imageReader2D1->GetOutput()->GetSpacing(); //const itk::Vector resolution2D2 = imageReader2D2->GetOutput()->GetSpacing(); typedef InternalImageType::RegionType ImageRegionType2D; typedef ImageRegionType2D::SizeType SizeType2D; // ImageRegionType2D region2D1 = rescaler2D1->GetOutput()->GetBufferedRegion(); //ORIGINAL 2d/3d ImageRegionType2D region2D1 = rescaler2D1->GetOutput()->GetLargestPossibleRegion(); // ImageRegionType2D region2D2 = rescaler2D2->GetOutput()->GetBufferedRegion(); SizeType2D size2D1 = region2D1.GetSize(); // SizeType2D size2D2 = region2D2.GetSize(); if (!customized_2DCX) { // Central axis positions are not given by the user. Use the image centers // as the central axis position. image1centerX = ((double) size2D1[0] - 1.)/2.; image1centerY = ((double) size2D1[1] - 1.)/2.; //image2centerX = ((double) size2D2[0] - 1.)/2.; // image2centerY = ((double) size2D2[1] - 1.)/2.; } // 2D Image 1 origin2D1[0] = - resolution2D1[0] * image1centerX; origin2D1[1] = - resolution2D1[1] * image1centerY; origin2D1[2] = - scd; imageReader2D1->GetOutput()->SetOrigin( origin2D1 ); rescaler2D1->GetOutput()->SetOrigin( origin2D1 ); //// 2D Image 2 //origin2D2[0] = - resolution2D2[0] * image2centerX; //origin2D2[1] = - resolution2D2[1] * image2centerY; //origin2D2[2] = - scd; //imageReader2D2->GetOutput()->SetOrigin( origin2D2 ); //rescaler2D2->GetOutput()->SetOrigin( origin2D2 ); registration->SetFixedImageRegion( rescaler2D1->GetOutput()->GetBufferedRegion() ); //registration->SetFixedImageRegion2( rescaler2D2->GetOutput()->GetBufferedRegion() ); if (verbose) { std::cout << "2D image 1 size: " << size2D1[0] << ", " << size2D1[1] << ", " << size2D1[2] << std::endl << " resolution: " << resolution2D1[0] << ", " << resolution2D1[1] << ", " << resolution2D1[2] << std::endl << " and position: " << origin2D1[0] << ", " << origin2D1[1] << ", " << origin2D1[2] << std::endl; // << "2D image 2 size: " //<< size2D2[0] << ", " << size2D2[1] << ", " << size2D2[2] << std::endl //<< " resolution: " // << resolution2D2[0] << ", " << resolution2D2[1] << ", " << resolution2D2[2] << std::endl // << " and position: " // << origin2D2[0] << ", " << origin2D2[1] << ", " << origin2D2[2] << std::endl; } //---------------------------------------------------------------------------- // Set the moving and fixed images' schedules //---------------------------------------------------------------------------- const unsigned int ResolutionLevels = 3; std::cout<<"\nSet the moving and fixed images' schedules"<SetSchedules( fixedSchedule, movingSchedule ); std::cout<<"\nSet the moving and fixed images' schedules to registration"< sampledRes2D; // std::vector imageRegionPyramid2D; // imagePyramid2D->SetNumberOfLevels( nScales ); // std::cout<<"imagepyramid 2d"<GetSchedule(); // for ( unsigned int dim = 0; dim < ImageType3D::ImageDimension; dim++ ) // { // schedule2D[ nScales-1 ][ dim ] = maxScale; //std::cout<<"schedule2D["<= 0; level-- ) // { // for ( unsigned int dim = 0; dim < ImageType3D::ImageDimension; dim++ ) // { // schedule2D[ level ][ dim ] = 2*schedule2D[ level+1 ][ dim ]; // std::cout<<"schedule2D["<( schedule2D[ level ][ dim ] ); // size[ dim ] = static_cast( // floor( static_cast( size2D1[ dim ] ) / scaleFactor ) ); // if( size[ dim ] < 1 ) // { // size[ dim ] = 1; // schedule2D[ level ][ dim ] = 1; // } // std::cout << level << " " << dim << " " // << size[ dim ] << " " << schedule2D[ level ][ dim ] // << std::endl; // scaleFactor = static_cast( schedule2D[ level ][ dim ] ); // start[ dim ] = static_cast( // ceil( static_cast( inputStart2D[ dim ] ) / scaleFactor ) ); // if ( dim < 2 ) // { // sampledRes2D[ level ] += scaleFactor*resolution2D1[ dim ] // *scaleFactor*resolution2D1[ dim ]; // } // } // sampledRes2D[ level ] = sqrt( sampledRes2D[ level ] ); // imageRegionPyramid2D[ level ].SetSize( size ); // imageRegionPyramid2D[ level ].SetIndex( start ); // } // imagePyramid2D->SetSchedule( schedule2D ); //// Set the pyramid schedule for the 3D image //// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ //// Software Guide : BeginLatex //// //// The 3D image pyramid naturally contains the same number of levels //// as the multi-resolution schedule for the 2D image. In addition //// the sub-sampling factors for each level are set such that //// resolution of the 3D image in each case is reduced to no greater //// than the corresponding 2D image resolution at that scale. This //// ensures that the 3D volume is reduced in size as far as possible, //// minimising ray-casting computation time, whilst retaining //// sufficient information to ensure accurate production of the DRR //// at the resolution of the 2D image. //// //// Software Guide : EndLatex //std::vector imageRegionPyramid3D; //imagePyramid3D->SetNumberOfLevels( nScales ); // //imageRegionPyramid3D.reserve( nScales ); //typedef ImagePyramidType3D::ScheduleType ScheduleType3D; //ScheduleType3D schedule3D = imagePyramid3D->GetSchedule(); // //// Compute the 2D image pyramid schedule such that the 3D volume //// resolution is no greater than the 2D image resolution. //for ( unsigned int level=0; level < nScales; level++ ) // { // for ( unsigned int dim = 0; dim < ImageType3D::ImageDimension; dim++) // { // double res = resolution3D[ dim ]; // schedule3D[ level ][ dim ] = 1; // while ( res*2. < sampledRes2D[ level ] ) // { // schedule3D[ level ][ dim ] *= 2; // res *= 2.; // } // } // } // //// Compute the 3D ImageRegion corresponding to each level of the //// pyramid. //typedef ImageRegionType3D::IndexType IndexType3D; //IndexType3D inputStart3D = region3D.GetIndex(); //for ( unsigned int level=0; level < nScales; level++ ) // { // SizeType3D size; // IndexType3D start; // for ( unsigned int dim = 0; dim < ImageType3D::ImageDimension; dim++) // { // float scaleFactor = static_cast( schedule3D[ level ][ dim ] ); // size[ dim ] = static_cast( // floor( static_cast( size3D[ dim ] ) / scaleFactor ) ); // if( size[ dim ] < 1 ) // { // size[ dim ] = 1; // schedule3D[ level ][ dim ] = 1; // } // scaleFactor = static_cast( schedule3D[ level ][ dim ] ); // start[ dim ] = static_cast( // ceil( static_cast( inputStart3D[ dim ] ) / scaleFactor ) ); // } // imageRegionPyramid3D[ level ].SetSize( size ); // imageRegionPyramid3D[ level ].SetIndex( start ); // } //imagePyramid3D->SetSchedule( schedule3D ); // Initialize the ray cast interpolator // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // The ray cast interpolator is used to project the 3D volume. It // does this by casting rays from the (transformed) focal point to // each (transformed) pixel coordinate in the 2D image. // // In addition a threshold may be specified to ensure that only // intensities greater than a given value contribute to the // projected volume. This can be used, for instance, to remove soft // tissue from projections of CT data and force the registration // to find a match which aligns bony structures in the images. // 2D Image 1 interpolator1->SetProjectionAngle( dtr*projAngle1 ); interpolator1->SetFocalPointToIsocenterDistance(scd); interpolator1->SetThreshold(threshold); interpolator1->SetTransform(transform); interpolator1->Initialize(); std::cout<<"\nInterpolator"<SetProjectionAngle( dtr*projAngle2 ); interpolator2->SetFocalPointToIsocenterDistance(scd); interpolator2->SetThreshold(threshold); interpolator2->SetTransform(transform); interpolator2->Initialize(); */ // Set up the transform and start position // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // The registration start position is intialised using the // transformation parameters. registration->SetInitialTransformParameters( transform->GetParameters() ); //trying to set the FIXED parameter //#if defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) // After 4.8.1 // TransformType::FixedParametersType fixedParameters(3); //#else //Pre 4.8.1 // TransformType::ParametersType fixedParameters(6); //#endif // fixedParameters[0] = 0.0; // fixedParameters[1] = 0.0; // fixedParameters[3] = 0.0; // fixedParameters[4] = 0.0; // fixedParameters[5] = 0.0; // transform->SetFixedParameters( fixedParameters ); // We wish to minimize the negative normalized correlation similarity measure. // optimizer->SetMaximize( true ); // for GradientDifferenceTwoImageToOneImageMetric optimizer->SetMaximize( false ); // for NCC ORIGINAL //optimizer->SetMaximize( true ); //NCC CHANGED optimizer->SetMaximumStepLength( maxStepSize ); optimizer->SetMinimumStepLength( minStepSize ); //optimizer->SetStepLength(2); // ORGINAL 4 //optimizer->SetStepTolerance( 0.01); //ORIGINAL 0.02 //optimizer->SetValueTolerance( 0.00001 );//ORIGINAL 0.001 //optimizer->SetMetricWorstPossibleValue(-0.2); optimizer->SetNumberOfIterations(200); // The optimizer weightings are set such that one degree equates to // one millimeter. itk::Optimizer::ScalesType weightings( transform->GetNumberOfParameters() ); std::cout<<"transform->GetNumberOfParameters()==>"<GetNumberOfParameters()<SetScales( weightings ); // optimizer->SetMetricWorstPossibleValue(0);//to change the stop condition if (verbose) { optimizer->Print( std::cout ); } // Create the observers // ~~~~~~~~~~~~~~~~~~~~ CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New(); optimizer->AddObserver( itk::IterationEvent(), observer ); // Software Guide : BeginLatex // // Once all the registration components are in place we can create // an instance of the interface command and connect it to the // registration object using the \code{AddObserver()} method. // // Software Guide : EndLatex // Software Guide : BeginCodeSnippet typedef RegistrationInterfaceCommand CommandType; CommandType::Pointer command = CommandType::New(); registration->AddObserver( itk::IterationEvent(), command ); // Software Guide : EndCodeSnippet // Software Guide : BeginLatex // // Finally we set the number of multi-resolution levels: // // Software Guide : EndLatex // Software Guide : BeginCodeSnippet //registration->SetNumberOfLevels( nScales ); //// Software Guide : EndCodeSnippet //imagePyramid3D->Print(std::cout); //imagePyramid2D->Print(std::cout); // Start the registration // ~~~~~~~~~~~~~~~~~~~~~~ // Create a timer to record calculation time. itk::TimeProbesCollectorBase timer; if (verbose) { std::cout << "Starting the registration now..." << std::endl; } try { timer.Start("Registration"); // Start the registration. registration->StartRegistration(); timer.Stop("Registration"); } catch( itk::ExceptionObject & err ) { std::cout << "ExceptionObject caught !" << std::endl; std::cout << err << std::endl; return -1; } typedef RegistrationType::ParametersType ParametersType; ParametersType finalParameters = registration->GetLastTransformParameters(); const double RotationAlongX = finalParameters[0]/dtr; // Convert radian to degree const double RotationAlongY = finalParameters[1]/dtr; const double RotationAlongZ = finalParameters[2]/dtr; const double TranslationAlongX = finalParameters[3]; const double TranslationAlongY = finalParameters[4]; const double TranslationAlongZ = finalParameters[5]; const int numberOfIterations = optimizer->GetCurrentIteration(); const double bestValue = optimizer->GetValue(); std::cout << "Result = " << std::endl; std::cout << " Rotation Along X = " << RotationAlongX << " deg" << std::endl; std::cout << " Rotation Along Y = " << RotationAlongY << " deg" << std::endl; std::cout << " Rotation Along Z = " << RotationAlongZ << " deg" << std::endl; std::cout << " Translation X = " << TranslationAlongX << " mm" << std::endl; std::cout << " Translation Y = " << TranslationAlongY << " mm" << std::endl; std::cout << " Translation Z = " << TranslationAlongZ << " mm" << std::endl; std::cout << " Number Of Iterations = " << numberOfIterations << std::endl; std::cout << " Metric value = " << bestValue << std::endl; std::cout<<"GET STOP "<GetStopConditionDescription()<SetParameters( finalParameters ); finalTransform->SetCenter(isocenter); typedef itk::ResampleImageFilter< InternalImageType, InternalImageType > ResampleFilterType; // The ResampleImageFilter is the driving force for the projection image generation. ResampleFilterType::Pointer resampleFilter1 = ResampleFilterType::New(); resampleFilter1->SetInput( caster3D->GetOutput() ); // Link the 3D volume. resampleFilter1->SetDefaultPixelValue( 0 ); // The parameters of interpolator1, such as ProjectionAngle and FocalPointToIsocenterDistance // have been set before registration. Here we only need to replace the initial // transform with the final transform. interpolator1->SetTransform( finalTransform ); interpolator1->Initialize(); resampleFilter1->SetInterpolator( interpolator1 ); // The output 2D projection image has the same image size, origin, and the pixel spacing as // those of the input 2D image. resampleFilter1->SetSize( rescaler2D1->GetOutput()->GetLargestPossibleRegion().GetSize() ); resampleFilter1->SetOutputOrigin( rescaler2D1->GetOutput()->GetOrigin() ); resampleFilter1->SetOutputSpacing( rescaler2D1->GetOutput()->GetSpacing() ); // Do the same thing for the output image 2. ResampleFilterType::Pointer resampleFilter2 = ResampleFilterType::New(); resampleFilter2->SetInput( caster3D->GetOutput() ); resampleFilter2->SetDefaultPixelValue( 0 ); // The parameters of interpolator2, such as ProjectionAngle and FocalPointToIsocenterDistance // have been set before registration. Here we only need to replace the initial // transform with the final transform. /* interpolator2->SetTransform( finalTransform ); interpolator2->Initialize(); resampleFilter2->SetInterpolator( interpolator2 ); resampleFilter2->SetSize( rescaler2D2->GetOutput()->GetLargestPossibleRegion().GetSize() ); resampleFilter2->SetOutputOrigin( rescaler2D2->GetOutput()->GetOrigin() ); resampleFilter2->SetOutputSpacing( rescaler2D2->GetOutput()->GetSpacing() ); */ /////////////////////////////---DEGUG--START----//////////////////////////////////// if (debug) { InternalImageType::PointType outputorigin2D1 = rescaler2D1->GetOutput()->GetOrigin(); std::cout << "Output image 1 origin: " << outputorigin2D1[0] << ", " << outputorigin2D1[1] << ", " << outputorigin2D1[2] << std::endl; /*InternalImageType::PointType outputorigin2D2 = rescaler2D2->GetOutput()->GetOrigin(); std::cout << "Output image 2 origin: " << outputorigin2D2[0] << ", " << outputorigin2D2[1] << ", " << outputorigin2D2[2] << std::endl;*/ } /////////////////////////////---DEGUG--END----////////////////////////////////////// // As explained before, the computed projection is upsided-down. // Here we use a FilpImageFilter to flip the images in y-direction. flipFilter1->SetInput( resampleFilter1->GetOutput() ); //flipFilter2->SetInput( resampleFilter2->GetOutput() ); //ORIGINAL // Rescale the intensity of the projection images to 0-255 for output. typedef itk::RescaleIntensityImageFilter< InternalImageType, OutputImageType > RescaleFilterType; RescaleFilterType::Pointer rescaler1 = RescaleFilterType::New(); rescaler1->SetOutputMinimum( 0 ); rescaler1->SetOutputMaximum( 255 ); rescaler1->SetInput( flipFilter1->GetOutput() ); //ORIGINAL // rescaler1->SetInput( resampleFilter1->GetOutput() ); //RescaleFilterType::Pointer rescaler2 = RescaleFilterType::New(); //rescaler2->SetOutputMinimum( 0 ); //rescaler2->SetOutputMaximum( 255 ); //rescaler2->SetInput( flipFilter2->GetOutput() ); //ORIGINAL // rescaler2->SetInput( resampleFilter2->GetOutput() ); typedef itk::ImageFileWriter< OutputImageType > WriterType; WriterType::Pointer writer1 = WriterType::New(); //WriterType::Pointer writer2 = WriterType::New(); writer1->SetFileName( fileOutput1 ); writer1->SetInput( rescaler1->GetOutput() ); try { std::cout << "Writing image: " << fileOutput1 << std::endl; writer1->Update(); } catch( itk::ExceptionObject & err ) { std::cerr << "ERROR: ExceptionObject caught !" << std::endl; std::cerr << err << std::endl; } //writer2->SetFileName( fileOutput2 ); //writer2->SetInput( rescaler2->GetOutput() ); //try // { // std::cout << "Writing image: " << fileOutput2 << std::endl; // writer2->Update(); // } //catch( itk::ExceptionObject & err ) // { // std::cerr << "ERROR: ExceptionObject caught !" << std::endl; // std::cerr << err << std::endl; // } timer.Report(); return EXIT_SUCCESS; } -- View this message in context: http://itk-users.7.n7.nabble.com/Multiresolution-Registration-error-while-trying-to-improve-a-journal-paper-tp36739p36751.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Mon Feb 8 09:45:07 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 8 Feb 2016 09:45:07 -0500 Subject: [ITK] [ITK-users] Multiresolution Registration error while trying to improve a journal paper In-Reply-To: <1454918603453-36751.post@n7.nabble.com> References: <1454670288825-36739.post@n7.nabble.com> <1454918603453-36751.post@n7.nabble.com> Message-ID: Can you attache the source code as a file? When you pasted it into the email, some long comments were wrapped and that made them non-comments. There is over a 100 compiler error messages. On Mon, Feb 8, 2016 at 3:03 AM, vishal wrote: > hey D?enan, > this is the code below is a multiresolution version of the registration > code > in this > https://github.com/InsightSoftwareConsortium/ITKTwoProjectionRegistration > project... first when i tried to build and execute the code it shows the > error "vector subscript is out of range".. then i tried to modified the > github code keeping IntensityBased2D3DRegistration(the code below) as a > reference it still shows another error called "access violation > location...." ... kindly help me out... > PLS NOTE:- i modified the code to take only one 2d image and one 3d volume > inorder to perform registration. to run this code u will have to build the > GetSiddonRayCastTracing.cxx code and obtain a projection. then build the > code below and give the following arguments: > Something.exe -v theProjectionFromtheStepAbove.dcm 0 3Dvolume.dcm > where > 0 is the projection angle. > regards > Vishal > > /*========================================================================= > * > * Copyright Insight Software Consortium > * > * Licensed under the Apache License, Version 2.0 (the "License"); > * you may not use this file except in compliance with the License. > * You may obtain a copy of the License at > * > * http://www.apache.org/licenses/LICENSE-2.0.txt > * > * Unless required by applicable law or agreed to in writing, software > * distributed under the License is distributed on an "AS IS" BASIS, > * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or > implied. > * See the License for the specific language governing permissions and > * limitations under the License. > * > > > *=========================================================================*/ > > /*========================================================================= > > This program implements an intensity based 2D-3D registration algorithm > using the > SiddonJacobsRayCastInterpolateImageFunction and > NormalizedCorrelationTwoImageToOneImageMetric > similarity measure > > PowellOptimizer is used as the optimization method to avoid gradient > calculation. > Euler3DTransform instead of CenteredEuler3DTransform is used to avoid the > shift of the center. > > When generating DRRs, the program attempts to simulate a 2D imaging system > attached to a linac > for radiation therapy. The program registers two 2D portal images with > their corresponding DRR > images generated from the 3D dataset. The portal images may be acquired at > any arbitrary projection > angles. The similarity measure is the summation of the measures calculated > each projection. > Multiresolution strategy was not implemented. > > This program was modified from the ITK > application--IntensityBased2D3DRegistration.cxx > > =========================================================================*/ > //#include "itkTwoProjectionImageRegistrationMethod.h" > > // The transformation used is a rigid 3D Euler transform with the > // provision of a center of rotation which defaults to the center of > // the 3D volume. In practice the center of the particular feature of > // interest in the 3D volume should be used. > #include > //WRITTEN USING > IntesityBased2D3dRegistration.cxx & > MultiResImageRegistration3.cxx > #include "itkEuler3DTransform.h" > > // We have chosen to implement the registration using the normalized > coorelation > // similarity measure. > > //#include "itkGradientDifferenceTwoImageToOneImageMetric.h" > //#include "itkNormalizedCorrelationTwoImageToOneImageMetric.h" > > // This is an intensity based registration algorithm so ray casting is > // used to project the 3D volume onto pixels in the target 2D image. > #include "itkSiddonJacobsRayCastInterpolateImageFunction.h" > #include "itkMultiResolutionImageRegistrationMethod.h" > // Finally the Powell optimizer is used to avoid requiring gradient > information. > //#include "itkPowellOptimizer.h" > #include "itkRegularStepGradientDescentOptimizer.h" > #include "itkImageFileReader.h" > #include "itkImageFileWriter.h" > > #include "itkResampleImageFilter.h" > #include "itkCastImageFilter.h" > #include "itkRescaleIntensityImageFilter.h" > #include "itkFlipImageFilter.h" > > #include "itkCommand.h" > #include "itkTimeProbesCollectorBase.h" > > //MODIFIED HEADERS > //#include "itkImageRegistrationMethodv4.h" > //#include > #include > //#include "itkMattesMutualInformationImageToImageMetric.h" > //#include > //#include "itkEuler3DTransform.h" > //#include "itkPowellOptimizer.h" > // > //#include "itkImageFileReader.h" > //#include "itkImageFileWriter.h" > // > //#include "itkResampleImageFilter.h" > //#include "itkCastImageFilter.h" > //#include "itkRescaleIntensityImageFilter.h" > //#include "itkFlipImageFilter.h" > // > //#include "itkCommand.h" > //#include "itkTimeProbesCollectorBase.h" > //#include "itkSiddonJacobsRayCastInterpolateImageFunction.h" > // First we define the command class to allow us to monitor the > registration. > > class CommandIterationUpdate : public itk::Command > { > public: > typedef CommandIterationUpdate Self; > typedef itk::Command Superclass; > typedef itk::SmartPointer Pointer; > itkNewMacro( Self ); > > protected: > CommandIterationUpdate() {}; > > public: > typedef itk::RegularStepGradientDescentOptimizer OptimizerType; > typedef const OptimizerType * OptimizerPointer; > > void Execute(itk::Object *caller, const itk::EventObject & event) > { > Execute( (const itk::Object *)caller, event); > } > > void Execute(const itk::Object *object, const itk::EventObject & event) > { > OptimizerPointer optimizer = > dynamic_cast< OptimizerPointer >( object ); > if( typeid( event ) != typeid( itk::IterationEvent ) ) > { > return; > } > std::cout << "Iteration: " << optimizer->GetCurrentIteration() << > std::endl; > std::cout << "Similarity: " << optimizer->GetValue() << std::endl; > std::cout << "Position: " << optimizer->GetCurrentPosition() << > std::endl; > //std::cout<<"GETCURRENT LINE VALUE > "<GetCurrentLineIteration()<< std::endl; > } > }; > > > // Software Guide : BeginLatex > // > // A second \emph{Command/Observer} is used to reduce the minimum > // registration step length on each occasion that the resolution of > // the multi-scale registration is increased (see > // \doxygen{MultiResImageRegistration1} for more info). > // > // Software Guide : EndLatex > // Software Guide : BeginCodeSnippet > template > class RegistrationInterfaceCommand : public itk::Command > { > public: > typedef RegistrationInterfaceCommand Self; > typedef itk::Command Superclass; > typedef itk::SmartPointer Pointer; > itkNewMacro( Self ); > > protected: > RegistrationInterfaceCommand() {}; > > public: > typedef TRegistration RegistrationType; > typedef RegistrationType * RegistrationPointer; > typedef itk::RegularStepGradientDescentOptimizer OptimizerType; > typedef OptimizerType * OptimizerPointer; > > void Execute(itk::Object * object, const itk::EventObject & event) > ITK_OVERRIDE > { > /* if( typeid( event ) != typeid( itk::IterationEvent ) ) > { > return; > }*/ //old > if( !(itk::IterationEvent().CheckEvent( &event )) ) > { > return; > } > > // RegistrationPointer registration = > // dynamic_cast( object ); > > RegistrationPointer registration = static_cast( > object ); > > // If this is the first resolution level we assume that the > // maximum step length (representing the first step size) and the > // minimum step length (representing the convergence criterion) > // have already been set. At each subsequent resolution level, we > // will reduce the minimum step length by a factor of four in order > // to allow the optimizer to focus on progressively smaller > // regions. The maximum step length is set to the current step > // length. In this way, when the optimizer is reinitialized at the > // beginning of the registration process for the next level, the > // step length will simply start with the last value used for the > // previous level. This will guarantee the continuity of the path > // taken by the optimizer through the parameter space. > if(registration == ITK_NULLPTR) > { > return; > } > /*OptimizerPointer optimizer = dynamic_cast< OptimizerPointer >( > registration->GetOptimizer() );*/ > OptimizerPointer optimizer = static_cast< OptimizerPointer > >(registration->GetModifiableOptimizer() ); > > std::cout << "-------------------------------------" << std::endl; > std::cout << "MultiResolution Level : " > << registration->GetCurrentLevel() << std::endl; > std::cout << std::endl; > > //if ( registration->GetCurrentLevel() != 0 ) //old > // { > // optimizer->SetMaximumStepLength( optimizer->GetCurrentStepLength() > ); > // optimizer->SetMinimumStepLength( optimizer->GetMinimumStepLength() > / > 4.0 ); > // } > if ( registration->GetCurrentLevel() == 0 ) > { > optimizer->SetMaximumStepLength( 16.00 ); > optimizer->SetMinimumStepLength( 0.01 ); > } > else > { > optimizer->SetMaximumStepLength( optimizer->GetMaximumStepLength() / > 4.0 ); > optimizer->SetMinimumStepLength( optimizer->GetMinimumStepLength() / > 10.0 ); > } //mulit3 > optimizer->Print( std::cout ); > } > > /* void Execute(const itk::Object * , const itk::EventObject & ) > { return; }*/ //old > void Execute(const itk::Object * , const itk::EventObject & ) > ITK_OVERRIDE > { return; } //multi3 > }; > // Software Guide : EndCodeSnippet > > > > > void exe_usage() > { > std::cerr << "\n"; > std::cerr << "Usage: TwoProjection2D3DRegistration Image2D1 > ProjAngle1 Image2D2 ProjAngle2 Volume3D\n"; > std::cerr << " Registers two 2D images to a 3D volume. \n\n"; > std::cerr << " where is one or more of the following:\n\n"; > std::cerr << " <-h> Display (this) usage > information\n"; > std::cerr << " <-v> Verbose output [default: > no]\n"; > std::cerr << " <-dbg> Debugging output [default: > no]\n"; > // old > std::cerr << " <-n int> The number of scales to > apply [default: 2]\n"; > std::cerr << " <-maxScale int> The scale factor > corresponding to max resolution [default: 1]\n"; > std::cerr << " <-step float float> Maximum and minimum step > sizes [default: 4 and 0.01]\n"; > //end old > std::cerr << " <-scd float> Source to isocenter > distance > [default: 1000mm]\n"; > std::cerr << " <-t float float float> CT volume translation in x, > y, and z direction in mm \n"; > std::cerr << " <-rx float> CT volume rotation about x > axis in degrees \n"; > std::cerr << " <-ry float> CT volume rotation about y > axis in degrees \n"; > std::cerr << " <-rz float> CT volume rotation about z > axis in degrees \n"; > std::cerr << " <-2dcx float float float float> Central axis > positions of the 2D images in continuous indices \n"; > std::cerr << " <-res float float float float> Pixel spacing of > projection images in the isocenter plane [default: 1x1 mm] \n"; > std::cerr << " <-iso float float float> Isocenter location in voxel > in indices (center of rotation and projection center)\n"; > std::cerr << " <-threshold float> Intensity threshold below > which are ignore [default: 0]\n"; > std::cerr << " <-o file> Output image filename\n\n"; > std::cerr << " by Jian Wu\n"; > std::cerr << " eewujian at hotmail.com\n"; > std::cerr << " (Univeristy of > Florida)\n\n"; > exit(EXIT_FAILURE); > } > > > int main( int argc, char *argv[] ) > { > char *fileImage2D1 = NULL; > double projAngle1 = -999; > /* char *fileImage2D2 = NULL; > double projAngle2 = -999;*/ > char *fileVolume3D = NULL; > // Default output file names > const char *fileOutput1 = "Image2D1_Registered.tif"; > //const char *fileOutput2 = "Image2D2_Registered.tif"; > > bool ok; > bool verbose = false; > bool debug = false; > bool customized_iso = false; > bool customized_2DCX = false; // Flag for customized 2D image central > axis > positions > bool customized_2DRES = false; // Flag for customized 2D image pixel > spacing > > unsigned int nScales = 2; //OLD PROG > int maxScale = 1; //OLD PROG > > double rx = 0.; > double ry = 0.; > double rz = 0.; > > double tx = 0.; > double ty = 0.; > double tz = 0.; > > double cx = 0.; > double cy = 0.; > double cz = 0.; > > double scd = 1000.; // Source to isocenter distance > > > double maxStepSize = 4.; //OLD PROG > double minStepSize = 1.; //OLD PROG > > double image1centerX = 0.0; > double image1centerY = 0.0; > double image2centerX = 0.0; > double image2centerY = 0.0; > > double image1resX = 1.0; > double image1resY = 1.0; > double image2resX = 1.0; > double image2resY = 1.0; > > double threshold = 0.0; > > // Parse command line parameters > > //if (argc <= 5) //ORIGINAL > if (argc <= 4) > exe_usage(); > > while (argc > 1) > { > ok = false; > > if ((ok == false) && (strcmp(argv[1], "-h") == 0)) > { > argc--; argv++; > ok = true; > exe_usage(); > } > > if ((ok == false) && (strcmp(argv[1], "-v") == 0)) > { > argc--; argv++; > ok = true; > verbose = true; > std::cout<<"INSIDE -v"< } > > if ((ok == false) && (strcmp(argv[1], "-dbg") == 0)) > { > argc--; argv++; > ok = true; > debug = true; > std::cout<<"INSIDE -debug"<<std::endl; > } > > if ((ok == false) && (strcmp(argv[1], "-scd") == 0)) > { > argc--; argv++; > ok = true; > scd = atof(argv[1]); > argc--; argv++; > std::cout<<"INSIDE -scd"<<std::endl; > } > > if ((ok == false) && (strcmp(argv[1], "-t") == 0)) > { > argc--; argv++; > ok = true; > tx=atof(argv[1]); > argc--; argv++; > ty=atof(argv[1]); > argc--; argv++; > tz=atof(argv[1]); > argc--; argv++; > std::cout<<"INSIDE -t"<<std::endl; > } > > if ((ok == false) && (strcmp(argv[1], "-rx") == 0)) > { > argc--; argv++; > ok = true; > rx=atof(argv[1]); > argc--; argv++; > std::cout<<"INSIDE -rx"<<std::endl; > } > > if ((ok == false) && (strcmp(argv[1], "-ry") == 0)) > { > argc--; argv++; > ok = true; > ry=atof(argv[1]); > argc--; argv++; > std::cout<<"INSIDE -ry"<<std::endl; > } > > if ((ok == false) && (strcmp(argv[1], "-rz") == 0)) > { > argc--; argv++; > ok = true; > rz=atof(argv[1]); > //std::cout<<"RZ > INTIALIZALIZES"<<std::endl; > argc--; argv++; > std::cout<<"INSIDE -rz"<<std::endl; > } > > if ((ok == false) && (strcmp(argv[1], "-2dcx") == 0)) > { > argc--; argv++; > ok = true; > image1centerX = atof(argv[1]); > argc--; argv++; > image1centerY = atof(argv[1]); > argc--; argv++; > image2centerX = atof(argv[1]); > argc--; argv++; > image2centerY = atof(argv[1]); > argc--; argv++; > customized_2DCX = true; > std::cout<<"INSIDE -2dcx"<<std::endl; > } > > if ((ok == false) && (strcmp(argv[1], "-res") == 0)) > { > argc--; argv++; > ok = true; > image1resX = atof(argv[1]); > argc--; argv++; > image1resY = atof(argv[1]); > argc--; argv++; > image2resX = atof(argv[1]); > argc--; argv++; > image2resY = atof(argv[1]); > argc--; argv++; > customized_2DRES = true; > std::cout<<"INSIDE -res"<<std::endl; > } > > if ((ok == false) && (strcmp(argv[1], "-iso") == 0)) > { > argc--; argv++; > ok = true; > cx=atof(argv[1]); > argc--; argv++; > cy=atof(argv[1]); > argc--; argv++; > cz=atof(argv[1]); > argc--; argv++; > customized_iso = true; > std::cout<<"INSIDE -iso"<<std::endl; > } > > if ((ok == false) && (strcmp(argv[1], "-threshold") > == > 0)) > { > argc--; argv++; > ok = true; > threshold=atof(argv[1]); > argc--; argv++; > std::cout<<"INSIDE > -threshold"<<std::endl; > } > > if ((ok == false) && (strcmp(argv[1], "-o") == 0)) > { > argc--; argv++; > ok = true; > fileOutput1 = argv[1]; > argc--; argv++; > std::cout<<"INSIDE -o"<<std::endl; > /*fileOutput2 = argv[1]; > argc--; argv++;*/ > } > > > if (ok == false) > { > > if (fileImage2D1 == NULL) > { > fileImage2D1 = argv[1]; > argc--; > argv++; > std::cout<<"INSIDE INTIALIZING FILE NAME > fileImage2D1"<<std::endl; > } > > if (projAngle1 == -999) > { > projAngle1 = atof(argv[1]); > argc--; > argv++; > std::cout<<"INSIDE INTIALIZING FILE NAME > projAngle1"<<std::endl; > } > > //if (fileImage2D2 == NULL) > // { > // fileImage2D2 = argv[1]; > // argc--; > // argv++; > // } > > //if (projAngle2 == -999) > // { > // projAngle2 = atof(argv[1]); > // argc--; > // argv++; > // } > > else if (fileVolume3D == NULL) > { > fileVolume3D = argv[1]; > argc--; > argv++; > std::cout<<"INSIDE INTIALIZING FILE NAME > FileVolume3D"<<std::endl; > } > > else > { > std::cerr << "ERROR: Cannot parse argument " > << argv[1] << std::endl; > exe_usage(); > } > } > } > > if (verbose) > { > if (fileImage2D1) std::cout << "Input 2D image 1: " > << fileImage2D1 << std::endl; > if (fileImage2D1) std::cout << "Projection Angle 1: " > << projAngle1 << std::endl; > //if (fileImage2D2) std::cout << "Input 2D image 2: " > << fileImage2D2 << std::endl; > //if (fileImage2D2) std::cout << "Projection Angle 2: > " > << projAngle2 << std::endl; > if (fileVolume3D) std::cout << "Input 3D image: " > << fileVolume3D << std::endl; > if (fileOutput1) std::cout << "Output image 1: " > << fileOutput1 << std::endl; > //if (fileOutput2) std::cout << "Output image 2: " > << fileOutput2 << std::endl; > } > > > // We begin the program proper by defining the 2D and 3D images. The > // {TwoProjectionImageRegistrationMethod} requires that both > // images have the same dimension so the 2D image is given > // dimension 3 and the size of the {z} dimension is set to unity. > std::cout<<"OUT OF THE INLIAZING LOOPS PROGRAM > STARTS!!"<<std::endl; > const unsigned int Dimension = 3; > typedef float InternalPixelType; > typedef short PixelType3D; > > typedef itk::Image< PixelType3D, Dimension > ImageType3D; > > typedef unsigned char OutputPixelType; > typedef itk::Image< OutputPixelType, Dimension > OutputImageType; > > // The following lines define each of the components used in the > // registration: The transform, optimizer, metric, interpolator and > // the registration method itself. > > typedef itk::Image< InternalPixelType, Dimension > InternalImageType; > > typedef itk::Euler3DTransform< double > TransformType; > > typedef itk::RegularStepGradientDescentOptimizer OptimizerType; > > //typedef itk::GradientDifferenceTwoImageToOneImageMetric< > /* typedef itk::NormalizedCorrelationTwoImageToOneImageMetric< > InternalImageType, > InternalImageType > MetricType;*/ > typedef itk::NormalizedCorrelationImageToImageMetric< > InternalImageType, > InternalImageType > MetricType; > > typedef itk::SiddonJacobsRayCastInterpolateImageFunction< > InternalImageType, > double > InterpolatorType; > > > /* typedef itk::TwoProjectionImageRegistrationMethod< > InternalImageType, > InternalImageType > RegistrationType;*/ > typedef itk::MultiResolutionImageRegistrationMethod< > InternalImageType, > InternalImageType > > RegistrationType; > > // Software Guide : BeginCodeSnippet //THESE ARE THE CHANGES MADE > typedef itk::MultiResolutionPyramidImageFilter< > InternalImageType, > InternalImageType > ImagePyramidType2D; > typedef itk::MultiResolutionPyramidImageFilter< > InternalImageType, > InternalImageType > ImagePyramidType3D; > // Software Guide : EndCodeSnippet > > > // Each of the registration components are instantiated in the > // usual way... > > ImagePyramidType2D::Pointer imagePyramid2D = > ImagePyramidType2D::New(); > ImagePyramidType3D::Pointer imagePyramid3D = > ImagePyramidType3D::New(); > > > std::cout<<"TYPES INTIALIZED"< MetricType::Pointer metric = MetricType::New(); > TransformType::Pointer transform = TransformType::New(); > OptimizerType::Pointer optimizer = OptimizerType::New(); > InterpolatorType::Pointer interpolator1 = InterpolatorType::New(); > //InterpolatorType::Pointer interpolator2 = InterpolatorType::New(); > RegistrationType::Pointer registration = RegistrationType::New(); > > //metric->ComputeGradientOff(); //ORIGINAL > metric->ComputeGradientOn(); > metric->SetSubtractMean( true ); > > // and passed to the registration method: > > registration->SetMetric( metric ); > registration->SetOptimizer( optimizer ); > registration->SetTransform( transform ); > registration->SetInterpolator( interpolator1 ); > // registration->SetInterpolator2( interpolator2 ); > registration->SetFixedImagePyramid( imagePyramid2D ); > registration->SetMovingImagePyramid( imagePyramid3D ); //changes made > from > 2d/3d > std::cout<<"REGISTRATION METHODS SET"< if (debug) > { > metric->DebugOn(); > //transform->DebugOn(); > //optimizer->DebugOn(); > interpolator1->DebugOn(); > // interpolator2->DebugOn(); > //registration->DebugOn(); > } > > > // The 2- and 3-D images are read from files, > > typedef itk::ImageFileReader< InternalImageType > ImageReaderType2D; > typedef itk::ImageFileReader< ImageType3D > ImageReaderType3D; > > ImageReaderType2D::Pointer imageReader2D1 = ImageReaderType2D::New(); > // ImageReaderType2D::Pointer imageReader2D2 = ImageReaderType2D::New(); > ImageReaderType3D::Pointer imageReader3D = ImageReaderType3D::New(); > > imageReader2D1->SetFileName( fileImage2D1 ); > //imageReader2D2->SetFileName( fileImage2D2 ); > imageReader3D->SetFileName( fileVolume3D ); > imageReader3D->Update(); > std::cout<<"2d 3d volume filename SET"< ImageType3D::Pointer image3DIn = imageReader3D->GetOutput(); > > // To simply Siddon-Jacob's fast ray-tracing algorithm, we force the > origin of the CT image > // to be (0,0,0). Because we align the CT isocenter with the central > axis, > the projection > // geometry is fully defined. The origin of the CT image becomes > irrelavent. > ImageType3D::PointType image3DOrigin; > image3DOrigin[0] = 0.0; > image3DOrigin[1] = 0.0; > image3DOrigin[2] = 0.0; > image3DIn->SetOrigin(image3DOrigin); > std::cout<<"VOLUME ORIGIN SET"< InternalImageType::Pointer image_tmp1 = imageReader2D1->GetOutput(); > //InternalImageType::Pointer image_tmp2 = imageReader2D2->GetOutput(); > > imageReader2D1->Update(); > // imageReader2D2->Update(); > > if (customized_2DRES) > { > InternalImageType::SpacingType spacing; > spacing[0] = image1resX; > spacing[1] = image1resY; > spacing[2] = 1.0; > image_tmp1->SetSpacing( spacing ); > > // spacing[0] = image2resX; > // spacing[1] = image2resY; > // image_tmp2->SetSpacing( spacing ); > > } > // The input 2D images were loaded as 3D images. They were considered > // as a single slice from a 3D volume. By default, images stored on the > // disk are treated as if they have RAI orientation. After view point > // transformation, the order of 2D image pixel reading is equivalent to > // from inferior to superior. This is contradictory to the traditional > // 2D x-ray image storage, in which a typical 2D image reader reads and > // writes images from superior to inferior. Thus the loaded 2D DICOM > // images should be flipped in y-direction. This was done by using a. > // FilpImageFilter. > typedef itk::FlipImageFilter< InternalImageType > FlipFilterType; > FlipFilterType::Pointer flipFilter1 = FlipFilterType::New(); > // FlipFilterType::Pointer flipFilter2 = FlipFilterType::New(); > > typedef FlipFilterType::FlipAxesArrayType FlipAxesArrayType; > FlipAxesArrayType flipArray; > flipArray[0] = 0; > flipArray[1] = 1; > flipArray[2] = 0; > > flipFilter1->SetFlipAxes( flipArray ); > // flipFilter2->SetFlipAxes( flipArray ); > > flipFilter1->SetInput( imageReader2D1->GetOutput() ); > //flipFilter2->SetInput( imageReader2D2->GetOutput() ); > > // The input 2D images may have 16 bits. We rescale the pixel value to > between 0-255. > typedef itk::RescaleIntensityImageFilter< > InternalImageType, InternalImageType > Input2DRescaleFilterType; > > Input2DRescaleFilterType::Pointer rescaler2D1 = > Input2DRescaleFilterType::New(); > rescaler2D1->SetOutputMinimum( 0 ); > rescaler2D1->SetOutputMaximum( 255 ); > rescaler2D1->SetInput( flipFilter1->GetOutput() ); > std::cout<<"flipFilter1->GetOutput() SET"< /*Input2DRescaleFilterType::Pointer rescaler2D2 = > Input2DRescaleFilterType::New(); > rescaler2D2->SetOutputMinimum( 0 ); > rescaler2D2->SetOutputMaximum( 255 ); > rescaler2D2->SetInput( flipFilter2->GetOutput() );*/ > > > // The 3D CT dataset is casted to the internal image type using > // {CastImageFilters}. > > typedef itk::CastImageFilter< > ImageType3D, InternalImageType > CastFilterType3D; > > CastFilterType3D::Pointer caster3D = CastFilterType3D::New(); > caster3D->SetInput( image3DIn ); > > rescaler2D1->Update(); > //rescaler2D2->Update(); > caster3D->Update(); > std::cout<<"caster3D->GetOutput() SET"< > registration->SetFixedImage( rescaler2D1->GetOutput() ); > //registration->SetFixedImage2( rescaler2D2->GetOutput() ); > registration->SetMovingImage( caster3D->GetOutput() ); > > registration->SetFixedImageRegion( > rescaler2D1->GetOutput()->GetBufferedRegion() ); //changes > made from 2d/3d > // Initialise the transform > // ~~~~~~~~~~~~~~~~~~~~~~~~ > > // Set the order of the computation. Default ZXY > transform->SetComputeZYX(true); > > > // The transform is initialised with the translation [tx,ty,tz] and > // rotation [rx,ry,rz] specified on the command line > > TransformType::OutputVectorType translation; > > translation[0] = tx; > translation[1] = ty; > translation[2] = tz; > > transform->SetTranslation(translation); > std::cout<<"transform->SetTranslation(translation); SET"< // constant for converting degrees to radians > const double dtr = ( atan(1.0) * 4.0 ) / 180.0; > transform->SetRotation(dtr*rx, dtr*ry, dtr*rz); > std::cout<<"transform->SetRotation(dtr*rx, dtr*ry, dtr*rz) > SET"< // The centre of rotation is set by default to the centre of the 3D > // volume but can be offset from this position using a command > // line specified translation [cx,cy,cz] > > ImageType3D::PointType origin3D = image3DIn->GetOrigin(); > const itk::Vector resolution3D = image3DIn->GetSpacing(); > > typedef ImageType3D::RegionType ImageRegionType3D; > typedef ImageRegionType3D::SizeType SizeType3D; > > ImageRegionType3D region3D = caster3D->GetOutput()->GetBufferedRegion(); > SizeType3D size3D = region3D.GetSize(); > > TransformType::InputPointType isocenter; > if (customized_iso) > { > // Isocenter location given by the user. > isocenter[0] = origin3D[0] + resolution3D[0] * cx; > isocenter[1] = origin3D[1] + resolution3D[1] * cy; > isocenter[2] = origin3D[2] + resolution3D[2] * cz; > } > else > { > // Set the center of the image as the isocenter. > isocenter[0] = origin3D[0] + resolution3D[0] * static_cast( > size3D[0] ) / 2.0; > isocenter[1] = origin3D[1] + resolution3D[1] * static_cast( > size3D[1] ) / 2.0; > isocenter[2] = origin3D[2] + resolution3D[2] * static_cast( > size3D[2] ) / 2.0; > } > > transform->SetCenter(isocenter); > > > if (verbose) > { > std::cout << "3D image size: " > << size3D[0] << ", " << size3D[1] << ", " << size3D[2] << > std::endl > << " resolution: " > << resolution3D[0] << ", " << resolution3D[1] << ", " << > resolution3D[2] << std::endl > << "Transform: " << transform << std::endl; > } > > > // Set the origin of the 2D image > // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > // For correct (perspective) projection of the 3D volume, the 2D > // image needs to be placed at a certain distance (the source-to- > // isocenter distance {scd} ) from the focal point, and the normal > // from the imaging plane to the focal point needs to be specified. > // > // By default, the imaging plane normal is set by default to the > // center of the 2D image but may be modified from this using the > // command line parameters [image1centerX, image1centerY, > // image2centerX, image2centerY]. > > double origin2D1[ Dimension ]; > // double origin2D2[ Dimension ]; > > // Note: Two 2D images may have different image sizes and pixel > dimensions, although > // scd are the same. > > const itk::Vector resolution2D1 = > imageReader2D1->GetOutput()->GetSpacing(); > //const itk::Vector resolution2D2 = > imageReader2D2->GetOutput()->GetSpacing(); > > typedef InternalImageType::RegionType ImageRegionType2D; > typedef ImageRegionType2D::SizeType SizeType2D; > > // ImageRegionType2D region2D1 = > rescaler2D1->GetOutput()->GetBufferedRegion(); //ORIGINAL 2d/3d > ImageRegionType2D region2D1 = > rescaler2D1->GetOutput()->GetLargestPossibleRegion(); > // ImageRegionType2D region2D2 = > rescaler2D2->GetOutput()->GetBufferedRegion(); > SizeType2D size2D1 = region2D1.GetSize(); > // SizeType2D size2D2 = region2D2.GetSize(); > > if (!customized_2DCX) > { // Central axis positions are not given by the user. Use the image > centers > // as the central axis position. > image1centerX = ((double) size2D1[0] - 1.)/2.; > image1centerY = ((double) size2D1[1] - 1.)/2.; > //image2centerX = ((double) size2D2[0] - 1.)/2.; > // image2centerY = ((double) size2D2[1] - 1.)/2.; > } > > // 2D Image 1 > origin2D1[0] = - resolution2D1[0] * image1centerX; > origin2D1[1] = - resolution2D1[1] * image1centerY; > origin2D1[2] = - scd; > > imageReader2D1->GetOutput()->SetOrigin( origin2D1 ); > rescaler2D1->GetOutput()->SetOrigin( origin2D1 ); > > //// 2D Image 2 > //origin2D2[0] = - resolution2D2[0] * image2centerX; > //origin2D2[1] = - resolution2D2[1] * image2centerY; > //origin2D2[2] = - scd; > > //imageReader2D2->GetOutput()->SetOrigin( origin2D2 ); > //rescaler2D2->GetOutput()->SetOrigin( origin2D2 ); > > registration->SetFixedImageRegion( > rescaler2D1->GetOutput()->GetBufferedRegion() ); > //registration->SetFixedImageRegion2( > rescaler2D2->GetOutput()->GetBufferedRegion() ); > > if (verbose) > { > std::cout << "2D image 1 size: " > << size2D1[0] << ", " << size2D1[1] << ", " << size2D1[2] << > std::endl > << " resolution: " > << resolution2D1[0] << ", " << resolution2D1[1] << ", " << > resolution2D1[2] << std::endl > << " and position: " > << origin2D1[0] << ", " << origin2D1[1] << ", " << > origin2D1[2] << std::endl; > // << "2D image 2 size: " > //<< size2D2[0] << ", " << size2D2[1] << ", " << size2D2[2] > << > std::endl > //<< " resolution: " > // << resolution2D2[0] << ", " << resolution2D2[1] << ", " << > resolution2D2[2] << std::endl > // << " and position: " > // << origin2D2[0] << ", " << origin2D2[1] << ", " << > origin2D2[2] << std::endl; > } > > > > //---------------------------------------------------------------------------- > // Set the moving and fixed images' schedules > > //---------------------------------------------------------------------------- > const unsigned int ResolutionLevels = 3; > std::cout<<"\nSet the moving and fixed images' schedules"< RegistrationType::ScheduleType fixedSchedule( ResolutionLevels,Dimension > ); > fixedSchedule[0][0] = 4; > fixedSchedule[0][1] = 4; > fixedSchedule[0][2] = 1; > fixedSchedule[1][0] = 2; > fixedSchedule[1][1] = 2; > fixedSchedule[1][2] = 1; > fixedSchedule[2][0] = 1; > fixedSchedule[2][1] = 1; > fixedSchedule[2][2] = 1; > > RegistrationType::ScheduleType movingSchedule( > ResolutionLevels,Dimension); > movingSchedule[0][0] = 4; > movingSchedule[0][1] = 4; > movingSchedule[0][2] = 4; > movingSchedule[1][0] = 2; > movingSchedule[1][1] = 2; > movingSchedule[1][2] = 2; > movingSchedule[2][0] = 1; > movingSchedule[2][1] = 1; > movingSchedule[2][2] = 1; > > registration->SetSchedules( fixedSchedule, movingSchedule ); > std::cout<<"\nSet the moving and fixed images' schedules to > registration"< > > > > > // //The old code start from here > // // Set the pyramid schedule for the 2D image > // // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > // // Software Guide : BeginLatex > // // > // // The multi-resolution hierachy is specified with respect to the 2D > // // image. The number of scales or levels defaults to two, with each > level > // // differing in resolution by a factor of two. The highest resolution > (final) > // // level corresponds to the resolution of the input 2D image but > // // this can be altered by the user via the \emph{maxScale} command > // // line parameter. The number of scales \emph{nScales} can also be > // // specified by the user. > // // > // // Software Guide : EndLatex > // std::vector<double> sampledRes2D; > // std::vector imageRegionPyramid2D; > > // imagePyramid2D->SetNumberOfLevels( nScales ); > // std::cout<<"imagepyramid 2d"< // > // sampledRes2D.reserve( nScales-1 ); > // std::cout<<"sampledRes2D > "<<sampledRes2D[0]<<std::endl; > // imageRegionPyramid2D.reserve( nScales ); > > // typedef ImagePyramidType2D::ScheduleType ScheduleType2D; > // ScheduleType2D schedule2D = imagePyramid2D->GetSchedule(); > > // for ( unsigned int dim = 0; dim < ImageType3D::ImageDimension; dim++ ) > // { > // schedule2D[ nScales-1 ][ dim ] = maxScale; > > //std::cout<<"schedule2D["< <<"] "<<schedule2D[ nScales-1 ][ dim > ]<<std::endl; > // } > > // for ( int level=nScales-2; level >= 0; level-- ) > // { > // for ( unsigned int dim = 0; dim < ImageType3D::ImageDimension; dim++ > ) > // { > // schedule2D[ level ][ dim ] = 2*schedule2D[ level+1 ][ dim ]; > // > std::cout<<"schedule2D["< <<"] "<< 2*schedule2D[ level+1 ][ dim > ]<<std::endl; > // } > // } > // std::cout<<"out of the imagepyramid type 2d > "<<std::endl; > // // Compute the 2D ImageRegion corresponding to each level of the > // // pyramid. > > // typedef ImageRegionType2D::IndexType IndexType2D; > // IndexType2D inputStart2D = region2D1.GetIndex(); > > // for ( unsigned int level=0; level < nScales; level++ ) > // { > // SizeType2D size; > // IndexType2D start; > // sampledRes2D[ level ] = 0.; //this is the error ORIGINAL > ////sampledRes2D[ level ] = 1.; //this is the error > // for ( unsigned int dim = 0; dim < ImageType3D::ImageDimension; > dim++ ) > // { > // float scaleFactor = static_cast<float>( schedule2D[ level ][ dim > ] ); > > // size[ dim ] = static_cast( > // floor( static_cast( size2D1[ dim ] ) / scaleFactor ) ); > > // if( size[ dim ] < 1 ) > // { > // size[ dim ] = 1; > // schedule2D[ level ][ dim ] = 1; > // } > > // std::cout << level << " " << dim << " " > // << size[ dim ] << " " << schedule2D[ level ][ dim ] > // << std::endl; > > // scaleFactor = static_cast( schedule2D[ level ][ dim ] ); > // start[ dim ] = static_cast( > // ceil( static_cast( inputStart2D[ dim ] ) / scaleFactor ) > ); > > // if ( dim < 2 ) > // { > // sampledRes2D[ level ] += scaleFactor*resolution2D1[ dim ] > // *scaleFactor*resolution2D1[ dim ]; > // } > // } > > // sampledRes2D[ level ] = sqrt( sampledRes2D[ level ] ); > > // imageRegionPyramid2D[ level ].SetSize( size ); > // imageRegionPyramid2D[ level ].SetIndex( start ); > // } > > // imagePyramid2D->SetSchedule( schedule2D ); > > > //// Set the pyramid schedule for the 3D image > //// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > //// Software Guide : BeginLatex > //// > //// The 3D image pyramid naturally contains the same number of levels > //// as the multi-resolution schedule for the 2D image. In addition > //// the sub-sampling factors for each level are set such that > //// resolution of the 3D image in each case is reduced to no greater > //// than the corresponding 2D image resolution at that scale. This > //// ensures that the 3D volume is reduced in size as far as possible, > //// minimising ray-casting computation time, whilst retaining > //// sufficient information to ensure accurate production of the DRR > //// at the resolution of the 2D image. > //// > //// Software Guide : EndLatex > > //std::vector imageRegionPyramid3D; > > //imagePyramid3D->SetNumberOfLevels( nScales ); > // > //imageRegionPyramid3D.reserve( nScales ); > > //typedef ImagePyramidType3D::ScheduleType ScheduleType3D; > //ScheduleType3D schedule3D = imagePyramid3D->GetSchedule(); > // > //// Compute the 2D image pyramid schedule such that the 3D volume > //// resolution is no greater than the 2D image resolution. > > //for ( unsigned int level=0; level < nScales; level++ ) > // { > // for ( unsigned int dim = 0; dim < ImageType3D::ImageDimension; dim++) > // { > // double res = resolution3D[ dim ]; > // schedule3D[ level ][ dim ] = 1; > // while ( res*2. < sampledRes2D[ level ] ) > // { > // schedule3D[ level ][ dim ] *= 2; > // res *= 2.; > // } > // } > // } > // > //// Compute the 3D ImageRegion corresponding to each level of the > //// pyramid. > > //typedef ImageRegionType3D::IndexType IndexType3D; > //IndexType3D inputStart3D = region3D.GetIndex(); > > //for ( unsigned int level=0; level < nScales; level++ ) > // { > // SizeType3D size; > // IndexType3D start; > // for ( unsigned int dim = 0; dim < ImageType3D::ImageDimension; dim++) > // { > // float scaleFactor = static_cast( schedule3D[ level ][ dim ] > ); > > // size[ dim ] = static_cast( > // floor( static_cast( size3D[ dim ] ) / scaleFactor ) ); > > // if( size[ dim ] < 1 ) > // { > // size[ dim ] = 1; > // schedule3D[ level ][ dim ] = 1; > // } > > // scaleFactor = static_cast( schedule3D[ level ][ dim ] ); > // start[ dim ] = static_cast( > // ceil( static_cast( inputStart3D[ dim ] ) / scaleFactor ) > ); > // } > // imageRegionPyramid3D[ level ].SetSize( size ); > // imageRegionPyramid3D[ level ].SetIndex( start ); > // } > > //imagePyramid3D->SetSchedule( schedule3D ); > > > // Initialize the ray cast interpolator > // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > // The ray cast interpolator is used to project the 3D volume. It > // does this by casting rays from the (transformed) focal point to > // each (transformed) pixel coordinate in the 2D image. > // > // In addition a threshold may be specified to ensure that only > // intensities greater than a given value contribute to the > // projected volume. This can be used, for instance, to remove soft > // tissue from projections of CT data and force the registration > // to find a match which aligns bony structures in the images. > > // 2D Image 1 > interpolator1->SetProjectionAngle( dtr*projAngle1 ); > interpolator1->SetFocalPointToIsocenterDistance(scd); > interpolator1->SetThreshold(threshold); > interpolator1->SetTransform(transform); > > interpolator1->Initialize(); > std::cout<<"\nInterpolator"< // 2D Image 2 > /* interpolator2->SetProjectionAngle( dtr*projAngle2 ); > interpolator2->SetFocalPointToIsocenterDistance(scd); > interpolator2->SetThreshold(threshold); > interpolator2->SetTransform(transform); > > interpolator2->Initialize(); > */ > > // Set up the transform and start position > // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > // The registration start position is intialised using the > // transformation parameters. > > > > registration->SetInitialTransformParameters( transform->GetParameters() > ); > //trying to set the FIXED parameter > //#if defined(ITK_FIXED_PARAMETERS_ARE_DOUBLE) // After 4.8.1 > // TransformType::FixedParametersType fixedParameters(3); > //#else //Pre 4.8.1 > // TransformType::ParametersType fixedParameters(6); > //#endif > // fixedParameters[0] = 0.0; > // fixedParameters[1] = 0.0; > // fixedParameters[3] = 0.0; > // fixedParameters[4] = 0.0; > // fixedParameters[5] = 0.0; > // transform->SetFixedParameters( fixedParameters ); > > // We wish to minimize the negative normalized correlation similarity > measure. > > // optimizer->SetMaximize( true ); // for > GradientDifferenceTwoImageToOneImageMetric > optimizer->SetMaximize( false ); // for NCC ORIGINAL > //optimizer->SetMaximize( true ); //NCC CHANGED > > optimizer->SetMaximumStepLength( maxStepSize ); > optimizer->SetMinimumStepLength( minStepSize ); > //optimizer->SetStepLength(2); // ORGINAL 4 > //optimizer->SetStepTolerance( 0.01); //ORIGINAL 0.02 > //optimizer->SetValueTolerance( 0.00001 );//ORIGINAL 0.001 > //optimizer->SetMetricWorstPossibleValue(-0.2); > optimizer->SetNumberOfIterations(200); > // The optimizer weightings are set such that one degree equates to > // one millimeter. > > itk::Optimizer::ScalesType weightings( transform->GetNumberOfParameters() > ); > > > std::cout<<"transform->GetNumberOfParameters()==>"<GetNumberOfParameters()< /* weightings[0] = 1./dtr; > weightings[1] = 1./dtr; //ORIGINAL > weightings[2] = 1./dtr; > weightings[3] = 1.; > weightings[4] = 1.; > weightings[5] = 1.;*/ > > weightings[0] = 1./dtr; > weightings[1] = 1./dtr; > weightings[2] = 1./dtr; > weightings[3] = 1.0; > weightings[4] = 1.0; > weightings[5] = 1.0; > > std::cout<<"WEIGHTINGS > "<<weightings[0]<<std::endl; > optimizer->SetScales( weightings ); > // optimizer->SetMetricWorstPossibleValue(0);//to change the stop > condition > if (verbose) > { > optimizer->Print( std::cout ); > } > > > // Create the observers > // ~~~~~~~~~~~~~~~~~~~~ > > CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New(); > > optimizer->AddObserver( itk::IterationEvent(), observer ); > > // Software Guide : BeginLatex > // > // Once all the registration components are in place we can create > // an instance of the interface command and connect it to the > // registration object using the \code{AddObserver()} method. > // > // Software Guide : EndLatex > // Software Guide : BeginCodeSnippet > typedef RegistrationInterfaceCommand CommandType; > CommandType::Pointer command = CommandType::New(); > registration->AddObserver( itk::IterationEvent(), command ); > // Software Guide : EndCodeSnippet > > // Software Guide : BeginLatex > // > // Finally we set the number of multi-resolution levels: > // > // Software Guide : EndLatex > // Software Guide : BeginCodeSnippet > //registration->SetNumberOfLevels( nScales ); > //// Software Guide : EndCodeSnippet > > //imagePyramid3D->Print(std::cout); > //imagePyramid2D->Print(std::cout); > > // Start the registration > // ~~~~~~~~~~~~~~~~~~~~~~ > > // Create a timer to record calculation time. > itk::TimeProbesCollectorBase timer; > > if (verbose) > { > std::cout << "Starting the registration now..." << std::endl; > } > > try > { > timer.Start("Registration"); > // Start the registration. > registration->StartRegistration(); > timer.Stop("Registration"); > } > catch( itk::ExceptionObject & err ) > { > std::cout << "ExceptionObject caught !" << std::endl; > std::cout << err << std::endl; > return -1; > } > > typedef RegistrationType::ParametersType ParametersType; > ParametersType finalParameters = > registration->GetLastTransformParameters(); > > const double RotationAlongX = finalParameters[0]/dtr; // Convert radian > to > degree > const double RotationAlongY = finalParameters[1]/dtr; > const double RotationAlongZ = finalParameters[2]/dtr; > const double TranslationAlongX = finalParameters[3]; > const double TranslationAlongY = finalParameters[4]; > const double TranslationAlongZ = finalParameters[5]; > > const int numberOfIterations = optimizer->GetCurrentIteration(); > > const double bestValue = optimizer->GetValue(); > > std::cout << "Result = " << std::endl; > std::cout << " Rotation Along X = " << RotationAlongX << " deg" << > std::endl; > std::cout << " Rotation Along Y = " << RotationAlongY << " deg" << > std::endl; > std::cout << " Rotation Along Z = " << RotationAlongZ << " deg" << > std::endl; > std::cout << " Translation X = " << TranslationAlongX << " mm" << > std::endl; > std::cout << " Translation Y = " << TranslationAlongY << " mm" << > std::endl; > std::cout << " Translation Z = " << TranslationAlongZ << " mm" << > std::endl; > std::cout << " Number Of Iterations = " << numberOfIterations << > std::endl; > std::cout << " Metric value = " << bestValue << std::endl; > std::cout<<"GET STOP > "<GetStopConditionDescription()< > // Write out the projection images at the registration position > // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > TransformType::Pointer finalTransform = TransformType::New(); > // The transform is determined by the parameters and the rotation center. > finalTransform->SetParameters( finalParameters ); > finalTransform->SetCenter(isocenter); > > typedef itk::ResampleImageFilter< InternalImageType, InternalImageType > > ResampleFilterType; > > // The ResampleImageFilter is the driving force for the projection image > generation. > ResampleFilterType::Pointer resampleFilter1 = ResampleFilterType::New(); > > resampleFilter1->SetInput( caster3D->GetOutput() ); // Link the 3D > volume. > resampleFilter1->SetDefaultPixelValue( 0 ); > > // The parameters of interpolator1, such as ProjectionAngle and > FocalPointToIsocenterDistance > // have been set before registration. Here we only need to replace the > initial > // transform with the final transform. > interpolator1->SetTransform( finalTransform ); > interpolator1->Initialize(); > resampleFilter1->SetInterpolator( interpolator1 ); > > // The output 2D projection image has the same image size, origin, and > the > pixel spacing as > // those of the input 2D image. > resampleFilter1->SetSize( > rescaler2D1->GetOutput()->GetLargestPossibleRegion().GetSize() ); > resampleFilter1->SetOutputOrigin( rescaler2D1->GetOutput()->GetOrigin() > ); > resampleFilter1->SetOutputSpacing( rescaler2D1->GetOutput()->GetSpacing() > ); > > // Do the same thing for the output image 2. > ResampleFilterType::Pointer resampleFilter2 = ResampleFilterType::New(); > resampleFilter2->SetInput( caster3D->GetOutput() ); > resampleFilter2->SetDefaultPixelValue( 0 ); > > // The parameters of interpolator2, such as ProjectionAngle and > FocalPointToIsocenterDistance > // have been set before registration. Here we only need to replace the > initial > // transform with the final transform. > /* interpolator2->SetTransform( finalTransform ); > interpolator2->Initialize(); > resampleFilter2->SetInterpolator( interpolator2 ); > > resampleFilter2->SetSize( > rescaler2D2->GetOutput()->GetLargestPossibleRegion().GetSize() ); > resampleFilter2->SetOutputOrigin( rescaler2D2->GetOutput()->GetOrigin() > ); > resampleFilter2->SetOutputSpacing( rescaler2D2->GetOutput()->GetSpacing() > ); > */ > > > /////////////////////////////---DEGUG--START----//////////////////////////////////// > if (debug) > { > InternalImageType::PointType outputorigin2D1 = > rescaler2D1->GetOutput()->GetOrigin(); > std::cout << "Output image 1 origin: " << outputorigin2D1[0] << ", " << > outputorigin2D1[1] > << ", " << outputorigin2D1[2] << std::endl; > /*InternalImageType::PointType outputorigin2D2 = > rescaler2D2->GetOutput()->GetOrigin(); > std::cout << "Output image 2 origin: " << outputorigin2D2[0] << ", " << > outputorigin2D2[1] > << ", " << outputorigin2D2[2] << std::endl;*/ > } > > > /////////////////////////////---DEGUG--END----////////////////////////////////////// > > > // As explained before, the computed projection is upsided-down. > // Here we use a FilpImageFilter to flip the images in y-direction. > flipFilter1->SetInput( resampleFilter1->GetOutput() ); > //flipFilter2->SetInput( resampleFilter2->GetOutput() ); //ORIGINAL > // Rescale the intensity of the projection images to 0-255 for output. > typedef itk::RescaleIntensityImageFilter< > InternalImageType, OutputImageType > RescaleFilterType; > > RescaleFilterType::Pointer rescaler1 = RescaleFilterType::New(); > rescaler1->SetOutputMinimum( 0 ); > rescaler1->SetOutputMaximum( 255 ); > rescaler1->SetInput( flipFilter1->GetOutput() ); //ORIGINAL > // rescaler1->SetInput( resampleFilter1->GetOutput() ); > > //RescaleFilterType::Pointer rescaler2 = RescaleFilterType::New(); > //rescaler2->SetOutputMinimum( 0 ); > //rescaler2->SetOutputMaximum( 255 ); > //rescaler2->SetInput( flipFilter2->GetOutput() ); //ORIGINAL > // rescaler2->SetInput( resampleFilter2->GetOutput() ); > > > typedef itk::ImageFileWriter< OutputImageType > WriterType; > WriterType::Pointer writer1 = WriterType::New(); > //WriterType::Pointer writer2 = WriterType::New(); > > writer1->SetFileName( fileOutput1 ); > writer1->SetInput( rescaler1->GetOutput() ); > > try > { > std::cout << "Writing image: " << fileOutput1 << std::endl; > writer1->Update(); > } > catch( itk::ExceptionObject & err ) > { > std::cerr << "ERROR: ExceptionObject caught !" << std::endl; > std::cerr << err << std::endl; > } > > //writer2->SetFileName( fileOutput2 ); > //writer2->SetInput( rescaler2->GetOutput() ); > > //try > // { > // std::cout << "Writing image: " << fileOutput2 << std::endl; > // writer2->Update(); > // } > //catch( itk::ExceptionObject & err ) > // { > // std::cerr << "ERROR: ExceptionObject caught !" << std::endl; > // std::cerr << err << std::endl; > // } > timer.Report(); > > return EXIT_SUCCESS; > } > > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/Multiresolution-Registration-error-while-trying-to-improve-a-journal-paper-tp36739p36751.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From artioml at post.bgu.ac.il Mon Feb 8 11:28:58 2016 From: artioml at post.bgu.ac.il (artioml) Date: Mon, 8 Feb 2016 09:28:58 -0700 (MST) Subject: [ITK] [ITK-users] Passing adapters to a metric Message-ID: <1454948938845-36755.post@n7.nabble.com> Hello, I want to calculate MSE between the red and the green channel of a given image. I have used an adapter as suggested in the examples section. But the metric throws an exception. What does the error mean? Anyone has an idea how to fix the problem? Thank you very much! Here is the error message: terminate called after throwing an instance of 'itk::ExceptionObject' what(): /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkDomainThreader.hxx:113: itk::ERROR: MeanSquaresImageToImageMetricv4GetValueAndDerivativeThreader(0x1c32950): A subclass of ThreadedDomainPartitioner::PartitionDomainreturned more subdomains than were requested Here is the code: typedef itk::RGBPixel InputPixelType; const unsigned int Dimension = 2; typedef itk::Image< InputPixelType, Dimension > ImageType; typedef itk::ImageAdaptor< ImageType, RedChannelPixelAccessor > RedImageAdaptorType; RedImageAdaptorType::Pointer red_adaptor = RedImageAdaptorType::New(); typedef itk::ImageAdaptor< ImageType, GreenChannelPixelAccessor > GreenImageAdaptorType; GreenImageAdaptorType::Pointer green_adaptor = GreenImageAdaptorType::New(); typedef itk::ImageFileReader< ImageType > ReaderType; ReaderType::Pointer reader = ReaderType::New(); reader->SetFileName( argv[1] ); ImageType::Pointer imageRGB = reader->GetOutput(); red_adaptor->SetImage( imageRGB ); green_adaptor->SetImage( imageRGB ); typedef itk::MeanSquaresImageToImageMetricv4< RedImageAdaptorType, GreenImageAdaptorType > MetricType; MetricType::Pointer metric = MetricType::New(); metric->SetFixedImage(red_adaptor); metric->SetMovingImage(green_adaptor); metric->SetMaximumNumberOfThreads(1); metric->Initialize(); std::cout << "Result: " << metric->GetValue() << std::endl; -- View this message in context: http://itk-users.7.n7.nabble.com/Passing-adapters-to-a-metric-tp36755.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From itkhelpacc at gmail.com Mon Feb 8 23:19:40 2016 From: itkhelpacc at gmail.com (vishal) Date: Mon, 8 Feb 2016 21:19:40 -0700 (MST) Subject: [ITK] [ITK-users] Multiresolution Registration error while trying to improve a journal paper In-Reply-To: References: <1454670288825-36739.post@n7.nabble.com> <1454918603453-36751.post@n7.nabble.com> Message-ID: <1454991580636-36756.post@n7.nabble.com> hi D?enan, Sorry.. I didnt no tat my bad.. Please find the source code attached with this mail.. Regards Vishal 2D3DRegistrationMultiResolution.cxx -- View this message in context: http://itk-users.7.n7.nabble.com/Multiresolution-Registration-error-while-trying-to-improve-a-journal-paper-tp36739p36756.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From gunjan_naik at persistent.com Tue Feb 9 01:12:45 2016 From: gunjan_naik at persistent.com (Gunjan Naik) Date: Tue, 9 Feb 2016 06:12:45 +0000 Subject: [ITK] [ITK-users] Issue with Seed points in Geodesic Active contour Message-ID: Hi All, I am using geodesic active contour for brain tumor segmentation. In that, I have to give seed points for creating level set. I have calculated seed points using opencv, but when I input these points using 'TransformPhysicalPointToIndex' it throws error stating that index out of bounds. It works for only points [(0,0)]. Please provide me directions. Thanks and Regards, Gunjan Naik Gunjan G. Naik | Persistent LABS | PhD Student - University of Pune gunjan_naik at persistent.com | Cell: +91-8087996979 | Tel: +91-20-670 34878 Persistent Systems Ltd. | Partners in Innovation | www.persistent.com DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From itkhelpacc at gmail.com Tue Feb 9 02:28:31 2016 From: itkhelpacc at gmail.com (vishal) Date: Tue, 9 Feb 2016 00:28:31 -0700 (MST) Subject: [ITK] [ITK-users] Multiresolution Registration error while trying to improve a journal paper In-Reply-To: <1454991580636-36756.post@n7.nabble.com> References: <1454670288825-36739.post@n7.nabble.com> <1454918603453-36751.post@n7.nabble.com> <1454991580636-36756.post@n7.nabble.com> Message-ID: <1455002911697-36758.post@n7.nabble.com> hi, I made some changes to the code i attached previously no i getting this error: Starting the registration now... Exception in the Metric )intialize caught!! itk::ERROR: NormalizedCorrelationImageToImageMetric(0000000002832510): Transform is not present ------------------------------------- MultiResolution Level : 0 ExceptionObject caught ! itk::ExceptionObject (000000000027E8A0) Location: "void __cdecl itk::NormalizedCorrelationImageToImageMetric,class itk::Image >::GetValueAndDerivative(const class it k::OptimizerParameters &,double &,class itk::Array &) const" File: c:\itk\insighttoolkit-4.8.2\modules\registration\common\include\itkNormali zedCorrelationImageToImageMetric.hxx Line: 332 Description: itk::ERROR: NormalizedCorrelationImageToImageMetric(000000000283251 0): The gradient image is null, maybe you forgot to call Initialize() Please find the modified code along with this post... please help me out with this problem!! regards Vishal code: RegularStepGradientDescentWithNGC.cxx -- View this message in context: http://itk-users.7.n7.nabble.com/Multiresolution-Registration-error-while-trying-to-improve-a-journal-paper-tp36739p36758.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Tue Feb 9 10:18:18 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 9 Feb 2016 10:18:18 -0500 Subject: [ITK] [ITK-users] Multiresolution Registration error while trying to improve a journal paper In-Reply-To: <1455002911697-36758.post@n7.nabble.com> References: <1454670288825-36739.post@n7.nabble.com> <1454918603453-36751.post@n7.nabble.com> <1454991580636-36756.post@n7.nabble.com> <1455002911697-36758.post@n7.nabble.com> Message-ID: Hey Vishal, I tried setting the transform to the metric, and that gets rid of the "transform not set" exception: metric->SetTransform(transform); metric->SetInterpolator(interpolator1); metric->Initialize(); Take a look at the Initialize method on line 300 in ITK-git\Modules\Registration\Common\include\itkImageToImageMetric.hxx to see all the things you need to provide to metric before a call to initialize. I guess that you are also migrating the code from registration V3 framework to V4, in addition to going from 2 projections to 1, which complicates your life. May I suggest you first do one, and once that works then the other? E.g. first update the example to use V4 registration framework, and then change the code to go from two projections to one. Regards On Tue, Feb 9, 2016 at 2:28 AM, vishal wrote: > hi, > I made some changes to the code i attached previously no i getting this > error: > > Starting the registration now... > Exception in the Metric )intialize caught!! > itk::ERROR: NormalizedCorrelationImageToImageMetric(0000000002832510): > Transform > is not present > ------------------------------------- > MultiResolution Level : 0 > > ExceptionObject caught ! > > itk::ExceptionObject (000000000027E8A0) > Location: "void __cdecl itk::NormalizedCorrelationImageToImageMetric itk:: > Image,class itk::Image >::GetValueAndDerivative(const > class it > k::OptimizerParameters &,double &,class itk::Array &) > const" > File: > c:\itk\insighttoolkit-4.8.2\modules\registration\common\include\itkNormali > zedCorrelationImageToImageMetric.hxx > Line: 332 > Description: itk::ERROR: > NormalizedCorrelationImageToImageMetric(000000000283251 > 0): The gradient image is null, maybe you forgot to call Initialize() > > Please find the modified code along with this post... please help me out > with this problem!! > regards > Vishal > > code: RegularStepGradientDescentWithNGC.cxx > < > http://itk-users.7.n7.nabble.com/file/n36758/RegularStepGradientDescentWithNGC.cxx > > > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/Multiresolution-Registration-error-while-trying-to-improve-a-journal-paper-tp36739p36758.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Tue Feb 9 10:23:01 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 9 Feb 2016 10:23:01 -0500 Subject: [ITK] [ITK-users] Issue with Seed points in Geodesic Active contour In-Reply-To: References: Message-ID: Hi Naik, you should provide your image's meta-information e.g. by: std::cout< wrote: > Hi All, > > > > I am using geodesic active contour for brain tumor segmentation. > > > > In that, I have to give seed points for creating level set. > > > > I have calculated seed points using opencv, but when I input these points > using ?TransformPhysicalPointToIndex? it throws error stating that index > out of bounds. > > > > It works for only points [(0,0)]. > > > > Please provide me directions. > > > > Thanks and Regards, > > Gunjan Naik > > > > > > *Gunjan G. Naik **|** Persistent LABS | PhD Student ? University of Pune* > > *gunjan_naik at persistent.com * *|** Cell: > +91-8087996979 <%2B91-8087996979> **| **Tel: +91-20-670 34878* > > *Persistent Systems Ltd. | **Partners in Innovation **| * > *www.persistent.com* > > > > DISCLAIMER ========== This e-mail may contain privileged and confidential > information which is the property of Persistent Systems Ltd. It is intended > only for the use of the individual or entity to which it is addressed. If > you are not the intended recipient, you are not authorized to read, retain, > copy, print, distribute or use this message. If you have received this > communication in error, please notify the sender and delete all copies of > this message. Persistent Systems Ltd. does not accept any liability for > virus infected mails. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Tue Feb 9 10:47:55 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 9 Feb 2016 10:47:55 -0500 Subject: [ITK] [ITK-users] Passing adapters to a metric In-Reply-To: <1454948938845-36755.post@n7.nabble.com> References: <1454948938845-36755.post@n7.nabble.com> Message-ID: You lack a reader->Update(); call before reader->GetOutput(); call. Without this the region passed to ThreadedDomainPartitioner is 0,0 which causes the exception. Regards On Mon, Feb 8, 2016 at 11:28 AM, artioml wrote: > Hello, > > I want to calculate MSE between the red and the green channel of a given > image. > I have used an adapter as suggested in the examples section. But the metric > throws an exception. > > What does the error mean? Anyone has an idea how to fix the problem? Thank > you very much! > > Here is the error message: > > terminate called after throwing an instance of 'itk::ExceptionObject' > what(): > > /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkDomainThreader.hxx:113: > itk::ERROR: > MeanSquaresImageToImageMetricv4GetValueAndDerivativeThreader(0x1c32950): A > subclass of ThreadedDomainPartitioner::PartitionDomainreturned more > subdomains than were requested > > Here is the code: > > typedef itk::RGBPixel InputPixelType; > const unsigned int Dimension = 2; > typedef itk::Image< InputPixelType, Dimension > ImageType; > > typedef itk::ImageAdaptor< ImageType, RedChannelPixelAccessor > > RedImageAdaptorType; > RedImageAdaptorType::Pointer red_adaptor = RedImageAdaptorType::New(); > typedef itk::ImageAdaptor< ImageType, GreenChannelPixelAccessor > > GreenImageAdaptorType; > GreenImageAdaptorType::Pointer green_adaptor = > GreenImageAdaptorType::New(); > > typedef itk::ImageFileReader< ImageType > ReaderType; > ReaderType::Pointer reader = ReaderType::New(); > reader->SetFileName( argv[1] ); > ImageType::Pointer imageRGB = reader->GetOutput(); > > red_adaptor->SetImage( imageRGB ); > green_adaptor->SetImage( imageRGB ); > > typedef itk::MeanSquaresImageToImageMetricv4< RedImageAdaptorType, > GreenImageAdaptorType > MetricType; > MetricType::Pointer metric = MetricType::New(); > > metric->SetFixedImage(red_adaptor); > metric->SetMovingImage(green_adaptor); > metric->SetMaximumNumberOfThreads(1); > metric->Initialize(); > std::cout << "Result: " << metric->GetValue() << std::endl; > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/Passing-adapters-to-a-metric-tp36755.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From artioml at post.bgu.ac.il Tue Feb 9 11:32:52 2016 From: artioml at post.bgu.ac.il (artioml) Date: Tue, 9 Feb 2016 09:32:52 -0700 (MST) Subject: [ITK] [ITK-users] Passing adapters to a metric In-Reply-To: References: <1454948938845-36755.post@n7.nabble.com> Message-ID: <1455035572947-36762.post@n7.nabble.com> That solved the problem thanks! -- View this message in context: http://itk-users.7.n7.nabble.com/Passing-adapters-to-a-metric-tp36755p36762.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From silvain.beriault at zimmercas.com Tue Feb 9 16:43:36 2016 From: silvain.beriault at zimmercas.com (=?iso-8859-1?Q?Silvain_B=E9riault?=) Date: Tue, 9 Feb 2016 21:43:36 +0000 Subject: [ITK] Using itk::TriangleMeshToBinaryImageFilter on a cube Message-ID: <351795E88040B54CAFE6E977EC789B180106DC08@SRV-EXCHANGE.zimmercas.com> Dear all, I am having difficulties with the use of itk::TriangleMeshToBinaryImageFilter on a cube mesh. There are many mislabled voxel at the surface of the cube (see attached images). The source code follows (Usage MeshToImageTest cube1.vtk cube1.nii 0.175). Thank you in advance for your help, Silvain B?riault #include #include #include #include #include #include typedef itk::Image VolumeType; typedef itk::Mesh MeshType; int main(int argc, char* argv[]) { if (argc != 4) { std::cerr << "Usage: MeshToImageTest inputMeshPath outputVolumePath spacing" << std::endl; } std::string inputFile = argv[1]; std::string outputFile = argv[2]; VolumeType::SpacingType spacing; spacing.Fill(atof(argv[3])); // read input mesh typedef itk::MeshFileReader MeshReaderType; MeshReaderType::Pointer reader = MeshReaderType::New(); reader->SetFileName(inputFile); reader->Update(); MeshType::Pointer mesh = reader->GetOutput(); // Compute OutputVolume's origin and size based on the mesh's bounding box + padding auto& bounds = mesh->GetBoundingBox()->GetBounds(); const int PADDING = 10; VolumeType::PointType origin; origin[0] = bounds[0] - PADDING * spacing[0]; origin[1] = bounds[2] - PADDING * spacing[1]; origin[2] = bounds[4] - PADDING * spacing[2]; VolumeType::SizeType size; size[0] = (bounds[1] - bounds[0]) / spacing[0] + 2*PADDING; size[1] = (bounds[3] - bounds[2]) / spacing[1] + 2*PADDING; size[2] = (bounds[5] - bounds[4]) / spacing[2] + 2*PADDING; // perform conversion between mesh to volume typedef itk::TriangleMeshToBinaryImageFilter MeshToImageFilter; MeshToImageFilter::Pointer meshToVol = MeshToImageFilter::New(); meshToVol->SetInput(mesh); meshToVol->SetOrigin(origin); meshToVol->SetSpacing(spacing); meshToVol->SetSize(size); meshToVol->SetInsideValue(1); meshToVol->SetOutsideValue(0); meshToVol->Update(); // write output volume typedef itk::ImageFileWriter ImageWriterType; ImageWriterType::Pointer writer = ImageWriterType::New(); writer->SetInput(meshToVol->GetOutput()); writer->SetFileName(outputFile); writer->Update(); } -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cube1.vtk Type: application/octet-stream Size: 494 bytes Desc: cube1.vtk URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: screenshot.png Type: image/png Size: 75676 bytes Desc: screenshot.png URL: From filippo.brogi at topic.nl Wed Feb 10 02:47:38 2016 From: filippo.brogi at topic.nl (Filippo Brogi) Date: Wed, 10 Feb 2016 00:47:38 -0700 (MST) Subject: [ITK] [ITK-users] 3D endocardium segmentation Message-ID: <1455090458497-36763.post@n7.nabble.com> Hello, I'm trying to perform a 3D segmentation of the endocardium (the inner part of the heart) using the Geodesic Active Contour pipeline. The current slice thickness is 8 mm. The result is not good as expected. Could be related to slice thickness? If so which one should be the max distance between slices? Thanks. Regards, Filippo -- View this message in context: http://itk-users.7.n7.nabble.com/3D-endocardium-segmentation-tp36763.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From filippo.brogi at topic.nl Wed Feb 10 03:35:06 2016 From: filippo.brogi at topic.nl (Filippo Brogi) Date: Wed, 10 Feb 2016 08:35:06 +0000 Subject: [ITK] [ITK-users] endocardium 3D segmentation Message-ID: <92C2B09BAC90E24EBC4250E7F22F153404049FFA@TOP-EX01.TOPIC.LOCAL> Hello, I'm trying to perform a 3D segmentation of the endocardium (the inner part of the heart) using the Geodesic Active Contour pipeline. The current slice thickness is 8 mm. The result is not good as expected. Could be related to slice thickness? If so which one should be the max distance between slices? Thanks. Regards, Filippo Met vriendelijke groet / kind regards, Filippo Brogi [cid:imageb7135d.PNG at c81a0bef.438d5b7e] Topic Embedded Systems Eindhovenseweg 32c 5683 KH Best T: +31 (0) 499 33 69 79 Postbus 440 E: filippo.brogi at topic.nl 5680 AK Best W: www.topic.nl [cid:imagecfecfd.JPG at 766fa2f5.469d984e][cid:imagebc20ea.JPG at 62dd7c97.4fb939e5][cid:image5bf11c.JPG at c97fc397.43af2edd] Please consider the environment before printing this e-mail Visit us at Embedded World 2016 Germany (23-25 feb 2016), Hall 1, stand number 220 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: image5bf11c.JPG Type: image/jpeg Size: 1060 bytes Desc: image5bf11c.JPG URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From filippo.brogi at topic.nl Wed Feb 10 03:24:22 2016 From: filippo.brogi at topic.nl (Filippo Brogi) Date: Wed, 10 Feb 2016 08:24:22 +0000 Subject: [ITK] [ITK-users] myocardium segmentation Message-ID: <92C2B09BAC90E24EBC4250E7F22F153404049FDE@TOP-EX01.TOPIC.LOCAL> Hello, I'm trying to perform a 3D segmentation of the endocardium (the inner part of the heart) using the Geodesic Active Contour pipeline. The current slice thickness is 8 mm. The result is not good as expected. Could be related to slice thickness? If so which one should be the max distance between slices? Thanks. Regards, Filippo Met vriendelijke groet / kind regards, Filippo Brogi [cid:image940d5e.PNG at 3eb0c3e3.41bfa2ce] Topic Embedded Systems Eindhovenseweg 32c 5683 KH Best T: +31 (0) 499 33 69 79 Postbus 440 E: filippo.brogi at topic.nl 5680 AK Best W: www.topic.nl [cid:image56f107.JPG at 810b3435.47a9a61b][cid:image7593bd.JPG at 2bc6c11d.41b36f83][cid:image6ee4f1.JPG at 6091fa57.4c8dfae2] Please consider the environment before printing this e-mail Visit us at Embedded World 2016 Germany (23-25 feb 2016), Hall 1, stand number 220 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... 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Name: image6ee4f1.JPG Type: image/jpeg Size: 1060 bytes Desc: image6ee4f1.JPG URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Wed Feb 10 06:53:21 2016 From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca) Date: Wed, 10 Feb 2016 12:53:21 +0100 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <729B1C07-6BAA-41AD-8B16-A1A2ECE039DF@mail.nih.gov> <1443521320260-7587935.post@n2.nabble.com> <84A225AE-400C-4FBA-97FA-6A027CB17208@mail.nih.gov> Message-ID: Hi Bradley again. I'm modifying your class in order to be able to set a mask image (a binary image) to be used as a limit in the histogram calculations, I mean, I set an input, a mask and the class should take into account to calculate the histograms only the voxels that belong to the input and to the mask image and having the value 1 in the mask image. The changes seem to be easy but I don?t know why my tests are not working. It seems that 2 threads are working at the same time and when I added my mask iterator, the code crashes. *** Consider that the input and mask images are the same origin, spacing and size. I attach the main changes I've done, and I would thank you a lot if you don't mind having a look and help me to find what I'm doing wrong: template< class TImageType, class TOutputImage > void TextureFeatureImageFilterV2< TImageType, TOutputImage >::*SetInput*(InputImageType *image) { // Process object is not const-correct so the const_cast is required here this->ProcessObject::SetNthInput( 0, const_cast< InputImageType * >( image ) ); } template< class TImageType, class TOutputImage > void TextureFeatureImageFilterV2< TImageType, TOutputImage >::*SetMaskImage*(InputImageType *image) { // Process object is not const-correct so the const_cast is required here this->ProcessObject::SetNthInput( 1, const_cast< InputImageType * >( image ) ); _maskImage = image; // _maskImage is a private member } In the *ThreadedGenerateData*(const RegionType& outputRegionForThread, ThreadIdType threadId ) method: { ... for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) { NeighborhoodIteratorType nIter( radius, input, *fit ); *NeighborhoodIteratorType maskIter( radius, _maskImage, *fit);* OutputIterator outIter(output, *fit); OutputPixelType out; NumericTraits::SetLength( out, this->GetNumberOfOutputComponents() ); while( !nIter.IsAtEnd() ) { this->FillHistogram( *histogram, nIter, *maskIter *); ... ++nIter; ++outIter; * ++maskIter;* ... In the *FillHistogram *method: { ... while( iter != m_CooccurenceOffsetVector.end() ) { const PixelType p1 = niter.GetPixel(iter->first); const PixelType p2 = niter.GetPixel(iter->second); std::cout << "Before p3" << std::endl; * const PixelType p3 = maskIter.GetPixel(iter->first); *std::cout << "After p3: " << p3 << std::endl; * const PixelType p4 = maskIter.GetPixel(iter->second); * std::cout << "After p4: " << p4 << std::endl; if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= m_Max *&& p3 == _insidePixelValue && p4 == _insidePixelValue* ) // The point { ... *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* Thank you so much. My kind regards. /Paco 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca < franciscolopezdelafranca at gmail.com>: > Hello Bradley again. > Sorry but I'd like to re-open this issue because I need your class but > with some modification. > I pass to tell you. > > As my tests with your external class were not good taking into account the > performance, I wonder if you could create a variant of it, but in which I > can set a mask image and your class just return the VectorImage with all > the features for that region (the masked locations) as > itk::ScalarImageToTextureFeaturesFilter class does. > I mean, to get the vector image with all the features but just calculate > it for the regions belonging to the mask image. Positions not belonging to > the mask region could have a pixel value of 0, for instance. > > I don?t know if it is very costly for you, but I would thank you so much. > Otherwise, I could try it but I'd need your suggestions on how to do it. > > Thanks a lot. > Best regards. > > 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca < > franciscolopezdelafranca at gmail.com>: > >> Hello Bradley again, >> I would like to ask you for a couple of favours. In the one hand, could >> you please send me your 3D image so that I can test on it? And on the other >> hand, could you test the example I have referenced in the previous email >> with your image, not changing anything in the code, such as it is, and tell >> me if the execution time is normal? >> Thank you very much. >> Regards, >> /Francisco >> >> PS: All my application trace is printed via standard 'cout' command, not >> due to a debugging compilation mode. >> >> >> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp < >> blowekamp at mail.nih.gov> escribi?: >> >>> Hello, >>> >>> Did you compile TextureFeatureImage in Release mode? >>> >>> 1) The filter does not scale well with a large radius. And given by your >>> initial report of print a very large number of offset you, it sounds like >>> you are using a large radius with many offsets. I created a 224x224x300 >>> unsigned short image and ran with the default offset and a radius of 2 in 5 >>> minutes on my laptop. When I wrote this filter is was ~10x faster than this >>> example... things change though... >>> >>> >>> 2) I sounds like the boundaries/limits of the histogram may be clipping >>> you values. I would inspect the co-occurance matrix. >>> >>> >>> HTH, >>> Brad >>> >>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca < >>> franciscolopezdelafranca at gmail.com> wrote: >>> >>> I've tested with itkTextureFeatureImageFilter, with >>> itk::ScalarImageToTextureFeaturesFilter and also with the >>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures example, >>> for a 3D image and here are my comments: >>> >>> >>> 1. I had to interrupt the test after several hours and it kept on >>> calculating. And this is for only a 3D image (224x224x300). I need to >>> process around 35 images. >>> 2. The result (texture features: entropy, energy, correlation, LH, >>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, 7.83083e+247]. >>> These values were not what I expected based on my experience on another >>> application I developed, but in that case, I calculated the texture >>> features for an image as a whole, not voxel by voxel. >>> >>> Regards. >>> >>> 2015-09-30 8:46 GMT+02:00 vis : >>> >>>> i yes i have tried radius = 3; >>>> still no luck >>>> >>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via ITK >>>> Insight >>>> Users] wrote: >>>> >>>> > Have you tried with a radius of 3 instead of 1? >>>> > >>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>> > >: >>>> > >>>> >> hey Matt, >>>> >> thanks for ur advice.. it did build successfully... but im not able >>>> to run >>>> >> the code for 2D png image... i tried to change the dimension to 2 and >>>> >> build >>>> >> it which it did.. but when i run the code using the command >>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png putput.png 1... >>>> i see >>>> >> this output >>>> >> >>>> >> offset: [-1, -1] [0, -1] >>>> >> offset: [0, -1] [1, -1] >>>> >> offset: [-1, 0] [0, 0] >>>> >> offset: [0, 0] [1, 0] >>>> >> offset: [-1, 1] [0, 1] >>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... if pls >>>> tel me >>>> >> how can i modify this code to work wid 2d image... forgive me if my >>>> ques >>>> >> are really silly im trying to learn something.. >>>> >> regards >>>> >> Vis >>>> >> >>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK Insight >>>> Users] >>>> >> < >>>> >> [hidden email] < >>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>>> >> wrote: >>>> >> >>>> >> > Hi, >>>> >> > >>>> >> > The function: >>>> >> > >>>> >> > itkTextureFeatureImageFilterTest(int argc, char *argv[]) >>>> >> > >>>> >> > must be renamed to >>>> >> > >>>> >> > main(int argc, char* argv[]) >>>> >> > >>>> >> > HTH, >>>> >> > Matt >>>> >> > >>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>> >> > > wrote: >>>> >> > >>>> >> > > hi all, >>>> >> > > im trying to build the itkTextureFeatureImageFilterTest.cxx code >>>> but >>>> >> im >>>> >> > not >>>> >> > > able to it is showing the following error >>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, Configuration: >>>> >> Debug >>>> >> > x64 >>>> >> > > ------ >>>> >> > > 1> Checking Build System >>>> >> > > 1> CMake does not need to re-run because >>>> >> > > >>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>> >> > is >>>> >> > > up-to-date. >>>> >> > > 2>------ Rebuild All started: Project: >>>> >> itkTextureFeatureImageFilterTest, >>>> >> > > Configuration: Debug x64 ------ >>>> >> > > 2> Building Custom Rule >>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>> >> > > 2> CMake does not need to re-run because >>>> >> > > >>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>> >> > is >>>> >> > > up-to-date. >>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: 'std::_Copy_impl': >>>> >> > Function >>>> >> > > call with parameters that may be unsafe - this call relies on the >>>> >> caller >>>> >> > to >>>> >> > > check that the passed values are correct. To disable this >>>> warning, use >>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to use >>>> Visual C++ >>>> >> > > 'Checked Iterators' >>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>> 'std::_Copy_impl' >>>> >> > > 2> >>>> >> > > >>>> >> >>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>> >> > see >>>> >> > > reference to function template instantiation '_OutIt >>>> std::copy>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' being >>>> compiled >>>> >> > > 2> with >>>> >> > > 2> [ >>>> >> > > 2> _OutIt=unsigned char *, >>>> >> > > 2> _InIt=const unsigned char * >>>> >> > > 2> ] >>>> >> > > 2> >>>> >> > > >>>> >> >>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>> >> > > while compiling class template member function 'void >>>> >> > > itk::ImageFileReader::GenerateData(void)' >>>> >> > > 2> with >>>> >> > > 2> [ >>>> >> > > 2> TOutputImage=InputImageType >>>> >> > > 2> ] >>>> >> > > 2> >>>> >> > > >>>> >> > >>>> >> >>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>> >> > >>>> >> > > : see reference to class template instantiation >>>> >> > > 'itk::ImageFileReader' being compiled >>>> >> > > 2> with >>>> >> > > 2> [ >>>> >> > > 2> TOutputImage=InputImageType >>>> >> > > 2> ] >>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>> 'std::_Copy_impl' >>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>> 'std::_Copy_impl' >>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>> 'std::_Copy_impl' >>>> >> > > 2> Creating library >>>> >> > > >>>> >> > >>>> >> >>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>> >> > >>>> >> > > and object >>>> >> > > >>>> >> > >>>> >> >>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>> >> > >>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved external >>>> symbol >>>> >> > main >>>> >> > > referenced in function __tmainCRTStartup >>>> >> > > >>>> >> > >>>> >> >>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>> >> > >>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, Configuration: >>>> Debug >>>> >> > x64 >>>> >> > > ------ >>>> >> > > 3> Building Custom Rule >>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>> >> > > 3> CMake does not need to re-run because >>>> >> > > >>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>> >> > is >>>> >> > > up-to-date. >>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 skipped >>>> ========== >>>> >> > > im using the follwing CMakeList.txt >>>> >> > > # This is the root ITK CMakeLists file. >>>> >> > > cmake_minimum_required(VERSION 2.4) >>>> >> > > if(COMMAND CMAKE_POLICY) >>>> >> > > cmake_policy(SET CMP0003 NEW) >>>> >> > > endif() >>>> >> > > >>>> >> > > >>>> >> > > # This project is designed to be built outside the Insight source >>>> >> tree. >>>> >> > > project(HelloWorld) >>>> >> > > >>>> >> > > # Find ITK. >>>> >> > > find_package(ITK REQUIRED) >>>> >> > > include(${ITK_USE_FILE}) >>>> >> > > >>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>> >> > > >>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest >>>> >> ${ITK_LIBRARIES}) >>>> >> > > >>>> >> > > please tel me wat the error is?? >>>> >> > > >>>> >> > > >>>> >> > > >>>> >> > > -- >>>> >> > > View this message in context: >>>> >> > >>>> >> >>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>> >> > > Sent from the ITK Insight Users mailing list archive at >>>> Nabble.com. >>>> >> > > _____________________________________ >>>> >> > > Powered by www.kitware.com >>>> >> > > >>>> >> > > Visit other Kitware open-source projects at >>>> >> > > http://www.kitware.com/opensource/opensource.html >>>> >> > > >>>> >> > > Kitware offers ITK Training Courses, for more information visit: >>>> >> > > http://www.kitware.com/products/protraining.php >>>> >> > > >>>> >> > > Please keep messages on-topic and check the ITK FAQ at: >>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >>>> >> > > >>>> >> > > Follow this link to subscribe/unsubscribe: >>>> >> > > http://public.kitware.com/mailman/listinfo/insight-users >>>> >> > _____________________________________ >>>> >> > Powered by www.kitware.com >>>> >> > >>>> >> > Visit other Kitware open-source projects at >>>> >> > http://www.kitware.com/opensource/opensource.html >>>> >> > >>>> >> > Kitware offers ITK Training Courses, for more information visit: >>>> >> > http://www.kitware.com/products/protraining.php >>>> >> > >>>> >> > Please keep messages on-topic and check the ITK FAQ at: >>>> >> > http://www.itk.org/Wiki/ITK_FAQ >>>> >> > >>>> >> > Follow this link to subscribe/unsubscribe: >>>> >> > http://public.kitware.com/mailman/listinfo/insight-users >>>> >> > >>>> >> > >>>> >> > ------------------------------ >>>> >> > If you reply to this email, your message will be added to the >>>> discussion >>>> >> > below: >>>> >> > >>>> >> > >>>> >> >>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587952.html >>>> >> > To unsubscribe from [ITK-users] Texture pixel by pixel, click here >>>> >> > < > . >>>> >> > NAML >>>> >> > < >>>> >> >>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>> >> > >>>> >> > >>>> >> >>>> >> >>>> >> >>>> >> >>>> >> -- >>>> >> View this message in context: >>>> >> >>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587960.html >>>> >> Sent from the ITK Insight Users mailing list archive at Nabble.com. >>>> >> _____________________________________ >>>> >> Powered by www.kitware.com >>>> >> >>>> >> Visit other Kitware open-source projects at >>>> >> http://www.kitware.com/opensource/opensource.html >>>> >> >>>> >> Kitware offers ITK Training Courses, for more information visit: >>>> >> http://www.kitware.com/products/protraining.php >>>> >> >>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>> >> >>>> >> Follow this link to subscribe/unsubscribe: >>>> >> http://public.kitware.com/mailman/listinfo/insight-users >>>> >> >>>> > >>>> > >>>> > _____________________________________ >>>> > Powered by www.kitware.com >>>> > >>>> > Visit other Kitware open-source projects at >>>> > http://www.kitware.com/opensource/opensource.html >>>> > >>>> > Kitware offers ITK Training Courses, for more information visit: >>>> > http://www.kitware.com/products/protraining.php >>>> > >>>> > Please keep messages on-topic and check the ITK FAQ at: >>>> > http://www.itk.org/Wiki/ITK_FAQ >>>> > >>>> > Follow this link to subscribe/unsubscribe: >>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>> > >>>> > >>>> > ------------------------------ >>>> > If you reply to this email, your message will be added to the >>>> discussion >>>> > below: >>>> > >>>> > >>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587961.html >>>> > To unsubscribe from [ITK-users] Texture pixel by pixel, click here >>>> > < >>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=7587867&code=aXRraGVscGFjY0BnbWFpbC5jb218NzU4Nzg2N3wzNzEzNjYzNzk= >>>> > >>>> > . >>>> > NAML >>>> > < >>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>> > >>>> > >>>> >>>> >>>> >>>> >>>> -- >>>> View this message in context: >>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587963.html >>>> Sent from the ITK Insight Users mailing list archive at Nabble.com. >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From suneezahanif02 at gmail.com Wed Feb 10 16:56:58 2016 From: suneezahanif02 at gmail.com (suneeza hanif) Date: Wed, 10 Feb 2016 22:56:58 +0100 Subject: [ITK] [ITK-users] Write a result image witout resampling In-Reply-To: References: Message-ID: Hello Gabriel, I have same problem when I do re-sampling, image quality is not same as before. You mentioned that you changed the cast filter type to RescaleIntensityImageFilter type but when I tried to change it I got an error. As RescaleIntensityImageFilter type already contains input and output image type and casting filter type also needs input and output image type. Can you please tell me in detail how did you manage to get the desired results. This would be of great help. Thanks. Best Regards, Suneeza On Tue, Jan 26, 2016 at 6:57 PM, Gabriel A. Gim?nez < gabrielgimenez85 at gmail.com> wrote: > Thanks D?enan Zuki?...., I changed the cast filter type > to RescaleIntensityImageFilter and I got the expected result. > > Best Regards... > > 2016-01-10 16:22 GMT-03:00 D?enan Zuki? : > >> Hi Gabriel, >> >> you probably need to use interpolation method of a higher quality for the >> final resampling, i.e. windowed sinc >> >> instead of linear >> >> . >> >> Regards, >> D?enan >> >> On Fri, Jan 8, 2016 at 9:17 PM, Gabriel A. Gim?nez < >> gabrielgimenez85 at gmail.com> wrote: >> >>> Hi everyone...how are you ? >>> >>> I'm going to point, to finish the registration process build the new >>> transformed fixed image (based on the manual examples), but the quality of >>> the generated image is degraded...how I can create a new image with the >>> same quality as the original image? I just need to apply the transformation >>> parameters. >>> >>> Regards and thanks in advance, >>> >>> -- >>> *Gabriel Alberto Gim?nez.* >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> > > > -- > *Gabriel Alberto Gim?nez.* > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Feb 11 01:12:55 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 11 Feb 2016 01:12:55 -0500 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: There are a couple of upcoming opportunities to share, discuss, design, and learn with your fellow ITK community members. On Thursday (tomorrow), 1:00 PM Eastern USA time, there will be a Google+ Hangout where we will be doing code reviews: https://plus.google.com/u/1/events/c8k1nvamslkhsqhiihnq07lobs4 On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/u/1/events/cvdcf8t1tg5cuung1p5gsl14tj0 For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 To get regular invites to these events, join the ITK Bar Camp G+ Community: https://plus.google.com/u/0/communities/111375098792764998322 All are welcome. Hope to talk to you then! From filippo.brogi at topic.nl Thu Feb 11 02:20:53 2016 From: filippo.brogi at topic.nl (Filippo Brogi) Date: Thu, 11 Feb 2016 00:20:53 -0700 (MST) Subject: [ITK] [ITK-users] zoom image content Message-ID: <1455175253042-36768.post@n7.nabble.com> Hello everyone. As a result of a 2D segmentation I get a binary image with the segmented part in white. I would like to enlarge the white part by a scalar factor, without changing the size the image. Is it possible? Thanks in advance. -- View this message in context: http://itk-users.7.n7.nabble.com/zoom-image-content-tp36768.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Thu Feb 11 04:55:42 2016 From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca) Date: Thu, 11 Feb 2016 10:55:42 +0100 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <729B1C07-6BAA-41AD-8B16-A1A2ECE039DF@mail.nih.gov> <1443521320260-7587935.post@n2.nabble.com> <84A225AE-400C-4FBA-97FA-6A027CB17208@mail.nih.gov> Message-ID: Hi, Please, someone that could help me. I'm working in a pre-doctorate project and I need this class to work. I've read the chapter 13 in the ITK Software Guide on how to write a filter and now I see the fact of the threads due to inheritance of ImageToImageFilter. But, I keep on without understanding why the code crashes just when calling *const PixelType p3 = maskIter.GetPixel(iter->first);* It is just a call to read data, not to write. I guess somebody that had worked with creation of filters might see "easily" the problem, but not me. So, again, please, I need someone to help me with this because I'm stuck on this point. Thank you very much. KR. /Francisco 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca < franciscolopezdelafranca at gmail.com>: > Hi Bradley again. > I'm modifying your class in order to be able to set a mask image (a binary > image) to be used as a limit in the histogram calculations, I mean, I set > an input, a mask and the class should take into account to calculate the > histograms only the voxels that belong to the input and to the mask image > and having the value 1 in the mask image. > The changes seem to be easy but I don?t know why my tests are not working. > It seems that 2 threads are working at the same time and when I added my > mask iterator, the code crashes. > > *** Consider that the input and mask images are the same origin, spacing > and size. > > I attach the main changes I've done, and I would thank you a lot if you > don't mind having a look and help me to find what I'm doing wrong: > > template< class TImageType, class TOutputImage > > void > TextureFeatureImageFilterV2< TImageType, TOutputImage >::*SetInput*(InputImageType > *image) > { > // Process object is not const-correct so the const_cast is required here > this->ProcessObject::SetNthInput( 0, > const_cast< InputImageType * >( image > ) ); > } > > template< class TImageType, class TOutputImage > > void > TextureFeatureImageFilterV2< TImageType, TOutputImage >::*SetMaskImage*(InputImageType > *image) > { > // Process object is not const-correct so the const_cast is required here > this->ProcessObject::SetNthInput( 1, const_cast< InputImageType * >( > image ) ); > > _maskImage = image; // _maskImage is a private member > } > > In the *ThreadedGenerateData*(const RegionType& outputRegionForThread, > ThreadIdType threadId ) method: > { > > ... > > for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) > { > NeighborhoodIteratorType nIter( radius, input, *fit ); > *NeighborhoodIteratorType maskIter( radius, _maskImage, *fit);* > OutputIterator outIter(output, *fit); > > OutputPixelType out; > NumericTraits::SetLength( out, > this->GetNumberOfOutputComponents() ); > > while( !nIter.IsAtEnd() ) > { > this->FillHistogram( *histogram, nIter, *maskIter *); > > ... > > ++nIter; > ++outIter; > * ++maskIter;* > ... > > In the *FillHistogram *method: > { > > ... > > while( iter != m_CooccurenceOffsetVector.end() ) > { > > const PixelType p1 = niter.GetPixel(iter->first); > const PixelType p2 = niter.GetPixel(iter->second); > std::cout << "Before p3" << std::endl; > > * const PixelType p3 = maskIter.GetPixel(iter->first); *std::cout > << "After p3: " << p3 << std::endl; > > * const PixelType p4 = maskIter.GetPixel(iter->second); * std::cout > << "After p4: " << p4 << std::endl; > > if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= m_Max > *&& p3 == _insidePixelValue && p4 == _insidePixelValue* ) // > The point > { > > ... > > > *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* > > Thank you so much. > My kind regards. > /Paco > > 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca < > franciscolopezdelafranca at gmail.com>: > >> Hello Bradley again. >> Sorry but I'd like to re-open this issue because I need your class but >> with some modification. >> I pass to tell you. >> >> As my tests with your external class were not good taking into account >> the performance, I wonder if you could create a variant of it, but in which >> I can set a mask image and your class just return the VectorImage with all >> the features for that region (the masked locations) as >> itk::ScalarImageToTextureFeaturesFilter class does. >> I mean, to get the vector image with all the features but just calculate >> it for the regions belonging to the mask image. Positions not belonging to >> the mask region could have a pixel value of 0, for instance. >> >> I don?t know if it is very costly for you, but I would thank you so >> much. Otherwise, I could try it but I'd need your suggestions on how to do >> it. >> >> Thanks a lot. >> Best regards. >> >> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca < >> franciscolopezdelafranca at gmail.com>: >> >>> Hello Bradley again, >>> I would like to ask you for a couple of favours. In the one hand, could >>> you please send me your 3D image so that I can test on it? And on the other >>> hand, could you test the example I have referenced in the previous email >>> with your image, not changing anything in the code, such as it is, and tell >>> me if the execution time is normal? >>> Thank you very much. >>> Regards, >>> /Francisco >>> >>> PS: All my application trace is printed via standard 'cout' command, not >>> due to a debugging compilation mode. >>> >>> >>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp < >>> blowekamp at mail.nih.gov> escribi?: >>> >>>> Hello, >>>> >>>> Did you compile TextureFeatureImage in Release mode? >>>> >>>> 1) The filter does not scale well with a large radius. And given by >>>> your initial report of print a very large number of offset you, it sounds >>>> like you are using a large radius with many offsets. I created a >>>> 224x224x300 unsigned short image and ran with the default offset and a >>>> radius of 2 in 5 minutes on my laptop. When I wrote this filter is was ~10x >>>> faster than this example... things change though... >>>> >>>> >>>> 2) I sounds like the boundaries/limits of the histogram may be clipping >>>> you values. I would inspect the co-occurance matrix. >>>> >>>> >>>> HTH, >>>> Brad >>>> >>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca < >>>> franciscolopezdelafranca at gmail.com> wrote: >>>> >>>> I've tested with itkTextureFeatureImageFilter, with >>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures example, >>>> for a 3D image and here are my comments: >>>> >>>> >>>> 1. I had to interrupt the test after several hours and it kept on >>>> calculating. And this is for only a 3D image (224x224x300). I need to >>>> process around 35 images. >>>> 2. The result (texture features: entropy, energy, correlation, LH, >>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, 7.83083e+247]. >>>> These values were not what I expected based on my experience on another >>>> application I developed, but in that case, I calculated the texture >>>> features for an image as a whole, not voxel by voxel. >>>> >>>> Regards. >>>> >>>> 2015-09-30 8:46 GMT+02:00 vis : >>>> >>>>> i yes i have tried radius = 3; >>>>> still no luck >>>>> >>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via ITK >>>>> Insight >>>>> Users] wrote: >>>>> >>>>> > Have you tried with a radius of 3 instead of 1? >>>>> > >>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>>> > >: >>>>> > >>>>> >> hey Matt, >>>>> >> thanks for ur advice.. it did build successfully... but im not able >>>>> to run >>>>> >> the code for 2D png image... i tried to change the dimension to 2 >>>>> and >>>>> >> build >>>>> >> it which it did.. but when i run the code using the command >>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png putput.png >>>>> 1... i see >>>>> >> this output >>>>> >> >>>>> >> offset: [-1, -1] [0, -1] >>>>> >> offset: [0, -1] [1, -1] >>>>> >> offset: [-1, 0] [0, 0] >>>>> >> offset: [0, 0] [1, 0] >>>>> >> offset: [-1, 1] [0, 1] >>>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... if pls >>>>> tel me >>>>> >> how can i modify this code to work wid 2d image... forgive me if my >>>>> ques >>>>> >> are really silly im trying to learn something.. >>>>> >> regards >>>>> >> Vis >>>>> >> >>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK Insight >>>>> Users] >>>>> >> < >>>>> >> [hidden email] < >>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>>>> >> wrote: >>>>> >> >>>>> >> > Hi, >>>>> >> > >>>>> >> > The function: >>>>> >> > >>>>> >> > itkTextureFeatureImageFilterTest(int argc, char *argv[]) >>>>> >> > >>>>> >> > must be renamed to >>>>> >> > >>>>> >> > main(int argc, char* argv[]) >>>>> >> > >>>>> >> > HTH, >>>>> >> > Matt >>>>> >> > >>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>>> >> > > wrote: >>>>> >> > >>>>> >> > > hi all, >>>>> >> > > im trying to build the itkTextureFeatureImageFilterTest.cxx >>>>> code but >>>>> >> im >>>>> >> > not >>>>> >> > > able to it is showing the following error >>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>>> Configuration: >>>>> >> Debug >>>>> >> > x64 >>>>> >> > > ------ >>>>> >> > > 1> Checking Build System >>>>> >> > > 1> CMake does not need to re-run because >>>>> >> > > >>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>>> >> > is >>>>> >> > > up-to-date. >>>>> >> > > 2>------ Rebuild All started: Project: >>>>> >> itkTextureFeatureImageFilterTest, >>>>> >> > > Configuration: Debug x64 ------ >>>>> >> > > 2> Building Custom Rule >>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>> >> > > 2> CMake does not need to re-run because >>>>> >> > > >>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>> >> > is >>>>> >> > > up-to-date. >>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>>> 'std::_Copy_impl': >>>>> >> > Function >>>>> >> > > call with parameters that may be unsafe - this call relies on >>>>> the >>>>> >> caller >>>>> >> > to >>>>> >> > > check that the passed values are correct. To disable this >>>>> warning, use >>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to use >>>>> Visual C++ >>>>> >> > > 'Checked Iterators' >>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>> 'std::_Copy_impl' >>>>> >> > > 2> >>>>> >> > > >>>>> >> >>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>>> >> > see >>>>> >> > > reference to function template instantiation '_OutIt >>>>> std::copy>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' being >>>>> compiled >>>>> >> > > 2> with >>>>> >> > > 2> [ >>>>> >> > > 2> _OutIt=unsigned char *, >>>>> >> > > 2> _InIt=const unsigned char * >>>>> >> > > 2> ] >>>>> >> > > 2> >>>>> >> > > >>>>> >> >>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>>> >> > > while compiling class template member function 'void >>>>> >> > > itk::ImageFileReader::GenerateData(void)' >>>>> >> > > 2> with >>>>> >> > > 2> [ >>>>> >> > > 2> TOutputImage=InputImageType >>>>> >> > > 2> ] >>>>> >> > > 2> >>>>> >> > > >>>>> >> > >>>>> >> >>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>>> >> > >>>>> >> > > : see reference to class template instantiation >>>>> >> > > 'itk::ImageFileReader' being compiled >>>>> >> > > 2> with >>>>> >> > > 2> [ >>>>> >> > > 2> TOutputImage=InputImageType >>>>> >> > > 2> ] >>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>> 'std::_Copy_impl' >>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>> 'std::_Copy_impl' >>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>> 'std::_Copy_impl' >>>>> >> > > 2> Creating library >>>>> >> > > >>>>> >> > >>>>> >> >>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>>> >> > >>>>> >> > > and object >>>>> >> > > >>>>> >> > >>>>> >> >>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>>> >> > >>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved external >>>>> symbol >>>>> >> > main >>>>> >> > > referenced in function __tmainCRTStartup >>>>> >> > > >>>>> >> > >>>>> >> >>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>>> >> > >>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>>> Configuration: Debug >>>>> >> > x64 >>>>> >> > > ------ >>>>> >> > > 3> Building Custom Rule >>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>> >> > > 3> CMake does not need to re-run because >>>>> >> > > >>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>> >> > is >>>>> >> > > up-to-date. >>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 skipped >>>>> ========== >>>>> >> > > im using the follwing CMakeList.txt >>>>> >> > > # This is the root ITK CMakeLists file. >>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>>> >> > > if(COMMAND CMAKE_POLICY) >>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>>> >> > > endif() >>>>> >> > > >>>>> >> > > >>>>> >> > > # This project is designed to be built outside the Insight >>>>> source >>>>> >> tree. >>>>> >> > > project(HelloWorld) >>>>> >> > > >>>>> >> > > # Find ITK. >>>>> >> > > find_package(ITK REQUIRED) >>>>> >> > > include(${ITK_USE_FILE}) >>>>> >> > > >>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>>> >> > > >>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest >>>>> >> ${ITK_LIBRARIES}) >>>>> >> > > >>>>> >> > > please tel me wat the error is?? >>>>> >> > > >>>>> >> > > >>>>> >> > > >>>>> >> > > -- >>>>> >> > > View this message in context: >>>>> >> > >>>>> >> >>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>>> >> > > Sent from the ITK Insight Users mailing list archive at >>>>> Nabble.com. >>>>> >> > > _____________________________________ >>>>> >> > > Powered by www.kitware.com >>>>> >> > > >>>>> >> > > Visit other Kitware open-source projects at >>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>>> >> > > >>>>> >> > > Kitware offers ITK Training Courses, for more information visit: >>>>> >> > > http://www.kitware.com/products/protraining.php >>>>> >> > > >>>>> >> > > Please keep messages on-topic and check the ITK FAQ at: >>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >>>>> >> > > >>>>> >> > > Follow this link to subscribe/unsubscribe: >>>>> >> > > http://public.kitware.com/mailman/listinfo/insight-users >>>>> >> > _____________________________________ >>>>> >> > Powered by www.kitware.com >>>>> >> > >>>>> >> > Visit other Kitware open-source projects at >>>>> >> > http://www.kitware.com/opensource/opensource.html >>>>> >> > >>>>> >> > Kitware offers ITK Training Courses, for more information visit: >>>>> >> > http://www.kitware.com/products/protraining.php >>>>> >> > >>>>> >> > Please keep messages on-topic and check the ITK FAQ at: >>>>> >> > http://www.itk.org/Wiki/ITK_FAQ >>>>> >> > >>>>> >> > Follow this link to subscribe/unsubscribe: >>>>> >> > http://public.kitware.com/mailman/listinfo/insight-users >>>>> >> > >>>>> >> > >>>>> >> > ------------------------------ >>>>> >> > If you reply to this email, your message will be added to the >>>>> discussion >>>>> >> > below: >>>>> >> > >>>>> >> > >>>>> >> >>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587952.html >>>>> >> > To unsubscribe from [ITK-users] Texture pixel by pixel, click here >>>>> >> > < > . >>>>> >> > NAML >>>>> >> > < >>>>> >> >>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>> >> > >>>>> >> > >>>>> >> >>>>> >> >>>>> >> >>>>> >> >>>>> >> -- >>>>> >> View this message in context: >>>>> >> >>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587960.html >>>>> >> Sent from the ITK Insight Users mailing list archive at Nabble.com. >>>>> >> _____________________________________ >>>>> >> Powered by www.kitware.com >>>>> >> >>>>> >> Visit other Kitware open-source projects at >>>>> >> http://www.kitware.com/opensource/opensource.html >>>>> >> >>>>> >> Kitware offers ITK Training Courses, for more information visit: >>>>> >> http://www.kitware.com/products/protraining.php >>>>> >> >>>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>> >> >>>>> >> Follow this link to subscribe/unsubscribe: >>>>> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >> >>>>> > >>>>> > >>>>> > _____________________________________ >>>>> > Powered by www.kitware.com >>>>> > >>>>> > Visit other Kitware open-source projects at >>>>> > http://www.kitware.com/opensource/opensource.html >>>>> > >>>>> > Kitware offers ITK Training Courses, for more information visit: >>>>> > http://www.kitware.com/products/protraining.php >>>>> > >>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>> > >>>>> > Follow this link to subscribe/unsubscribe: >>>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>> > >>>>> > >>>>> > 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http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>> > >>>>> > >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> View this message in context: >>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587963.html >>>>> Sent from the ITK Insight Users mailing list archive at Nabble.com. >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> >>>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From samah.bouzidi at gmail.com Thu Feb 11 06:13:41 2016 From: samah.bouzidi at gmail.com (samah) Date: Thu, 11 Feb 2016 04:13:41 -0700 (MST) Subject: [ITK] [ITK-users] airway enhancement using Hessian3DToVesselnessMeasureImageFilter Message-ID: <1455189221682-7588475.post@n2.nabble.com> Hi, I tried to use Hessian3DToVesselnessMeasureImageFilter to segment airways tree in the lung. i have modified the Hessian3DToVesselnessMeasureImageFilter.hxx as follow: // Get the eigen value eigenValue = it.Get(); // dark tubular structures will have a low value of $\lambda_1$ and large positive values of $\lambda_2$ and $\lambda_3$ double normalizeValue = vnl_math_min( eigenValue[1], eigenValue[0]); // Similarity measure to a line structure if ( normalizeValue > 0 ) { double lineMeasure; if ( eigenValue[2] <= 0 ) { lineMeasure = std::exp( -0.5 * vnl_math_sqr( eigenValue[2] / ( m_Alpha1 * normalizeValue ) ) ); } else { lineMeasure = std::exp( -0.5 * vnl_math_sqr( eigenValue[2] / ( m_Alpha2 * normalizeValue ) ) ); } lineMeasure *= normalizeValue; oit.Set( static_cast< OutputPixelType >( lineMeasure ) ); } else { oit.Set(NumericTraits< OutputPixelType >::ZeroValue()); } ++it; ++oit; } but it doesn't work, any suggestion please. Regards Samah, -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/airway-enhancement-using-Hessian3DToVesselnessMeasureImageFilter-tp7588475.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From skalexander at gmail.com Thu Feb 11 10:41:13 2016 From: skalexander at gmail.com (Simon Alexander) Date: Thu, 11 Feb 2016 15:41:13 +0000 Subject: [ITK] [ITK-users] Write a result image witout resampling In-Reply-To: References: Message-ID: In general it is only going to be possible to avoid re-sampling when your transform is strictly rigid (i.e. the sampling lattice of the image can be rigidly transformed and remain regularly shaped). Rescaling the intensity is a completely different issue, but can be used to avoid introducing extra quantization error, for example if you use floating point images in ways that will adjust the value range and then casting them to an integer type. What are you trying to achieve? On Wed, 10 Feb 2016 at 16:57 suneeza hanif wrote: > Hello Gabriel, > > I have same problem when I do re-sampling, image quality is not same as > before. You mentioned that you changed the cast filter type to RescaleIntensityImageFilter > type but when I tried to change it I got an error. As RescaleIntensityImageFilter > type already contains input and output image type and casting filter type > also needs input and output image type. > > Can you please tell me in detail how did you manage to get the desired > results. This would be of great help. > > Thanks. > > Best Regards, > Suneeza > > On Tue, Jan 26, 2016 at 6:57 PM, Gabriel A. Gim?nez < > gabrielgimenez85 at gmail.com> wrote: > >> Thanks D?enan Zuki?...., I changed the cast filter type >> to RescaleIntensityImageFilter and I got the expected result. >> >> Best Regards... >> >> 2016-01-10 16:22 GMT-03:00 D?enan Zuki? : >> >>> Hi Gabriel, >>> >>> you probably need to use interpolation method of a higher quality for >>> the final resampling, i.e. windowed sinc >>> >>> instead of linear >>> >>> . >>> >>> Regards, >>> D?enan >>> >>> On Fri, Jan 8, 2016 at 9:17 PM, Gabriel A. Gim?nez < >>> gabrielgimenez85 at gmail.com> wrote: >>> >>>> Hi everyone...how are you ? >>>> >>>> I'm going to point, to finish the registration process build the new >>>> transformed fixed image (based on the manual examples), but the quality of >>>> the generated image is degraded...how I can create a new image with the >>>> same quality as the original image? I just need to apply the transformation >>>> parameters. >>>> >>>> Regards and thanks in advance, >>>> >>>> -- >>>> *Gabriel Alberto Gim?nez.* >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> >>> >> >> >> -- >> *Gabriel Alberto Gim?nez.* >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Thu Feb 11 11:16:08 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 11 Feb 2016 11:16:08 -0500 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <729B1C07-6BAA-41AD-8B16-A1A2ECE039DF@mail.nih.gov> <1443521320260-7587935.post@n2.nabble.com> <84A225AE-400C-4FBA-97FA-6A027CB17208@mail.nih.gov> Message-ID: Hi Francisco, "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the error message that goes along with the crash? In which file and line does it crash? Regards On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca < franciscolopezdelafranca at gmail.com> wrote: > Hi, > Please, someone that could help me. I'm working in a pre-doctorate project > and I need this class to work. > I've read the chapter 13 in the ITK Software Guide on how to write a > filter and now I see the fact of the threads due to inheritance of > ImageToImageFilter. > But, I keep on without understanding why the code crashes just when > calling > *const PixelType p3 = maskIter.GetPixel(iter->first);* > It is just a call to read data, not to write. > > I guess somebody that had worked with creation of filters might see > "easily" the problem, but not me. > > So, again, please, I need someone to help me with this because I'm stuck > on this point. > > Thank you very much. > KR. > /Francisco > > 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca < > franciscolopezdelafranca at gmail.com>: > >> Hi Bradley again. >> I'm modifying your class in order to be able to set a mask image (a >> binary image) to be used as a limit in the histogram calculations, I mean, >> I set an input, a mask and the class should take into account to calculate >> the histograms only the voxels that belong to the input and to the mask >> image and having the value 1 in the mask image. >> The changes seem to be easy but I don?t know why my tests are not >> working. It seems that 2 threads are working at the same time and when I >> added my mask iterator, the code crashes. >> >> *** Consider that the input and mask images are the same origin, spacing >> and size. >> >> I attach the main changes I've done, and I would thank you a lot if you >> don't mind having a look and help me to find what I'm doing wrong: >> >> template< class TImageType, class TOutputImage > >> void >> TextureFeatureImageFilterV2< TImageType, TOutputImage >::*SetInput*(InputImageType >> *image) >> { >> // Process object is not const-correct so the const_cast is required >> here >> this->ProcessObject::SetNthInput( 0, >> const_cast< InputImageType * >( image >> ) ); >> } >> >> template< class TImageType, class TOutputImage > >> void >> TextureFeatureImageFilterV2< TImageType, TOutputImage >::*SetMaskImage*(InputImageType >> *image) >> { >> // Process object is not const-correct so the const_cast is required >> here >> this->ProcessObject::SetNthInput( 1, const_cast< InputImageType * >( >> image ) ); >> >> _maskImage = image; // _maskImage is a private member >> } >> >> In the *ThreadedGenerateData*(const RegionType& outputRegionForThread, >> ThreadIdType threadId ) method: >> { >> >> ... >> >> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >> { >> NeighborhoodIteratorType nIter( radius, input, *fit ); >> *NeighborhoodIteratorType maskIter( radius, _maskImage, *fit);* >> OutputIterator outIter(output, *fit); >> >> OutputPixelType out; >> NumericTraits::SetLength( out, >> this->GetNumberOfOutputComponents() ); >> >> while( !nIter.IsAtEnd() ) >> { >> this->FillHistogram( *histogram, nIter, *maskIter *); >> >> ... >> >> ++nIter; >> ++outIter; >> * ++maskIter;* >> ... >> >> In the *FillHistogram *method: >> { >> >> ... >> >> while( iter != m_CooccurenceOffsetVector.end() ) >> { >> >> const PixelType p1 = niter.GetPixel(iter->first); >> const PixelType p2 = niter.GetPixel(iter->second); >> std::cout << "Before p3" << std::endl; >> >> * const PixelType p3 = maskIter.GetPixel(iter->first); *std::cout >> << "After p3: " << p3 << std::endl; >> >> * const PixelType p4 = maskIter.GetPixel(iter->second); * std::cout >> << "After p4: " << p4 << std::endl; >> >> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= m_Max >> *&& p3 == _insidePixelValue && p4 == _insidePixelValue* ) // >> The point >> { >> >> ... >> >> >> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >> >> Thank you so much. >> My kind regards. >> /Paco >> >> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca < >> franciscolopezdelafranca at gmail.com>: >> >>> Hello Bradley again. >>> Sorry but I'd like to re-open this issue because I need your class but >>> with some modification. >>> I pass to tell you. >>> >>> As my tests with your external class were not good taking into account >>> the performance, I wonder if you could create a variant of it, but in which >>> I can set a mask image and your class just return the VectorImage with all >>> the features for that region (the masked locations) as >>> itk::ScalarImageToTextureFeaturesFilter class does. >>> I mean, to get the vector image with all the features but just calculate >>> it for the regions belonging to the mask image. Positions not belonging to >>> the mask region could have a pixel value of 0, for instance. >>> >>> I don?t know if it is very costly for you, but I would thank you so >>> much. Otherwise, I could try it but I'd need your suggestions on how to do >>> it. >>> >>> Thanks a lot. >>> Best regards. >>> >>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca < >>> franciscolopezdelafranca at gmail.com>: >>> >>>> Hello Bradley again, >>>> I would like to ask you for a couple of favours. In the one hand, could >>>> you please send me your 3D image so that I can test on it? And on the other >>>> hand, could you test the example I have referenced in the previous email >>>> with your image, not changing anything in the code, such as it is, and tell >>>> me if the execution time is normal? >>>> Thank you very much. >>>> Regards, >>>> /Francisco >>>> >>>> PS: All my application trace is printed via standard 'cout' command, >>>> not due to a debugging compilation mode. >>>> >>>> >>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp < >>>> blowekamp at mail.nih.gov> escribi?: >>>> >>>>> Hello, >>>>> >>>>> Did you compile TextureFeatureImage in Release mode? >>>>> >>>>> 1) The filter does not scale well with a large radius. And given by >>>>> your initial report of print a very large number of offset you, it sounds >>>>> like you are using a large radius with many offsets. I created a >>>>> 224x224x300 unsigned short image and ran with the default offset and a >>>>> radius of 2 in 5 minutes on my laptop. When I wrote this filter is was ~10x >>>>> faster than this example... things change though... >>>>> >>>>> >>>>> 2) I sounds like the boundaries/limits of the histogram may be >>>>> clipping you values. I would inspect the co-occurance matrix. >>>>> >>>>> >>>>> HTH, >>>>> Brad >>>>> >>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca < >>>>> franciscolopezdelafranca at gmail.com> wrote: >>>>> >>>>> I've tested with itkTextureFeatureImageFilter, with >>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures example, >>>>> for a 3D image and here are my comments: >>>>> >>>>> >>>>> 1. I had to interrupt the test after several hours and it kept on >>>>> calculating. And this is for only a 3D image (224x224x300). I need to >>>>> process around 35 images. >>>>> 2. The result (texture features: entropy, energy, correlation, LH, >>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, 7.83083e+247]. >>>>> These values were not what I expected based on my experience on another >>>>> application I developed, but in that case, I calculated the texture >>>>> features for an image as a whole, not voxel by voxel. >>>>> >>>>> Regards. >>>>> >>>>> 2015-09-30 8:46 GMT+02:00 vis : >>>>> >>>>>> i yes i have tried radius = 3; >>>>>> still no luck >>>>>> >>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via ITK >>>>>> Insight >>>>>> Users] wrote: >>>>>> >>>>>> > Have you tried with a radius of 3 instead of 1? >>>>>> > >>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>>>> > >: >>>>>> > >>>>>> >> hey Matt, >>>>>> >> thanks for ur advice.. it did build successfully... but im not >>>>>> able to run >>>>>> >> the code for 2D png image... i tried to change the dimension to 2 >>>>>> and >>>>>> >> build >>>>>> >> it which it did.. but when i run the code using the command >>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png putput.png >>>>>> 1... i see >>>>>> >> this output >>>>>> >> >>>>>> >> offset: [-1, -1] [0, -1] >>>>>> >> offset: [0, -1] [1, -1] >>>>>> >> offset: [-1, 0] [0, 0] >>>>>> >> offset: [0, 0] [1, 0] >>>>>> >> offset: [-1, 1] [0, 1] >>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... if pls >>>>>> tel me >>>>>> >> how can i modify this code to work wid 2d image... forgive me if >>>>>> my ques >>>>>> >> are really silly im trying to learn something.. >>>>>> >> regards >>>>>> >> Vis >>>>>> >> >>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK Insight >>>>>> Users] >>>>>> >> < >>>>>> >> [hidden email] < >>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>>>>> >> wrote: >>>>>> >> >>>>>> >> > Hi, >>>>>> >> > >>>>>> >> > The function: >>>>>> >> > >>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char *argv[]) >>>>>> >> > >>>>>> >> > must be renamed to >>>>>> >> > >>>>>> >> > main(int argc, char* argv[]) >>>>>> >> > >>>>>> >> > HTH, >>>>>> >> > Matt >>>>>> >> > >>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>>>> >> > > wrote: >>>>>> >> > >>>>>> >> > > hi all, >>>>>> >> > > im trying to build the itkTextureFeatureImageFilterTest.cxx >>>>>> code but >>>>>> >> im >>>>>> >> > not >>>>>> >> > > able to it is showing the following error >>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>>>> Configuration: >>>>>> >> Debug >>>>>> >> > x64 >>>>>> >> > > ------ >>>>>> >> > > 1> Checking Build System >>>>>> >> > > 1> CMake does not need to re-run because >>>>>> >> > > >>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>>>> >> > is >>>>>> >> > > up-to-date. >>>>>> >> > > 2>------ Rebuild All started: Project: >>>>>> >> itkTextureFeatureImageFilterTest, >>>>>> >> > > Configuration: Debug x64 ------ >>>>>> >> > > 2> Building Custom Rule >>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>> >> > > 2> CMake does not need to re-run because >>>>>> >> > > >>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>> >> > is >>>>>> >> > > up-to-date. >>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>>>> 'std::_Copy_impl': >>>>>> >> > Function >>>>>> >> > > call with parameters that may be unsafe - this call relies on >>>>>> the >>>>>> >> caller >>>>>> >> > to >>>>>> >> > > check that the passed values are correct. To disable this >>>>>> warning, use >>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to use >>>>>> Visual C++ >>>>>> >> > > 'Checked Iterators' >>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>> 'std::_Copy_impl' >>>>>> >> > > 2> >>>>>> >> > > >>>>>> >> >>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>>>> >> > see >>>>>> >> > > reference to function template instantiation '_OutIt >>>>>> std::copy>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' being >>>>>> compiled >>>>>> >> > > 2> with >>>>>> >> > > 2> [ >>>>>> >> > > 2> _OutIt=unsigned char *, >>>>>> >> > > 2> _InIt=const unsigned char * >>>>>> >> > > 2> ] >>>>>> >> > > 2> >>>>>> >> > > >>>>>> >> >>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>>>> >> > > while compiling class template member function 'void >>>>>> >> > > itk::ImageFileReader::GenerateData(void)' >>>>>> >> > > 2> with >>>>>> >> > > 2> [ >>>>>> >> > > 2> TOutputImage=InputImageType >>>>>> >> > > 2> ] >>>>>> >> > > 2> >>>>>> >> > > >>>>>> >> > >>>>>> >> >>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>>>> >> > >>>>>> >> > > : see reference to class template instantiation >>>>>> >> > > 'itk::ImageFileReader' being compiled >>>>>> >> > > 2> with >>>>>> >> > > 2> [ >>>>>> >> > > 2> TOutputImage=InputImageType >>>>>> >> > > 2> ] >>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>> 'std::_Copy_impl' >>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>> 'std::_Copy_impl' >>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>> 'std::_Copy_impl' >>>>>> >> > > 2> Creating library >>>>>> >> > > >>>>>> >> > >>>>>> >> >>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>>>> >> > >>>>>> >> > > and object >>>>>> >> > > >>>>>> >> > >>>>>> >> >>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>>>> >> > >>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved external >>>>>> symbol >>>>>> >> > main >>>>>> >> > > referenced in function __tmainCRTStartup >>>>>> >> > > >>>>>> >> > >>>>>> >> >>>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>>>> >> > >>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>>>> Configuration: Debug >>>>>> >> > x64 >>>>>> >> > > ------ >>>>>> >> > > 3> Building Custom Rule >>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>> >> > > 3> CMake does not need to re-run because >>>>>> >> > > >>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>> >> > is >>>>>> >> > > up-to-date. >>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 skipped >>>>>> ========== >>>>>> >> > > im using the follwing CMakeList.txt >>>>>> >> > > # This is the root ITK CMakeLists file. >>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>>>> >> > > if(COMMAND CMAKE_POLICY) >>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>>>> >> > > endif() >>>>>> >> > > >>>>>> >> > > >>>>>> >> > > # This project is designed to be built outside the Insight >>>>>> source >>>>>> >> tree. >>>>>> >> > > project(HelloWorld) >>>>>> >> > > >>>>>> >> > > # Find ITK. >>>>>> >> > > find_package(ITK REQUIRED) >>>>>> >> > > include(${ITK_USE_FILE}) >>>>>> >> > > >>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>>>> >> > > >>>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest >>>>>> >> ${ITK_LIBRARIES}) >>>>>> >> > > >>>>>> >> > > please tel me wat the error is?? >>>>>> >> > > >>>>>> >> > > >>>>>> >> > > >>>>>> >> > > -- >>>>>> >> > > View this message in context: >>>>>> >> > >>>>>> >> >>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>>>> >> > > Sent from the ITK Insight Users mailing list archive at >>>>>> Nabble.com. >>>>>> >> > > _____________________________________ >>>>>> >> > > Powered by www.kitware.com >>>>>> >> > > >>>>>> >> > > Visit other Kitware open-source projects at >>>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>>>> >> > > >>>>>> >> > > Kitware offers ITK Training Courses, for more information >>>>>> visit: >>>>>> >> > > http://www.kitware.com/products/protraining.php >>>>>> >> > > >>>>>> >> > > Please keep messages on-topic and check the ITK FAQ at: >>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >>>>>> >> > > >>>>>> >> > > Follow this link to subscribe/unsubscribe: >>>>>> >> > > http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >> > _____________________________________ >>>>>> >> > Powered by www.kitware.com >>>>>> >> > >>>>>> >> > Visit other Kitware open-source projects at >>>>>> >> > http://www.kitware.com/opensource/opensource.html >>>>>> >> > >>>>>> >> > Kitware offers ITK Training Courses, for more information visit: >>>>>> >> > http://www.kitware.com/products/protraining.php >>>>>> >> > >>>>>> >> > Please keep messages on-topic and check the ITK FAQ at: >>>>>> >> > http://www.itk.org/Wiki/ITK_FAQ >>>>>> >> > >>>>>> >> > Follow this link to subscribe/unsubscribe: >>>>>> >> > http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >> > >>>>>> >> > >>>>>> >> > ------------------------------ >>>>>> >> > If you reply to this email, your message will be added to the >>>>>> discussion >>>>>> >> > below: >>>>>> >> > >>>>>> >> > >>>>>> >> >>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587952.html >>>>>> >> > To unsubscribe from [ITK-users] Texture pixel by pixel, click >>>>>> here >>>>>> >> > < > . >>>>>> >> > NAML >>>>>> >> > < >>>>>> >> >>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>> >> > >>>>>> >> > >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> -- >>>>>> >> View this message in context: >>>>>> >> >>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587960.html >>>>>> >> Sent from the ITK Insight Users 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http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>> > >>>>>> > >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> View this message in context: >>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587963.html >>>>>> Sent from the ITK Insight Users mailing list archive at Nabble.com. >>>>>> _____________________________________ >>>>>> Powered by www.kitware.com >>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>> http://www.kitware.com/products/protraining.php >>>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>>> >>>>> >>> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From suneezahanif02 at gmail.com Thu Feb 11 11:16:57 2016 From: suneezahanif02 at gmail.com (suneeza hanif) Date: Thu, 11 Feb 2016 17:16:57 +0100 Subject: [ITK] [ITK-users] Write a result image witout resampling In-Reply-To: References: Message-ID: Hello Simon, Thank you for your reply. The problem is after doing registration, the transformed image is written in a file. The quality of transformed image is not same as moving image. When I change the window and level of an image then it look similar. Best Regards, Suneeza On Thu, Feb 11, 2016 at 4:41 PM, Simon Alexander wrote: > In general it is only going to be possible to avoid re-sampling when your > transform is strictly rigid (i.e. the sampling lattice of the image can be > rigidly transformed and remain regularly shaped). Rescaling the intensity > is a completely different issue, but can be used to avoid introducing extra > quantization error, for example if you use floating point images in ways > that will adjust the value range and then casting them to an integer type. > > What are you trying to achieve? > > On Wed, 10 Feb 2016 at 16:57 suneeza hanif > wrote: > >> Hello Gabriel, >> >> I have same problem when I do re-sampling, image quality is not same as >> before. You mentioned that you changed the cast filter type to RescaleIntensityImageFilter >> type but when I tried to change it I got an error. As RescaleIntensityImageFilter >> type already contains input and output image type and casting filter type >> also needs input and output image type. >> >> Can you please tell me in detail how did you manage to get the desired >> results. This would be of great help. >> >> Thanks. >> >> Best Regards, >> Suneeza >> >> On Tue, Jan 26, 2016 at 6:57 PM, Gabriel A. Gim?nez < >> gabrielgimenez85 at gmail.com> wrote: >> >>> Thanks D?enan Zuki?...., I changed the cast filter type >>> to RescaleIntensityImageFilter and I got the expected result. >>> >>> Best Regards... >>> >>> 2016-01-10 16:22 GMT-03:00 D?enan Zuki? : >>> >>>> Hi Gabriel, >>>> >>>> you probably need to use interpolation method of a higher quality for >>>> the final resampling, i.e. windowed sinc >>>> >>>> instead of linear >>>> >>>> . >>>> >>>> Regards, >>>> D?enan >>>> >>>> On Fri, Jan 8, 2016 at 9:17 PM, Gabriel A. Gim?nez < >>>> gabrielgimenez85 at gmail.com> wrote: >>>> >>>>> Hi everyone...how are you ? >>>>> >>>>> I'm going to point, to finish the registration process build the new >>>>> transformed fixed image (based on the manual examples), but the quality of >>>>> the generated image is degraded...how I can create a new image with the >>>>> same quality as the original image? I just need to apply the transformation >>>>> parameters. >>>>> >>>>> Regards and thanks in advance, >>>>> >>>>> -- >>>>> *Gabriel Alberto Gim?nez.* >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>>> >>>> >>> >>> >>> -- >>> *Gabriel Alberto Gim?nez.* >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Thu Feb 11 11:20:12 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 11 Feb 2016 11:20:12 -0500 Subject: [ITK] [ITK-users] zoom image content In-Reply-To: <1455175253042-36768.post@n7.nabble.com> References: <1455175253042-36768.post@n7.nabble.com> Message-ID: Hi Filippo, depending on what kind of enlargement you want, you might use resample filter , dilate filter , or do some manual hacking of the image's metadata (double the image spacing, reduce the LargestPossibleRegion and possibly shift its center). HTH, D?enan On Thu, Feb 11, 2016 at 2:20 AM, Filippo Brogi wrote: > Hello everyone. > As a result of a 2D segmentation I get a binary image with the segmented > part in white. I would like to enlarge the white part by a scalar factor, > without changing the size the image. Is it possible? Thanks in advance. > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/zoom-image-content-tp36768.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Thu Feb 11 11:25:31 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 11 Feb 2016 11:25:31 -0500 Subject: [ITK] [ITK-users] Write a result image witout resampling In-Reply-To: References: Message-ID: Hi Suneeza, what is your input data format? Which tool are you using to visualize the images? DICOM can have a lot of metadata, including a predefined window and level. To eliminate some of the variables, can you use .mha or .nrrd format for both input and output, and use a simple viewer such as ITK-SNAP to view and compare the images? Also worth verifying is that both input and output format have the same pixel type e.g. unsigned short. Regards, D?enan On Thu, Feb 11, 2016 at 11:16 AM, suneeza hanif wrote: > Hello Simon, > > Thank you for your reply. > > The problem is after doing registration, the transformed image is written > in a file. The quality of transformed image is not same as moving image. > When I change the window and level of an image then it look similar. > > Best Regards, > Suneeza > > On Thu, Feb 11, 2016 at 4:41 PM, Simon Alexander > wrote: > >> In general it is only going to be possible to avoid re-sampling when your >> transform is strictly rigid (i.e. the sampling lattice of the image can be >> rigidly transformed and remain regularly shaped). Rescaling the intensity >> is a completely different issue, but can be used to avoid introducing extra >> quantization error, for example if you use floating point images in ways >> that will adjust the value range and then casting them to an integer type. >> >> What are you trying to achieve? >> >> On Wed, 10 Feb 2016 at 16:57 suneeza hanif >> wrote: >> >>> Hello Gabriel, >>> >>> I have same problem when I do re-sampling, image quality is not same as >>> before. You mentioned that you changed the cast filter type to RescaleIntensityImageFilter >>> type but when I tried to change it I got an error. As RescaleIntensityImageFilter >>> type already contains input and output image type and casting filter type >>> also needs input and output image type. >>> >>> Can you please tell me in detail how did you manage to get the desired >>> results. This would be of great help. >>> >>> Thanks. >>> >>> Best Regards, >>> Suneeza >>> >>> On Tue, Jan 26, 2016 at 6:57 PM, Gabriel A. Gim?nez < >>> gabrielgimenez85 at gmail.com> wrote: >>> >>>> Thanks D?enan Zuki?...., I changed the cast filter type >>>> to RescaleIntensityImageFilter and I got the expected result. >>>> >>>> Best Regards... >>>> >>>> 2016-01-10 16:22 GMT-03:00 D?enan Zuki? : >>>> >>>>> Hi Gabriel, >>>>> >>>>> you probably need to use interpolation method of a higher quality for >>>>> the final resampling, i.e. windowed sinc >>>>> >>>>> instead of linear >>>>> >>>>> . >>>>> >>>>> Regards, >>>>> D?enan >>>>> >>>>> On Fri, Jan 8, 2016 at 9:17 PM, Gabriel A. Gim?nez < >>>>> gabrielgimenez85 at gmail.com> wrote: >>>>> >>>>>> Hi everyone...how are you ? >>>>>> >>>>>> I'm going to point, to finish the registration process build the new >>>>>> transformed fixed image (based on the manual examples), but the quality of >>>>>> the generated image is degraded...how I can create a new image with the >>>>>> same quality as the original image? I just need to apply the transformation >>>>>> parameters. >>>>>> >>>>>> Regards and thanks in advance, >>>>>> >>>>>> -- >>>>>> *Gabriel Alberto Gim?nez.* >>>>>> >>>>>> _____________________________________ >>>>>> Powered by www.kitware.com >>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>> http://www.kitware.com/products/protraining.php >>>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >>>>>> >>>>> >>>> >>>> >>>> -- >>>> *Gabriel Alberto Gim?nez.* >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Thu Feb 11 12:07:52 2016 From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca) Date: Thu, 11 Feb 2016 18:07:52 +0100 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <84A225AE-400C-4FBA-97FA-6A027CB17208@mail.nih.gov> Message-ID: Hi Dzenan, The original class is here: https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx I've just added setInput and setMaskImage methods and modify some lines in the original class as I indicated in the yesterday mail within this thread. I'm running it on Windows, and there is no error at all, just a crash. I may have to include exceptions management. The crash occurs just when calling p3 = maskIter.GetPixel(iter->first) If you know why it could be or if you need more clarification, please let me know. Many thanks 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < ml-node+s2283740n7588477h22 at n2.nabble.com>: > Hi Francisco, > > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the error message > that goes along with the crash? In which file and line does it crash? > > Regards > > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca <[hidden > email] > wrote: > >> Hi, >> Please, someone that could help me. I'm working in a pre-doctorate >> project and I need this class to work. >> I've read the chapter 13 in the ITK Software Guide on how to write a >> filter and now I see the fact of the threads due to inheritance of >> ImageToImageFilter. >> But, I keep on without understanding why the code crashes just when >> calling >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >> It is just a call to read data, not to write. >> >> I guess somebody that had worked with creation of filters might see >> "easily" the problem, but not me. >> >> So, again, please, I need someone to help me with this because I'm stuck >> on this point. >> >> Thank you very much. >> KR. >> /Francisco >> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden email] >> >: >> >>> Hi Bradley again. >>> I'm modifying your class in order to be able to set a mask image (a >>> binary image) to be used as a limit in the histogram calculations, I mean, >>> I set an input, a mask and the class should take into account to calculate >>> the histograms only the voxels that belong to the input and to the mask >>> image and having the value 1 in the mask image. >>> The changes seem to be easy but I don?t know why my tests are not >>> working. It seems that 2 threads are working at the same time and when I >>> added my mask iterator, the code crashes. >>> >>> *** Consider that the input and mask images are the same origin, spacing >>> and size. >>> >>> I attach the main changes I've done, and I would thank you a lot if you >>> don't mind having a look and help me to find what I'm doing wrong: >>> >>> template< class TImageType, class TOutputImage > >>> void >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >::*SetInput*(InputImageType >>> *image) >>> { >>> // Process object is not const-correct so the const_cast is required >>> here >>> this->ProcessObject::SetNthInput( 0, >>> const_cast< InputImageType * >( >>> image ) ); >>> } >>> >>> template< class TImageType, class TOutputImage > >>> void >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >::*SetMaskImage*(InputImageType >>> *image) >>> { >>> // Process object is not const-correct so the const_cast is required >>> here >>> this->ProcessObject::SetNthInput( 1, const_cast< InputImageType * >( >>> image ) ); >>> >>> _maskImage = image; // _maskImage is a private member >>> } >>> >>> In the *ThreadedGenerateData*(const RegionType& outputRegionForThread, >>> ThreadIdType threadId ) method: >>> { >>> >>> ... >>> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >>> { >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, *fit);* >>> OutputIterator outIter(output, *fit); >>> >>> OutputPixelType out; >>> NumericTraits::SetLength( out, >>> this->GetNumberOfOutputComponents() ); >>> >>> while( !nIter.IsAtEnd() ) >>> { >>> this->FillHistogram( *histogram, nIter, *maskIter *); >>> >>> ... >>> >>> ++nIter; >>> ++outIter; >>> * ++maskIter;* >>> ... >>> >>> In the *FillHistogram *method: >>> { >>> >>> ... >>> >>> while( iter != m_CooccurenceOffsetVector.end() ) >>> { >>> >>> const PixelType p1 = niter.GetPixel(iter->first); >>> const PixelType p2 = niter.GetPixel(iter->second); >>> std::cout << "Before p3" << std::endl; >>> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); *std::cout >>> << "After p3: " << p3 << std::endl; >>> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >>> std::cout << "After p4: " << p4 << std::endl; >>> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= m_Max >>> *&& p3 == _insidePixelValue && p4 == _insidePixelValue* ) >>> // The point >>> { >>> >>> ... >>> >>> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >>> >>> Thank you so much. >>> My kind regards. >>> /Paco >>> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca <[hidden email] >>> >: >>> >>>> Hello Bradley again. >>>> Sorry but I'd like to re-open this issue because I need your class but >>>> with some modification. >>>> I pass to tell you. >>>> >>>> As my tests with your external class were not good taking into account >>>> the performance, I wonder if you could create a variant of it, but in which >>>> I can set a mask image and your class just return the VectorImage with all >>>> the features for that region (the masked locations) as >>>> itk::ScalarImageToTextureFeaturesFilter class does. >>>> I mean, to get the vector image with all the features but just >>>> calculate it for the regions belonging to the mask image. Positions not >>>> belonging to the mask region could have a pixel value of 0, for instance. >>>> >>>> I don?t know if it is very costly for you, but I would thank you so >>>> much. Otherwise, I could try it but I'd need your suggestions on how to do >>>> it. >>>> >>>> Thanks a lot. >>>> Best regards. >>>> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca <[hidden email] >>>> >: >>>> >>>>> Hello Bradley again, >>>>> I would like to ask you for a couple of favours. In the one hand, >>>>> could you please send me your 3D image so that I can test on it? And on the >>>>> other hand, could you test the example I have referenced in the previous >>>>> email with your image, not changing anything in the code, such as it is, >>>>> and tell me if the execution time is normal? >>>>> Thank you very much. >>>>> Regards, >>>>> /Francisco >>>>> >>>>> PS: All my application trace is printed via standard 'cout' command, >>>>> not due to a debugging compilation mode. >>>>> >>>>> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp <[hidden >>>>> email] > >>>>> escribi?: >>>>> >>>>>> Hello, >>>>>> >>>>>> Did you compile TextureFeatureImage in Release mode? >>>>>> >>>>>> 1) The filter does not scale well with a large radius. And given by >>>>>> your initial report of print a very large number of offset you, it sounds >>>>>> like you are using a large radius with many offsets. I created a >>>>>> 224x224x300 unsigned short image and ran with the default offset and a >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this filter is was ~10x >>>>>> faster than this example... things change though... >>>>>> >>>>>> >>>>>> 2) I sounds like the boundaries/limits of the histogram may be >>>>>> clipping you values. I would inspect the co-occurance matrix. >>>>>> >>>>>> >>>>>> HTH, >>>>>> Brad >>>>>> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca <[hidden >>>>>> email] > >>>>>> wrote: >>>>>> >>>>>> I've tested with itkTextureFeatureImageFilter, with >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures example, >>>>>> for a 3D image and here are my comments: >>>>>> >>>>>> >>>>>> 1. I had to interrupt the test after several hours and it kept on >>>>>> calculating. And this is for only a 3D image (224x224x300). I need to >>>>>> process around 35 images. >>>>>> 2. The result (texture features: entropy, energy, correlation, LH, >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, 7.83083e+247]. >>>>>> These values were not what I expected based on my experience on another >>>>>> application I developed, but in that case, I calculated the texture >>>>>> features for an image as a whole, not voxel by voxel. >>>>>> >>>>>> Regards. >>>>>> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >>>>>> >: >>>>>> >>>>>>> i yes i have tried radius = 3; >>>>>>> still no luck >>>>>>> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via ITK >>>>>>> Insight >>>>>>> Users] <[hidden email] >>>>>>> > wrote: >>>>>>> >>>>>>> > Have you tried with a radius of 3 instead of 1? >>>>>>> > >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>>>>> > >: >>>>>>> > >>>>>>> >> hey Matt, >>>>>>> >> thanks for ur advice.. it did build successfully... but im not >>>>>>> able to run >>>>>>> >> the code for 2D png image... i tried to change the dimension to 2 >>>>>>> and >>>>>>> >> build >>>>>>> >> it which it did.. but when i run the code using the command >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png putput.png >>>>>>> 1... i see >>>>>>> >> this output >>>>>>> >> >>>>>>> >> offset: [-1, -1] [0, -1] >>>>>>> >> offset: [0, -1] [1, -1] >>>>>>> >> offset: [-1, 0] [0, 0] >>>>>>> >> offset: [0, 0] [1, 0] >>>>>>> >> offset: [-1, 1] [0, 1] >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... if pls >>>>>>> tel me >>>>>>> >> how can i modify this code to work wid 2d image... forgive me if >>>>>>> my ques >>>>>>> >> are really silly im trying to learn something.. >>>>>>> >> regards >>>>>>> >> Vis >>>>>>> >> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK >>>>>>> Insight Users] >>>>>>> >> < >>>>>>> >> [hidden email] < >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>>>>>> >> wrote: >>>>>>> >> >>>>>>> >> > Hi, >>>>>>> >> > >>>>>>> >> > The function: >>>>>>> >> > >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char *argv[]) >>>>>>> >> > >>>>>>> >> > must be renamed to >>>>>>> >> > >>>>>>> >> > main(int argc, char* argv[]) >>>>>>> >> > >>>>>>> >> > HTH, >>>>>>> >> > Matt >>>>>>> >> > >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>>>>> >> > > wrote: >>>>>>> >> > >>>>>>> >> > > hi all, >>>>>>> >> > > im trying to build the itkTextureFeatureImageFilterTest.cxx >>>>>>> code but >>>>>>> >> im >>>>>>> >> > not >>>>>>> >> > > able to it is showing the following error >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>>>>> Configuration: >>>>>>> >> Debug >>>>>>> >> > x64 >>>>>>> >> > > ------ >>>>>>> >> > > 1> Checking Build System >>>>>>> >> > > 1> CMake does not need to re-run because >>>>>>> >> > > >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>>>>> >> > is >>>>>>> >> > > up-to-date. >>>>>>> >> > > 2>------ Rebuild All started: Project: >>>>>>> >> itkTextureFeatureImageFilterTest, >>>>>>> >> > > Configuration: Debug x64 ------ >>>>>>> >> > > 2> Building Custom Rule >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>> >> > > 2> CMake does not need to re-run because >>>>>>> >> > > >>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>> >> > is >>>>>>> >> > > up-to-date. >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>>>>> 'std::_Copy_impl': >>>>>>> >> > Function >>>>>>> >> > > call with parameters that may be unsafe - this call relies on >>>>>>> the >>>>>>> >> caller >>>>>>> >> > to >>>>>>> >> > > check that the passed values are correct. To disable this >>>>>>> warning, use >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to use >>>>>>> Visual C++ >>>>>>> >> > > 'Checked Iterators' >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>> 'std::_Copy_impl' >>>>>>> >> > > 2> >>>>>>> >> > > >>>>>>> >> >>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>>>>> >> > see >>>>>>> >> > > reference to function template instantiation '_OutIt >>>>>>> std::copy>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' being >>>>>>> compiled >>>>>>> >> > > 2> with >>>>>>> >> > > 2> [ >>>>>>> >> > > 2> _OutIt=unsigned char *, >>>>>>> >> > > 2> _InIt=const unsigned char * >>>>>>> >> > > 2> ] >>>>>>> >> > > 2> >>>>>>> >> > > >>>>>>> >> >>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>>>>> >> > > while compiling class template member function 'void >>>>>>> >> > > itk::ImageFileReader::GenerateData(void)' >>>>>>> >> > > 2> with >>>>>>> >> > > 2> [ >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>> >> > > 2> ] >>>>>>> >> > > 2> >>>>>>> >> > > >>>>>>> >> > >>>>>>> >> >>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>>>>> >> > >>>>>>> >> > > : see reference to class template instantiation >>>>>>> >> > > 'itk::ImageFileReader' being compiled >>>>>>> >> > > 2> with >>>>>>> >> > > 2> [ >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>> >> > > 2> ] >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>> 'std::_Copy_impl' >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>> 'std::_Copy_impl' >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>> 'std::_Copy_impl' >>>>>>> >> > > 2> Creating library >>>>>>> >> > > >>>>>>> >> > >>>>>>> >> >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>>>>> >> > >>>>>>> >> > > and object >>>>>>> >> > > >>>>>>> >> > >>>>>>> >> >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>>>>> >> > >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved >>>>>>> external symbol >>>>>>> >> > main >>>>>>> >> > > referenced in function __tmainCRTStartup >>>>>>> >> > > >>>>>>> >> > >>>>>>> >> >>>>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>>>>> >> > >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>>>>> Configuration: Debug >>>>>>> >> > x64 >>>>>>> >> > > ------ >>>>>>> >> > > 3> Building Custom Rule >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>> >> > > 3> CMake does not need to re-run because >>>>>>> >> > > >>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>> >> > is >>>>>>> >> > > up-to-date. >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 skipped >>>>>>> ========== >>>>>>> >> > > im using the follwing CMakeList.txt >>>>>>> >> > > # This is the root ITK CMakeLists file. >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>>>>> >> > > endif() >>>>>>> >> > > >>>>>>> >> > > >>>>>>> >> > > # This project is designed to be built outside the Insight >>>>>>> source >>>>>>> >> tree. >>>>>>> >> > > project(HelloWorld) >>>>>>> >> > > >>>>>>> >> > > # Find ITK. >>>>>>> >> > > find_package(ITK REQUIRED) >>>>>>> >> > > include(${ITK_USE_FILE}) >>>>>>> >> > > >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>>>>> >> > > >>>>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest >>>>>>> >> ${ITK_LIBRARIES}) >>>>>>> >> > > >>>>>>> >> > > please tel me wat the error is?? >>>>>>> >> > > >>>>>>> >> > > >>>>>>> >> > > >>>>>>> >> > > -- >>>>>>> >> > > View this message in context: >>>>>>> >> > >>>>>>> >> >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>>>>> >> > > Sent from the ITK Insight Users mailing list archive at >>>>>>> Nabble.com. >>>>>>> >> > > _____________________________________ >>>>>>> >> > > Powered by www.kitware.com >>>>>>> >> > > >>>>>>> >> > > Visit other Kitware open-source projects at >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>>>>> >> > > >>>>>>> >> > > Kitware offers ITK Training Courses, for more information >>>>>>> visit: >>>>>>> >> > > http://www.kitware.com/products/protraining.php >>>>>>> >> > > >>>>>>> >> > > Please keep messages on-topic and check the ITK FAQ at: >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >>>>>>> >> > > >>>>>>> >> > > Follow this link to subscribe/unsubscribe: >>>>>>> >> > > http://public.kitware.com/mailman/listinfo/insight-users >>>>>>> >> > _____________________________________ >>>>>>> >> > Powered by www.kitware.com >>>>>>> >> > >>>>>>> >> > Visit other Kitware open-source projects at >>>>>>> >> > http://www.kitware.com/opensource/opensource.html >>>>>>> >> > >>>>>>> >> > Kitware offers ITK Training Courses, for more information visit: >>>>>>> >> > http://www.kitware.com/products/protraining.php >>>>>>> >> > >>>>>>> >> > Please keep messages on-topic and check the ITK FAQ at: >>>>>>> >> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>> >> > >>>>>>> >> > Follow this link to subscribe/unsubscribe: >>>>>>> >> > http://public.kitware.com/mailman/listinfo/insight-users >>>>>>> >> > >>>>>>> >> > >>>>>>> >> > ------------------------------ >>>>>>> >> > If you reply to this email, your message will be added to the >>>>>>> discussion >>>>>>> >> > below: >>>>>>> >> > >>>>>>> >> > >>>>>>> >> >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587952.html >>>>>>> >> > To unsubscribe from [ITK-users] Texture pixel by pixel, click >>>>>>> here >>>>>>> >> > < > . >>>>>>> >> > NAML >>>>>>> >> > < >>>>>>> >> >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>>> >> > >>>>>>> >> > >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> >> -- >>>>>>> >> View this message in context: >>>>>>> >> >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587960.html >>>>>>> >> Sent from the ITK Insight Users mailing list archive at >>>>>>> Nabble.com. >>>>>>> >> _____________________________________ >>>>>>> >> Powered by www.kitware.com >>>>>>> >> >>>>>>> >> Visit other Kitware open-source projects at >>>>>>> >> http://www.kitware.com/opensource/opensource.html >>>>>>> >> >>>>>>> >> Kitware offers ITK Training Courses, for more information visit: >>>>>>> >> http://www.kitware.com/products/protraining.php >>>>>>> >> >>>>>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>> >> >>>>>>> >> Follow this link to subscribe/unsubscribe: >>>>>>> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>> >> >>>>>>> > >>>>>>> > >>>>>>> > _____________________________________ >>>>>>> > Powered by www.kitware.com >>>>>>> > >>>>>>> > Visit other Kitware open-source projects at >>>>>>> > http://www.kitware.com/opensource/opensource.html >>>>>>> > >>>>>>> > Kitware offers ITK Training Courses, for more information visit: >>>>>>> > http://www.kitware.com/products/protraining.php >>>>>>> > >>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>> > >>>>>>> > Follow this link to subscribe/unsubscribe: >>>>>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>>>> > >>>>>>> > >>>>>>> > ------------------------------ >>>>>>> > If you reply to this email, your message will be added to the >>>>>>> discussion >>>>>>> > below: >>>>>>> > >>>>>>> > >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587961.html >>>>>>> > To unsubscribe from [ITK-users] Texture pixel by pixel, click here >>>>>>> > < > . >>>>>>> > NAML >>>>>>> > < >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>>> > >>>>>>> > >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> View this message in context: >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587963.html >>>>>>> Sent from the ITK Insight Users mailing list archive at Nabble.com. >>>>>>> _____________________________________ >>>>>>> Powered by www.kitware.com >>>>>>> >>>>>>> Visit other Kitware open-source projects at >>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>> >>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>> http://www.kitware.com/products/protraining.php >>>>>>> >>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>> >>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>> >>>>>> >>>>>> _____________________________________ >>>>>> Powered by www.kitware.com >>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>> http://www.kitware.com/products/protraining.php >>>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >>>>>> >>>>>> >>>> >>> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588477.html > To start a new topic under ITK Insight Users, email > ml-node+s2283740n2283740h75 at n2.nabble.com > To unsubscribe from ITK Insight Users, click here > > . > NAML > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Thu Feb 11 12:08:12 2016 From: franciscolopezdelafranca at gmail.com (=?UTF-8?Q?Francisco_L=C3=B3pez-Franca?=) Date: Thu, 11 Feb 2016 10:08:12 -0700 (MST) Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <84A225AE-400C-4FBA-97FA-6A027CB17208@mail.nih.gov> Message-ID: Hi Dzenan, The original class is here: https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx I've just added setInput and setMaskImage methods and modify some lines in the original class as I indicated in the yesterday mail within this thread. I'm running it on Windows, and there is no error at all, just a crash. I may have to include exceptions management. The crash occurs just when calling p3 = maskIter.GetPixel(iter->first) If you know why it could be or if you need more clarification, please let me know. Many thanks 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < ml-node+s2283740n7588477h22 at n2.nabble.com>: > Hi Francisco, > > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the error message > that goes along with the crash? In which file and line does it crash? > > Regards > > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca <[hidden > email] > wrote: > >> Hi, >> Please, someone that could help me. I'm working in a pre-doctorate >> project and I need this class to work. >> I've read the chapter 13 in the ITK Software Guide on how to write a >> filter and now I see the fact of the threads due to inheritance of >> ImageToImageFilter. >> But, I keep on without understanding why the code crashes just when >> calling >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >> It is just a call to read data, not to write. >> >> I guess somebody that had worked with creation of filters might see >> "easily" the problem, but not me. >> >> So, again, please, I need someone to help me with this because I'm stuck >> on this point. >> >> Thank you very much. >> KR. >> /Francisco >> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden email] >> >: >> >>> Hi Bradley again. >>> I'm modifying your class in order to be able to set a mask image (a >>> binary image) to be used as a limit in the histogram calculations, I mean, >>> I set an input, a mask and the class should take into account to calculate >>> the histograms only the voxels that belong to the input and to the mask >>> image and having the value 1 in the mask image. >>> The changes seem to be easy but I don?t know why my tests are not >>> working. It seems that 2 threads are working at the same time and when I >>> added my mask iterator, the code crashes. >>> >>> *** Consider that the input and mask images are the same origin, spacing >>> and size. >>> >>> I attach the main changes I've done, and I would thank you a lot if you >>> don't mind having a look and help me to find what I'm doing wrong: >>> >>> template< class TImageType, class TOutputImage > >>> void >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >::*SetInput*(InputImageType >>> *image) >>> { >>> // Process object is not const-correct so the const_cast is required >>> here >>> this->ProcessObject::SetNthInput( 0, >>> const_cast< InputImageType * >( >>> image ) ); >>> } >>> >>> template< class TImageType, class TOutputImage > >>> void >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >::*SetMaskImage*(InputImageType >>> *image) >>> { >>> // Process object is not const-correct so the const_cast is required >>> here >>> this->ProcessObject::SetNthInput( 1, const_cast< InputImageType * >( >>> image ) ); >>> >>> _maskImage = image; // _maskImage is a private member >>> } >>> >>> In the *ThreadedGenerateData*(const RegionType& outputRegionForThread, >>> ThreadIdType threadId ) method: >>> { >>> >>> ... >>> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >>> { >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, *fit);* >>> OutputIterator outIter(output, *fit); >>> >>> OutputPixelType out; >>> NumericTraits::SetLength( out, >>> this->GetNumberOfOutputComponents() ); >>> >>> while( !nIter.IsAtEnd() ) >>> { >>> this->FillHistogram( *histogram, nIter, *maskIter *); >>> >>> ... >>> >>> ++nIter; >>> ++outIter; >>> * ++maskIter;* >>> ... >>> >>> In the *FillHistogram *method: >>> { >>> >>> ... >>> >>> while( iter != m_CooccurenceOffsetVector.end() ) >>> { >>> >>> const PixelType p1 = niter.GetPixel(iter->first); >>> const PixelType p2 = niter.GetPixel(iter->second); >>> std::cout << "Before p3" << std::endl; >>> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); *std::cout >>> << "After p3: " << p3 << std::endl; >>> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >>> std::cout << "After p4: " << p4 << std::endl; >>> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= m_Max >>> *&& p3 == _insidePixelValue && p4 == _insidePixelValue* ) >>> // The point >>> { >>> >>> ... >>> >>> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >>> >>> Thank you so much. >>> My kind regards. >>> /Paco >>> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca <[hidden email] >>> >: >>> >>>> Hello Bradley again. >>>> Sorry but I'd like to re-open this issue because I need your class but >>>> with some modification. >>>> I pass to tell you. >>>> >>>> As my tests with your external class were not good taking into account >>>> the performance, I wonder if you could create a variant of it, but in which >>>> I can set a mask image and your class just return the VectorImage with all >>>> the features for that region (the masked locations) as >>>> itk::ScalarImageToTextureFeaturesFilter class does. >>>> I mean, to get the vector image with all the features but just >>>> calculate it for the regions belonging to the mask image. Positions not >>>> belonging to the mask region could have a pixel value of 0, for instance. >>>> >>>> I don?t know if it is very costly for you, but I would thank you so >>>> much. Otherwise, I could try it but I'd need your suggestions on how to do >>>> it. >>>> >>>> Thanks a lot. >>>> Best regards. >>>> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca <[hidden email] >>>> >: >>>> >>>>> Hello Bradley again, >>>>> I would like to ask you for a couple of favours. In the one hand, >>>>> could you please send me your 3D image so that I can test on it? And on the >>>>> other hand, could you test the example I have referenced in the previous >>>>> email with your image, not changing anything in the code, such as it is, >>>>> and tell me if the execution time is normal? >>>>> Thank you very much. >>>>> Regards, >>>>> /Francisco >>>>> >>>>> PS: All my application trace is printed via standard 'cout' command, >>>>> not due to a debugging compilation mode. >>>>> >>>>> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp <[hidden >>>>> email] > >>>>> escribi?: >>>>> >>>>>> Hello, >>>>>> >>>>>> Did you compile TextureFeatureImage in Release mode? >>>>>> >>>>>> 1) The filter does not scale well with a large radius. And given by >>>>>> your initial report of print a very large number of offset you, it sounds >>>>>> like you are using a large radius with many offsets. I created a >>>>>> 224x224x300 unsigned short image and ran with the default offset and a >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this filter is was ~10x >>>>>> faster than this example... things change though... >>>>>> >>>>>> >>>>>> 2) I sounds like the boundaries/limits of the histogram may be >>>>>> clipping you values. I would inspect the co-occurance matrix. >>>>>> >>>>>> >>>>>> HTH, >>>>>> Brad >>>>>> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca <[hidden >>>>>> email] > >>>>>> wrote: >>>>>> >>>>>> I've tested with itkTextureFeatureImageFilter, with >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures example, >>>>>> for a 3D image and here are my comments: >>>>>> >>>>>> >>>>>> 1. I had to interrupt the test after several hours and it kept on >>>>>> calculating. And this is for only a 3D image (224x224x300). I need to >>>>>> process around 35 images. >>>>>> 2. The result (texture features: entropy, energy, correlation, LH, >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, 7.83083e+247]. >>>>>> These values were not what I expected based on my experience on another >>>>>> application I developed, but in that case, I calculated the texture >>>>>> features for an image as a whole, not voxel by voxel. >>>>>> >>>>>> Regards. >>>>>> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >>>>>> >: >>>>>> >>>>>>> i yes i have tried radius = 3; >>>>>>> still no luck >>>>>>> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via ITK >>>>>>> Insight >>>>>>> Users] <[hidden email] >>>>>>> > wrote: >>>>>>> >>>>>>> > Have you tried with a radius of 3 instead of 1? >>>>>>> > >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>>>>> > >: >>>>>>> > >>>>>>> >> hey Matt, >>>>>>> >> thanks for ur advice.. it did build successfully... but im not >>>>>>> able to run >>>>>>> >> the code for 2D png image... i tried to change the dimension to 2 >>>>>>> and >>>>>>> >> build >>>>>>> >> it which it did.. but when i run the code using the command >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png putput.png >>>>>>> 1... i see >>>>>>> >> this output >>>>>>> >> >>>>>>> >> offset: [-1, -1] [0, -1] >>>>>>> >> offset: [0, -1] [1, -1] >>>>>>> >> offset: [-1, 0] [0, 0] >>>>>>> >> offset: [0, 0] [1, 0] >>>>>>> >> offset: [-1, 1] [0, 1] >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... if pls >>>>>>> tel me >>>>>>> >> how can i modify this code to work wid 2d image... forgive me if >>>>>>> my ques >>>>>>> >> are really silly im trying to learn something.. >>>>>>> >> regards >>>>>>> >> Vis >>>>>>> >> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK >>>>>>> Insight Users] >>>>>>> >> < >>>>>>> >> [hidden email] < >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>>>>>> >> wrote: >>>>>>> >> >>>>>>> >> > Hi, >>>>>>> >> > >>>>>>> >> > The function: >>>>>>> >> > >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char *argv[]) >>>>>>> >> > >>>>>>> >> > must be renamed to >>>>>>> >> > >>>>>>> >> > main(int argc, char* argv[]) >>>>>>> >> > >>>>>>> >> > HTH, >>>>>>> >> > Matt >>>>>>> >> > >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>>>>> >> > > wrote: >>>>>>> >> > >>>>>>> >> > > hi all, >>>>>>> >> > > im trying to build the itkTextureFeatureImageFilterTest.cxx >>>>>>> code but >>>>>>> >> im >>>>>>> >> > not >>>>>>> >> > > able to it is showing the following error >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>>>>> Configuration: >>>>>>> >> Debug >>>>>>> >> > x64 >>>>>>> >> > > ------ >>>>>>> >> > > 1> Checking Build System >>>>>>> >> > > 1> CMake does not need to re-run because >>>>>>> >> > > >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>>>>> >> > is >>>>>>> >> > > up-to-date. >>>>>>> >> > > 2>------ Rebuild All started: Project: >>>>>>> >> itkTextureFeatureImageFilterTest, >>>>>>> >> > > Configuration: Debug x64 ------ >>>>>>> >> > > 2> Building Custom Rule >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>> >> > > 2> CMake does not need to re-run because >>>>>>> >> > > >>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>> >> > is >>>>>>> >> > > up-to-date. >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>>>>> 'std::_Copy_impl': >>>>>>> >> > Function >>>>>>> >> > > call with parameters that may be unsafe - this call relies on >>>>>>> the >>>>>>> >> caller >>>>>>> >> > to >>>>>>> >> > > check that the passed values are correct. To disable this >>>>>>> warning, use >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to use >>>>>>> Visual C++ >>>>>>> >> > > 'Checked Iterators' >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>> 'std::_Copy_impl' >>>>>>> >> > > 2> >>>>>>> >> > > >>>>>>> >> >>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>>>>> >> > see >>>>>>> >> > > reference to function template instantiation '_OutIt >>>>>>> std::copy>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' being >>>>>>> compiled >>>>>>> >> > > 2> with >>>>>>> >> > > 2> [ >>>>>>> >> > > 2> _OutIt=unsigned char *, >>>>>>> >> > > 2> _InIt=const unsigned char * >>>>>>> >> > > 2> ] >>>>>>> >> > > 2> >>>>>>> >> > > >>>>>>> >> >>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>>>>> >> > > while compiling class template member function 'void >>>>>>> >> > > itk::ImageFileReader::GenerateData(void)' >>>>>>> >> > > 2> with >>>>>>> >> > > 2> [ >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>> >> > > 2> ] >>>>>>> >> > > 2> >>>>>>> >> > > >>>>>>> >> > >>>>>>> >> >>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>>>>> >> > >>>>>>> >> > > : see reference to class template instantiation >>>>>>> >> > > 'itk::ImageFileReader' being compiled >>>>>>> >> > > 2> with >>>>>>> >> > > 2> [ >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>> >> > > 2> ] >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>> 'std::_Copy_impl' >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>> 'std::_Copy_impl' >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>> 'std::_Copy_impl' >>>>>>> >> > > 2> Creating library >>>>>>> >> > > >>>>>>> >> > >>>>>>> >> >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>>>>> >> > >>>>>>> >> > > and object >>>>>>> >> > > >>>>>>> >> > >>>>>>> >> >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>>>>> >> > >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved >>>>>>> external symbol >>>>>>> >> > main >>>>>>> >> > > referenced in function __tmainCRTStartup >>>>>>> >> > > >>>>>>> >> > >>>>>>> >> >>>>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>>>>> >> > >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>>>>> Configuration: Debug >>>>>>> >> > x64 >>>>>>> >> > > ------ >>>>>>> >> > > 3> Building Custom Rule >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>> >> > > 3> CMake does not need to re-run because >>>>>>> >> > > >>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>> >> > is >>>>>>> >> > > up-to-date. >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 skipped >>>>>>> ========== >>>>>>> >> > > im using the follwing CMakeList.txt >>>>>>> >> > > # This is the root ITK CMakeLists file. >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>>>>> >> > > endif() >>>>>>> >> > > >>>>>>> >> > > >>>>>>> >> > > # This project is designed to be built outside the Insight >>>>>>> source >>>>>>> >> tree. >>>>>>> >> > > project(HelloWorld) >>>>>>> >> > > >>>>>>> >> > > # Find ITK. >>>>>>> >> > > find_package(ITK REQUIRED) >>>>>>> >> > > include(${ITK_USE_FILE}) >>>>>>> >> > > >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>>>>> >> > > >>>>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest >>>>>>> >> ${ITK_LIBRARIES}) >>>>>>> >> > > >>>>>>> >> > > please tel me wat the error is?? >>>>>>> >> > > >>>>>>> >> > > >>>>>>> >> > > >>>>>>> >> > > -- >>>>>>> >> > > View this message in context: >>>>>>> >> > >>>>>>> >> >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>>>>> >> > > Sent from the ITK Insight Users mailing list archive at >>>>>>> Nabble.com. >>>>>>> >> > > _____________________________________ >>>>>>> >> > > Powered by www.kitware.com >>>>>>> >> > > >>>>>>> >> > > Visit other Kitware open-source projects at >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>>>>> >> > > >>>>>>> >> > > Kitware offers ITK Training Courses, for more information >>>>>>> visit: >>>>>>> >> > > http://www.kitware.com/products/protraining.php >>>>>>> >> > > >>>>>>> >> > > Please keep messages on-topic and check the ITK FAQ at: >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >>>>>>> >> > > >>>>>>> >> > > Follow this link to subscribe/unsubscribe: >>>>>>> >> > > http://public.kitware.com/mailman/listinfo/insight-users >>>>>>> >> > _____________________________________ >>>>>>> >> > Powered by www.kitware.com >>>>>>> >> > >>>>>>> >> > Visit other Kitware open-source projects at >>>>>>> >> > http://www.kitware.com/opensource/opensource.html >>>>>>> >> > >>>>>>> >> > Kitware offers ITK Training Courses, for more information visit: >>>>>>> >> > http://www.kitware.com/products/protraining.php >>>>>>> >> > >>>>>>> >> > Please keep messages on-topic and check the ITK FAQ at: >>>>>>> >> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>> >> > >>>>>>> >> > Follow this link to subscribe/unsubscribe: >>>>>>> >> > http://public.kitware.com/mailman/listinfo/insight-users >>>>>>> >> > >>>>>>> >> > >>>>>>> >> > ------------------------------ >>>>>>> >> > If you reply to this email, your message will be added to the >>>>>>> discussion >>>>>>> >> > below: >>>>>>> >> > >>>>>>> >> > >>>>>>> >> >>>>>>> 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Insight Users mailing list archive at >>>>>>> Nabble.com. >>>>>>> >> _____________________________________ >>>>>>> >> Powered by www.kitware.com >>>>>>> >> >>>>>>> >> Visit other Kitware open-source projects at >>>>>>> >> http://www.kitware.com/opensource/opensource.html >>>>>>> >> >>>>>>> >> Kitware offers ITK Training Courses, for more information visit: >>>>>>> >> http://www.kitware.com/products/protraining.php >>>>>>> >> >>>>>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>> >> >>>>>>> >> Follow this link to subscribe/unsubscribe: >>>>>>> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>> >> >>>>>>> > >>>>>>> > >>>>>>> > _____________________________________ >>>>>>> > Powered by www.kitware.com >>>>>>> > >>>>>>> > Visit other Kitware open-source projects at >>>>>>> > http://www.kitware.com/opensource/opensource.html >>>>>>> > >>>>>>> > Kitware offers ITK Training Courses, for more information visit: >>>>>>> > http://www.kitware.com/products/protraining.php >>>>>>> > >>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>> > >>>>>>> > Follow this link to subscribe/unsubscribe: >>>>>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>>>> > >>>>>>> > >>>>>>> > ------------------------------ >>>>>>> > If you reply to this email, your message will be added to the >>>>>>> discussion >>>>>>> > below: >>>>>>> > >>>>>>> > >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587961.html >>>>>>> > To unsubscribe from [ITK-users] Texture pixel by pixel, click here >>>>>>> > < > . >>>>>>> > NAML >>>>>>> > < >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>>> > >>>>>>> > >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> View this message in context: >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587963.html >>>>>>> Sent from the ITK Insight Users mailing list archive at Nabble.com. >>>>>>> _____________________________________ >>>>>>> Powered by www.kitware.com >>>>>>> >>>>>>> Visit other Kitware open-source projects at >>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>> >>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>> http://www.kitware.com/products/protraining.php >>>>>>> >>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>> >>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>> >>>>>> >>>>>> _____________________________________ >>>>>> Powered by www.kitware.com >>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>> http://www.kitware.com/products/protraining.php >>>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >>>>>> >>>>>> >>>> >>> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588477.html > To start a new topic under ITK Insight Users, email > ml-node+s2283740n2283740h75 at n2.nabble.com > To unsubscribe from ITK Insight Users, click here > > . > NAML > > -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588483.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From filippo.brogi at topic.nl Thu Feb 11 11:17:10 2016 From: filippo.brogi at topic.nl (Filippo Brogi) Date: Thu, 11 Feb 2016 09:17:10 -0700 (MST) Subject: [ITK] [ITK-users] zoom image content In-Reply-To: References: <1455175253042-36768.post@n7.nabble.com> Message-ID: <1455207430903-36778.post@n7.nabble.com> Hi Dzenan, thank for your answer. I think I'm going to use the dilate filter. I basically need to enlarge the image and use as a mask for removing the segmented part from the original image. Thanks a lot. -- View this message in context: http://itk-users.7.n7.nabble.com/zoom-image-content-tp36768p36778.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From filippo.brogi at topic.nl Thu Feb 11 11:36:51 2016 From: filippo.brogi at topic.nl (Filippo Brogi) Date: Thu, 11 Feb 2016 09:36:51 -0700 (MST) Subject: [ITK] [ITK-users] zoom image content In-Reply-To: <20160211163320.GA20819@jerng.de> References: <1455175253042-36768.post@n7.nabble.com> <20160211163320.GA20819@jerng.de> Message-ID: <1455208611962-36779.post@n7.nabble.com> Hi JE, a morphological operation is definitely what I need. Thanks. -- View this message in context: http://itk-users.7.n7.nabble.com/zoom-image-content-tp36768p36779.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From Ryan.Young at seattlechildrens.org Thu Feb 11 20:00:46 2016 From: Ryan.Young at seattlechildrens.org (Young, Ryan) Date: Fri, 12 Feb 2016 01:00:46 +0000 Subject: [ITK] [ITK-users] rigid landmark registartion simpleITK (python) Message-ID: <06D6E971FE505044A365F05BD51FFD830A531FB3@PPWEXD01d.childrens.sea.kids> Hello, I am trying to rigidly align a group of landmarked samples. I have calculated a rigid transformation matrix. When I apply this to the sample (see code below) is sample is commonly clipped. It seems like the transformation is pushing the sample out out its physically defined space and the data is lost. How should I set things up to that large translations and rotations do not result in parts of the image being lost. affine_center = (0,0,0) affine_translation =translation affine_matrix =T.flatten(order='C') affine = sitk.AffineTransform(affine_matrix, affine_translation, affine_center) imAffine = sitk.Resample(im, imRef, affine,sitk.sitkLinear, sitk.sitkUInt32) CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From hans-johnson at uiowa.edu Thu Feb 11 20:37:55 2016 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Fri, 12 Feb 2016 01:37:55 +0000 Subject: [ITK] [ITK-users] rigid landmark registartion simpleITK (python) Message-ID: <89A1A7A5-C1F9-4AEB-950D-0FCE88262560@uiowa.edu> Ryan, Have you tried applying the inverse of the rigid transform defined by landmarks? A common mistake is apply the transform that works for aligning landmarks points to an image. They are inverse problems. The transform that is applied to align landmarks is the inverse of the transform that is needed to resample images. Hans -- From: Insight-users > on behalf of "Young, Ryan" > Date: Thursday, February 11, 2016 at 7:00 PM To: "insight-users at itk.org" > Subject: [ITK-users] rigid landmark registartion simpleITK (python) Hello, I am trying to rigidly align a group of landmarked samples. I have calculated a rigid transformation matrix. When I apply this to the sample (see code below) is sample is commonly clipped. It seems like the transformation is pushing the sample out out its physically defined space and the data is lost. How should I set things up to that large translations and rotations do not result in parts of the image being lost. affine_center = (0,0,0) affine_translation =translation affine_matrix =T.flatten(order='C') affine = sitk.AffineTransform(affine_matrix, affine_translation, affine_center) imAffine = sitk.Resample(im, imRef, affine,sitk.sitkLinear, sitk.sitkUInt32) CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From seidel at cvrti.utah.edu Thu Feb 11 23:32:15 2016 From: seidel at cvrti.utah.edu (Thomas Seidel) Date: Thu, 11 Feb 2016 21:32:15 -0700 Subject: [ITK] [ITK-users] Error in BinaryThinningImageFilter ? Message-ID: Hi all, I am using the BinaryThinningImageFilter to create the skeleton of 3D binary objects. I now found that the skeleton of a tilted object (let?s say I permute the x and z axis) is NOT the same as the tilted skeleton. This must be an error. Or doesn?t it work in 3D and only creates a slice-by-slice 2D skeleton??? I?d appreciate your help. Best, Thomas -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From tevain at telecom-paristech.fr Fri Feb 12 03:16:25 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Fri, 12 Feb 2016 09:16:25 +0100 (CET) Subject: [ITK] [ITK-users] Error in BinaryThinningImageFilter ? In-Reply-To: References: Message-ID: <2008803167.18213214.1455264985587.JavaMail.zimbra@enst.fr> Hello Thomas, As you can see in the documentation http://www.itk.org/Doxygen/html/classitk_1_1BinaryThinningImageFilter.html, this filter is made from a 2D implementation, and is not ready for nD. For 3D, you can refer to the journal entry here http://www.insight-journal.org/browse/publication/181 based on another publication. Last time I used the code, it's worked easily. HTH, Tim ----- Mail original ----- De: "Thomas Seidel" ?: insight-users at itk.org Envoy?: Vendredi 12 F?vrier 2016 05:32:15 Objet: [ITK] [ITK-users] Error in BinaryThinningImageFilter ? Hi all, I am using the BinaryThinningImageFilter to create the skeleton of 3D binary objects. I now found that the skeleton of a tilted object (let?s say I permute the x and z axis) is NOT the same as the tilted skeleton. This must be an error. Or doesn?t it work in 3D and only creates a slice-by-slice 2D skeleton??? I?d appreciate your help. Best, Thomas _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Fri Feb 12 10:21:46 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 12 Feb 2016 10:21:46 -0500 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <84A225AE-400C-4FBA-97FA-6A027CB17208@mail.nih.gov> Message-ID: Hi Francisco, do you mind attaching the modified files or pointing to your fork of it on GitHub? Regards On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca < franciscolopezdelafranca at gmail.com> wrote: > Hi Dzenan, > The original class is here: > > > https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h > > https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx > > I've just added setInput and setMaskImage methods and modify some lines in > the original class as I indicated in the yesterday mail within this thread. > I'm running it on Windows, and there is no error at all, just a crash. I > may have to include exceptions management. > The crash occurs just when calling p3 = maskIter.GetPixel(iter->first) > > If you know why it could be or if you need more clarification, please let > me know. > Many thanks > > 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < > ml-node+s2283740n7588477h22 at n2.nabble.com>: > > > Hi Francisco, > > > > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the error > message > > that goes along with the crash? In which file and line does it crash? > > > > Regards > > > > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca <[hidden > > email] > wrote: > > > >> Hi, > >> Please, someone that could help me. I'm working in a pre-doctorate > >> project and I need this class to work. > >> I've read the chapter 13 in the ITK Software Guide on how to write a > >> filter and now I see the fact of the threads due to inheritance of > >> ImageToImageFilter. > >> But, I keep on without understanding why the code crashes just when > >> calling > >> *const PixelType p3 = maskIter.GetPixel(iter->first);* > >> It is just a call to read data, not to write. > >> > >> I guess somebody that had worked with creation of filters might see > >> "easily" the problem, but not me. > >> > >> So, again, please, I need someone to help me with this because I'm stuck > >> on this point. > >> > >> Thank you very much. > >> KR. > >> /Francisco > >> > >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden email] > >> >: > >> > >>> Hi Bradley again. > >>> I'm modifying your class in order to be able to set a mask image (a > >>> binary image) to be used as a limit in the histogram calculations, I > mean, > >>> I set an input, a mask and the class should take into account to > calculate > >>> the histograms only the voxels that belong to the input and to the mask > >>> image and having the value 1 in the mask image. > >>> The changes seem to be easy but I don?t know why my tests are not > >>> working. It seems that 2 threads are working at the same time and when > I > >>> added my mask iterator, the code crashes. > >>> > >>> *** Consider that the input and mask images are the same origin, > spacing > >>> and size. > >>> > >>> I attach the main changes I've done, and I would thank you a lot if you > >>> don't mind having a look and help me to find what I'm doing wrong: > >>> > >>> template< class TImageType, class TOutputImage > > >>> void > >>> TextureFeatureImageFilterV2< TImageType, TOutputImage > >::*SetInput*(InputImageType > >>> *image) > >>> { > >>> // Process object is not const-correct so the const_cast is required > >>> here > >>> this->ProcessObject::SetNthInput( 0, > >>> const_cast< InputImageType * >( > >>> image ) ); > >>> } > >>> > >>> template< class TImageType, class TOutputImage > > >>> void > >>> TextureFeatureImageFilterV2< TImageType, TOutputImage > >::*SetMaskImage*(InputImageType > >>> *image) > >>> { > >>> // Process object is not const-correct so the const_cast is required > >>> here > >>> this->ProcessObject::SetNthInput( 1, const_cast< InputImageType * >( > >>> image ) ); > >>> > >>> _maskImage = image; // _maskImage is a private member > >>> } > >>> > >>> In the *ThreadedGenerateData*(const RegionType& outputRegionForThread, > >>> ThreadIdType threadId ) method: > >>> { > >>> > >>> ... > >>> > >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) > >>> { > >>> NeighborhoodIteratorType nIter( radius, input, *fit ); > >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, *fit);* > >>> OutputIterator outIter(output, *fit); > >>> > >>> OutputPixelType out; > >>> NumericTraits::SetLength( out, > >>> this->GetNumberOfOutputComponents() ); > >>> > >>> while( !nIter.IsAtEnd() ) > >>> { > >>> this->FillHistogram( *histogram, nIter, *maskIter *); > >>> > >>> ... > >>> > >>> ++nIter; > >>> ++outIter; > >>> * ++maskIter;* > >>> ... > >>> > >>> In the *FillHistogram *method: > >>> { > >>> > >>> ... > >>> > >>> while( iter != m_CooccurenceOffsetVector.end() ) > >>> { > >>> > >>> const PixelType p1 = niter.GetPixel(iter->first); > >>> const PixelType p2 = niter.GetPixel(iter->second); > >>> std::cout << "Before p3" << std::endl; > >>> > >>> * const PixelType p3 = maskIter.GetPixel(iter->first); *std::cout > >>> << "After p3: " << p3 << std::endl; > >>> > >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * > >>> std::cout << "After p4: " << p4 << std::endl; > >>> > >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= m_Max > >>> *&& p3 == _insidePixelValue && p4 == _insidePixelValue* ) > >>> // The point > >>> { > >>> > >>> ... > >>> > >>> > >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* > >>> > >>> Thank you so much. > >>> My kind regards. > >>> /Paco > >>> > >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca <[hidden email] > >>> >: > >>> > >>>> Hello Bradley again. > >>>> Sorry but I'd like to re-open this issue because I need your class but > >>>> with some modification. > >>>> I pass to tell you. > >>>> > >>>> As my tests with your external class were not good taking into account > >>>> the performance, I wonder if you could create a variant of it, but in > which > >>>> I can set a mask image and your class just return the VectorImage > with all > >>>> the features for that region (the masked locations) as > >>>> itk::ScalarImageToTextureFeaturesFilter class does. > >>>> I mean, to get the vector image with all the features but just > >>>> calculate it for the regions belonging to the mask image. Positions > not > >>>> belonging to the mask region could have a pixel value of 0, for > instance. > >>>> > >>>> I don?t know if it is very costly for you, but I would thank you so > >>>> much. Otherwise, I could try it but I'd need your suggestions on how > to do > >>>> it. > >>>> > >>>> Thanks a lot. > >>>> Best regards. > >>>> > >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca <[hidden > email] > >>>> >: > >>>> > >>>>> Hello Bradley again, > >>>>> I would like to ask you for a couple of favours. In the one hand, > >>>>> could you please send me your 3D image so that I can test on it? And > on the > >>>>> other hand, could you test the example I have referenced in the > previous > >>>>> email with your image, not changing anything in the code, such as it > is, > >>>>> and tell me if the execution time is normal? > >>>>> Thank you very much. > >>>>> Regards, > >>>>> /Francisco > >>>>> > >>>>> PS: All my application trace is printed via standard 'cout' command, > >>>>> not due to a debugging compilation mode. > >>>>> > >>>>> > >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp <[hidden > >>>>> email] > > >>>>> escribi?: > >>>>> > >>>>>> Hello, > >>>>>> > >>>>>> Did you compile TextureFeatureImage in Release mode? > >>>>>> > >>>>>> 1) The filter does not scale well with a large radius. And given by > >>>>>> your initial report of print a very large number of offset you, it > sounds > >>>>>> like you are using a large radius with many offsets. I created a > >>>>>> 224x224x300 unsigned short image and ran with the default offset > and a > >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this filter is > was ~10x > >>>>>> faster than this example... things change though... > >>>>>> > >>>>>> > >>>>>> 2) I sounds like the boundaries/limits of the histogram may be > >>>>>> clipping you values. I would inspect the co-occurance matrix. > >>>>>> > >>>>>> > >>>>>> HTH, > >>>>>> Brad > >>>>>> > >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca <[hidden > >>>>>> email] > > >>>>>> wrote: > >>>>>> > >>>>>> I've tested with itkTextureFeatureImageFilter, with > >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the > >>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures > example, > >>>>>> for a 3D image and here are my comments: > >>>>>> > >>>>>> > >>>>>> 1. I had to interrupt the test after several hours and it kept on > >>>>>> calculating. And this is for only a 3D image (224x224x300). I need > to > >>>>>> process around 35 images. > >>>>>> 2. The result (texture features: entropy, energy, correlation, LH, > >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, > 7.83083e+247]. > >>>>>> These values were not what I expected based on my experience on > another > >>>>>> application I developed, but in that case, I calculated the texture > >>>>>> features for an image as a whole, not voxel by voxel. > >>>>>> > >>>>>> Regards. > >>>>>> > >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] > >>>>>> >: > >>>>>> > >>>>>>> i yes i have tried radius = 3; > >>>>>>> still no luck > >>>>>>> > >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via ITK > >>>>>>> Insight > >>>>>>> Users] <[hidden email] > >>>>>>> > wrote: > >>>>>>> > >>>>>>> > Have you tried with a radius of 3 instead of 1? > >>>>>>> > > >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] > >>>>>>> > >: > >>>>>>> > > >>>>>>> >> hey Matt, > >>>>>>> >> thanks for ur advice.. it did build successfully... but im not > >>>>>>> able to run > >>>>>>> >> the code for 2D png image... i tried to change the dimension to > 2 > >>>>>>> and > >>>>>>> >> build > >>>>>>> >> it which it did.. but when i run the code using the command > >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png putput.png > >>>>>>> 1... i see > >>>>>>> >> this output > >>>>>>> >> > >>>>>>> >> offset: [-1, -1] [0, -1] > >>>>>>> >> offset: [0, -1] [1, -1] > >>>>>>> >> offset: [-1, 0] [0, 0] > >>>>>>> >> offset: [0, 0] [1, 0] > >>>>>>> >> offset: [-1, 1] [0, 1] > >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... if > pls > >>>>>>> tel me > >>>>>>> >> how can i modify this code to work wid 2d image... forgive me if > >>>>>>> my ques > >>>>>>> >> are really silly im trying to learn something.. > >>>>>>> >> regards > >>>>>>> >> Vis > >>>>>>> >> > >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK > >>>>>>> Insight Users] > >>>>>>> >> < > >>>>>>> >> [hidden email] < > >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> > >>>>>>> >> wrote: > >>>>>>> >> > >>>>>>> >> > Hi, > >>>>>>> >> > > >>>>>>> >> > The function: > >>>>>>> >> > > >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char *argv[]) > >>>>>>> >> > > >>>>>>> >> > must be renamed to > >>>>>>> >> > > >>>>>>> >> > main(int argc, char* argv[]) > >>>>>>> >> > > >>>>>>> >> > HTH, > >>>>>>> >> > Matt > >>>>>>> >> > > >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] > >>>>>>> >> > > > wrote: > >>>>>>> >> > > >>>>>>> >> > > hi all, > >>>>>>> >> > > im trying to build the itkTextureFeatureImageFilterTest.cxx > >>>>>>> code but > >>>>>>> >> im > >>>>>>> >> > not > >>>>>>> >> > > able to it is showing the following error > >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, > >>>>>>> Configuration: > >>>>>>> >> Debug > >>>>>>> >> > x64 > >>>>>>> >> > > ------ > >>>>>>> >> > > 1> Checking Build System > >>>>>>> >> > > 1> CMake does not need to re-run because > >>>>>>> >> > > > >>>>>>> > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp > >>>>>>> >> > is > >>>>>>> >> > > up-to-date. > >>>>>>> >> > > 2>------ Rebuild All started: Project: > >>>>>>> >> itkTextureFeatureImageFilterTest, > >>>>>>> >> > > Configuration: Debug x64 ------ > >>>>>>> >> > > 2> Building Custom Rule > >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt > >>>>>>> >> > > 2> CMake does not need to re-run because > >>>>>>> >> > > > >>>>>>> > D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp > >>>>>>> >> > is > >>>>>>> >> > > up-to-date. > >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx > >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio > >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: > >>>>>>> 'std::_Copy_impl': > >>>>>>> >> > Function > >>>>>>> >> > > call with parameters that may be unsafe - this call relies > on > >>>>>>> the > >>>>>>> >> caller > >>>>>>> >> > to > >>>>>>> >> > > check that the passed values are correct. To disable this > >>>>>>> warning, use > >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to use > >>>>>>> Visual C++ > >>>>>>> >> > > 'Checked Iterators' > >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio > >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of > >>>>>>> 'std::_Copy_impl' > >>>>>>> >> > > 2> > >>>>>>> >> > > > >>>>>>> >> > >>>>>>> > c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : > >>>>>>> >> > see > >>>>>>> >> > > reference to function template instantiation '_OutIt > >>>>>>> std::copy >>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' being > >>>>>>> compiled > >>>>>>> >> > > 2> with > >>>>>>> >> > > 2> [ > >>>>>>> >> > > 2> _OutIt=unsigned char *, > >>>>>>> >> > > 2> _InIt=const unsigned char * > >>>>>>> >> > > 2> ] > >>>>>>> >> > > 2> > >>>>>>> >> > > > >>>>>>> >> > >>>>>>> > c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : > >>>>>>> >> > > while compiling class template member function 'void > >>>>>>> >> > > itk::ImageFileReader::GenerateData(void)' > >>>>>>> >> > > 2> with > >>>>>>> >> > > 2> [ > >>>>>>> >> > > 2> TOutputImage=InputImageType > >>>>>>> >> > > 2> ] > >>>>>>> >> > > 2> > >>>>>>> >> > > > >>>>>>> >> > > >>>>>>> >> > >>>>>>> > D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) > >>>>>>> >> > > >>>>>>> >> > > : see reference to class template instantiation > >>>>>>> >> > > 'itk::ImageFileReader' being compiled > >>>>>>> >> > > 2> with > >>>>>>> >> > > 2> [ > >>>>>>> >> > > 2> TOutputImage=InputImageType > >>>>>>> >> > > 2> ] > >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio > >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of > >>>>>>> 'std::_Copy_impl' > >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio > >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of > >>>>>>> 'std::_Copy_impl' > >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio > >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of > >>>>>>> 'std::_Copy_impl' > >>>>>>> >> > > 2> Creating library > >>>>>>> >> > > > >>>>>>> >> > > >>>>>>> >> > >>>>>>> > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib > >>>>>>> >> > > >>>>>>> >> > > and object > >>>>>>> >> > > > >>>>>>> >> > > >>>>>>> >> > >>>>>>> > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp > >>>>>>> >> > > >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved > >>>>>>> external symbol > >>>>>>> >> > main > >>>>>>> >> > > referenced in function __tmainCRTStartup > >>>>>>> >> > > > >>>>>>> >> > > >>>>>>> >> > >>>>>>> > 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe > >>>>>>> >> > > >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals > >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, > >>>>>>> Configuration: Debug > >>>>>>> >> > x64 > >>>>>>> >> > > ------ > >>>>>>> >> > > 3> Building Custom Rule > >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt > >>>>>>> >> > > 3> CMake does not need to re-run because > >>>>>>> >> > > > >>>>>>> > D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp > >>>>>>> >> > is > >>>>>>> >> > > up-to-date. > >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 skipped > >>>>>>> ========== > >>>>>>> >> > > im using the follwing CMakeList.txt > >>>>>>> >> > > # This is the root ITK CMakeLists file. > >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) > >>>>>>> >> > > if(COMMAND CMAKE_POLICY) > >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) > >>>>>>> >> > > endif() > >>>>>>> >> > > > >>>>>>> >> > > > >>>>>>> >> > > # This project is designed to be built outside the Insight > >>>>>>> source > >>>>>>> >> tree. > >>>>>>> >> > > project(HelloWorld) > >>>>>>> >> > > > >>>>>>> >> > > # Find ITK. > >>>>>>> >> > > find_package(ITK REQUIRED) > >>>>>>> >> > > include(${ITK_USE_FILE}) > >>>>>>> >> > > > >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest > >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) > >>>>>>> >> > > > >>>>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest > >>>>>>> >> ${ITK_LIBRARIES}) > >>>>>>> >> > > > >>>>>>> >> > > please tel me wat the error is?? > >>>>>>> >> > > > >>>>>>> >> > > > >>>>>>> >> > > > >>>>>>> >> > > -- > >>>>>>> >> > > View this message in context: > >>>>>>> >> > > >>>>>>> >> > >>>>>>> > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html > >>>>>>> >> > > Sent from the ITK Insight Users mailing list archive at > >>>>>>> Nabble.com. > >>>>>>> >> > > _____________________________________ > >>>>>>> >> > > Powered by www.kitware.com > >>>>>>> >> > > > >>>>>>> >> > > Visit other Kitware open-source projects at > >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html > >>>>>>> >> > > > >>>>>>> >> > > Kitware offers ITK Training Courses, for more information > >>>>>>> visit: > >>>>>>> >> > > http://www.kitware.com/products/protraining.php > >>>>>>> >> > > > >>>>>>> >> > > Please keep messages on-topic and check the ITK FAQ at: > >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ > >>>>>>> >> > > > >>>>>>> >> > > Follow this link to subscribe/unsubscribe: > >>>>>>> >> > > http://public.kitware.com/mailman/listinfo/insight-users > >>>>>>> >> > _____________________________________ > >>>>>>> >> > Powered by www.kitware.com > >>>>>>> >> > > >>>>>>> >> > Visit other Kitware open-source projects at > >>>>>>> >> > http://www.kitware.com/opensource/opensource.html > >>>>>>> >> > > >>>>>>> >> > Kitware offers ITK Training Courses, for more information > visit: > >>>>>>> >> > http://www.kitware.com/products/protraining.php > >>>>>>> >> > > >>>>>>> >> > Please keep messages on-topic and check the ITK FAQ at: > >>>>>>> >> > http://www.itk.org/Wiki/ITK_FAQ > >>>>>>> >> > > >>>>>>> >> > Follow this link to 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URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From filippo.brogi at topic.nl Fri Feb 12 10:55:41 2016 From: filippo.brogi at topic.nl (Filippo Brogi) Date: Fri, 12 Feb 2016 08:55:41 -0700 (MST) Subject: [ITK] [ITK-users] ContourExtractor2DImageFilter issue Message-ID: <1455292541350-36785.post@n7.nabble.com> I have segmented a binary 2D image and then I'm trying to extract the level set 255. using the ContourExtractor2DImageFilter but sometimes the number of extracted contours is 0, even when the image contains valid pixels. This is the way I'm using the filter ContourExtractor2DImageFilterType::Pointer pContour = ContourExtractor2DImageFilterType::New(); pContour->SetContourValue(0); pContour->VertexConnectHighPixelsOff(); pContour->ReverseContourOrientationOff(); I also tried with different contour values, but stil facing with the same issue. For sure the input image contains only 0-255 values. Thanks -- View this message in context: http://itk-users.7.n7.nabble.com/ContourExtractor2DImageFilter-issue-tp36785.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From artioml at post.bgu.ac.il Sat Feb 13 01:53:45 2016 From: artioml at post.bgu.ac.il (artioml) Date: Fri, 12 Feb 2016 23:53:45 -0700 (MST) Subject: [ITK] [ITK-users] Deformable registration of RGB image Message-ID: <1455346424847-36786.post@n7.nabble.com> Hello, I try to perform B-Spline deformable registration of RGB images. I found a test named 'itkMeanSquaresImageToImageMetricv4VectorRegistrationTest', which uses itkVectorImageToImageMetricTraitsv4. I tried to edit DeformaleRegistration7 example and replaced the lines that defines image and metric to: ... const unsigned int ImageDimension = 2; //typedef float PixelType; typedef itk::Vector PixelType; typedef itk::Image< PixelType, ImageDimension > FixedImageType; typedef itk::Image< PixelType, ImageDimension > MovingImageType; ... typedef itk::Image< float, ImageDimension> VirtualImageType; typedef itk::VectorImageToImageMetricTraitsv4< FixedImageType, MovingImageType, VirtualImageType, PixelType::Length> MetricTraitsType; typedef itk::MeanSquaresImageToImageMetricv4 < FixedImageType, MovingImageType, VirtualImageType, float, MetricTraitsType > MetricType; typedef MetricType::FixedSampledPointSetType PointSetType; When i try to compile the code I get a really long error message, I will put it bellow. Any idea how can I fix it? Is it possible to perform deformable registration on vector images? Thank you! In file included from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkLightObject.h:21:0, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkObject.h:31, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkDataObject.h:31, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkProcessObject.h:31, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:21, from /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:1: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkConceptChecking.h: In instantiation of ?struct itk::Concept::IsFloatingPoint >?: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkDefaultImageToImageMetricTraitsv4.h:146:3: required from ?class itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double>? /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.h:291:60: required from ?class itk::ImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >? /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:184:71: required from ?class itk::ImageRegistrationMethodv4, 2u>, itk::Image, 2u> >? /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:99:19: required from here /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkMacro.h:699:53: error: ?is_integer? is not a member of ?itk::NumericTraits >? #define itkStaticConstMacro(name, type, value) enum { name = value } ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkConceptChecking.h:782:3: note: in expansion of macro ?itkStaticConstMacro? itkStaticConstMacro(Integral, bool, NumericTraits< T >::is_integer); ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkMacro.h:699:53: error: ?is_exact? is not a member of ?itk::NumericTraits >? #define itkStaticConstMacro(name, type, value) enum { name = value } ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkConceptChecking.h:783:3: note: in expansion of macro ?itkStaticConstMacro? itkStaticConstMacro(IsExact, bool, NumericTraits< T >::is_exact); ^ /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx: In function ?int main(int, char**)?: /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:102:49: error: no matching function for call to ?itk::ImageRegistrationMethodv4, 2u>, itk::Image, 2u> >::SetMetric(itk::MeanSquaresImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, float, itk::VectorImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 3u> >::Pointer&)? registration->SetMetric( metric ); ^ /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:102:49: note: candidate is: In file included from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkLightObject.h:21:0, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkObject.h:31, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkDataObject.h:31, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkProcessObject.h:31, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:21, from /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:1: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkMacro.h:963:16: note: void itk::ImageRegistrationMethodv4::SetMetric(itk::ImageRegistrationMethodv4::MetricType*) [with TFixedImage = itk::Image, 2u>; TMovingImage = itk::Image, 2u>; TOutputTransform = itk::Transform; TVirtualImage = itk::Image, 2u>; TPointSet = itk::PointSet >; itk::ImageRegistrationMethodv4::MetricType = itk::ObjectToObjectMetricBaseTemplate; typename TOutputTransform::ScalarType = double] virtual void Set##name (type * _arg) \ ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:250:3: note: in expansion of macro ?itkSetObjectMacro? itkSetObjectMacro( Metric, MetricType ); ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkMacro.h:963:16: note: no known conversion for argument 1 from ?itk::MeanSquaresImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, float, itk::VectorImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 3u> >::Pointer {aka itk::SmartPointer, 2u>, itk::Image, 2u>, itk::Image, float, itk::VectorImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 3u> > >}? to ?itk::ImageRegistrationMethodv4, 2u>, itk::Image, 2u> >::MetricType* {aka itk::ObjectToObjectMetricBaseTemplate*}? virtual void Set##name (type * _arg) \ ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:250:3: note: in expansion of macro ?itkSetObjectMacro? itkSetObjectMacro( Metric, MetricType ); ^ In file included from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkAtomicInt.h:38:0, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkLightObject.h:25, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkObject.h:31, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkDataObject.h:31, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkProcessObject.h:31, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:21, from /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:1: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkConceptChecking.h: In instantiation of ?void itk::Concept::Convertible::Constraints::constraints() [with T1 = itk::Vector; T2 = unsigned char]?: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkConceptChecking.h:192:3: required from ?struct itk::Concept::Convertible, unsigned char>? /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageFilterBase/include/itkCastImageFilter.h:126:3: required from ?class itk::CastImageFilter, 2u>, itk::Image >? /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:260:17: required from here /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkConceptChecking.h:185:35: error: invalid static_cast from type ?itk::Vector? to type ?unsigned char? T2 b = static_cast< T2 >( a ); ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkConceptChecking.h: In instantiation of ?void itk::Concept::Convertible::Constraints::constraints() [with T1 = itk::Vector; T2 = double]?: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkConceptChecking.h:192:3: required from ?struct itk::Concept::Convertible, double>? /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageCompare/include/itkSquaredDifferenceImageFilter.h:115:3: required from ?class itk::SquaredDifferenceImageFilter, 2u>, itk::Image, 2u>, itk::Image >? /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:286:23: required from here /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkConceptChecking.h:185:35: error: invalid static_cast from type ?itk::Vector? to type ?double? In file included from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader.h:138:0, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4.h:22, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.hxx:29, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:518, from /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:1: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader.hxx: In instantiation of ?bool itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::ProcessPoint(const VirtualIndexType&, const VirtualPointType&, const FixedImagePointType&, const FixedImagePixelType&, const FixedImageGradientType&, const MovingImagePointType&, const MovingImagePixelType&, const MovingImageGradientType&, itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::MeasureType&, itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::DerivativeType&, itk::ThreadIdType) const [with TDomainPartitioner = itk::ThreadedIndexedContainerPartitioner; TImageToImageMetric = itk::ImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >; TMattesMutualInformationMetric = itk::MattesMutualInformationImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::VirtualIndexType = itk::Index<2u>; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::VirtualPointType = itk::Point; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::FixedImagePointType = itk::Point; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::FixedImagePixelType = itk::Vector; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::FixedImageGradientType = itk::CovariantVector; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::MovingImagePointType = itk::Point; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::MovingImagePixelType = itk::Vector; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::MovingImageGradientType = itk::CovariantVector; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::MeasureType = double; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::DerivativeType = itk::Array; itk::ThreadIdType = unsigned int]?: /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:378:1: required from here /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:236:24: error: no match for ?operator}? and ?itk::MattesMutualInformationImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >::PDFValueType {aka double}?) if( movingImageValue < this->m_MattesAssociate->m_MovingImageTrueMin ) ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:240:29: error: no match for ?operator>? (operand types are ?const MovingImagePixelType {aka const itk::Vector}? and ?itk::MattesMutualInformationImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >::PDFValueType {aka double}?) else if( movingImageValue > this->m_MattesAssociate->m_MovingImageTrueMax ) ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:246:144: error: cannot convert ?itk::Vector? to ?const PDFValueType {aka const double}? in initialization const PDFValueType movingImageParzenWindowTerm = movingImageValue / this->m_MattesAssociate->m_MovingImageBinSize - this->m_MattesAssociate->m_MovingImageNormalizedMin; ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader.hxx: In instantiation of ?bool itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::ProcessPoint(const VirtualIndexType&, const VirtualPointType&, const FixedImagePointType&, const FixedImagePixelType&, const FixedImageGradientType&, const MovingImagePointType&, const MovingImagePixelType&, const MovingImageGradientType&, itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::MeasureType&, itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::DerivativeType&, itk::ThreadIdType) const [with TDomainPartitioner = itk::ThreadedImageRegionPartitioner<2u>; TImageToImageMetric = itk::ImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >; TMattesMutualInformationMetric = itk::MattesMutualInformationImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::VirtualIndexType = itk::Index<2u>; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::VirtualPointType = itk::Point; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::FixedImagePointType = itk::Point; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::FixedImagePixelType = itk::Vector; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::FixedImageGradientType = itk::CovariantVector; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::MovingImagePointType = itk::Point; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::MovingImagePixelType = itk::Vector; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::MovingImageGradientType = itk::CovariantVector; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::MeasureType = double; itk::MattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader::DerivativeType = itk::Array; itk::ThreadIdType = unsigned int]?: /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:378:1: required from here /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:236:24: error: no match for ?operator}? and ?itk::MattesMutualInformationImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >::PDFValueType {aka double}?) if( movingImageValue < this->m_MattesAssociate->m_MovingImageTrueMin ) ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:240:29: error: no match for ?operator>? (operand types are ?const MovingImagePixelType {aka const itk::Vector}? and ?itk::MattesMutualInformationImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >::PDFValueType {aka double}?) else if( movingImageValue > this->m_MattesAssociate->m_MovingImageTrueMax ) ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4GetValueAndDerivativeThreader.hxx:246:144: error: cannot convert ?itk::Vector? to ?const PDFValueType {aka const double}? in initialization const PDFValueType movingImageParzenWindowTerm = movingImageValue / this->m_MattesAssociate->m_MovingImageBinSize - this->m_MattesAssociate->m_MovingImageNormalizedMin; ^ In file included from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4.h:290:0, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.hxx:29, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:518, from /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:1: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4.hxx: In instantiation of ?void itk::MattesMutualInformationImageToImageMetricv4::Initialize() [with TFixedImage = itk::Image, 2u>; TMovingImage = itk::Image, 2u>; TVirtualImage = itk::Image, 2u>; TInternalComputationValueType = double; TMetricTraits = itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double>]?: /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:378:1: required from here /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4.hxx:101:29: error: cannot convert ?const Self {aka const itk::Vector}? to ?itk::MattesMutualInformationImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >::PDFValueType {aka double}? in assignment this->m_FixedImageTrueMin = NumericTraits::max(); ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4.hxx:102:29: error: cannot convert ?const Self {aka const itk::Vector}? to ?itk::MattesMutualInformationImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >::PDFValueType {aka double}? in assignment this->m_FixedImageTrueMax = NumericTraits::NonpositiveMin(); ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4.hxx:103:30: error: cannot convert ?const Self {aka const itk::Vector}? to ?itk::MattesMutualInformationImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >::PDFValueType {aka double}? in assignment this->m_MovingImageTrueMin = NumericTraits::max(); ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4.hxx:104:30: error: cannot convert ?const Self {aka const itk::Vector}? to ?itk::MattesMutualInformationImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >::PDFValueType {aka double}? in assignment this->m_MovingImageTrueMax = NumericTraits::NonpositiveMin(); ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4.hxx:121:56: error: no match for ?operator, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >::PDFValueType {aka double}? and ?const PixelType {aka const itk::Vector}?) this->m_FixedImageTrueMin = (m_FixedImageTrueMin < currValue) ? this->m_FixedImageTrueMin : currValue; ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4.hxx:122:56: error: no match for ?operator>? (operand types are ?itk::MattesMutualInformationImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >::PDFValueType {aka double}? and ?const PixelType {aka const itk::Vector}?) this->m_FixedImageTrueMax = (m_FixedImageTrueMax > currValue) ? this->m_FixedImageTrueMax : currValue; ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4.hxx:142:58: error: no match for ?operator, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >::PDFValueType {aka double}? and ?const PixelType {aka const itk::Vector}?) this->m_MovingImageTrueMin = (m_MovingImageTrueMin < currValue) ? this->m_MovingImageTrueMin : currValue; ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkMattesMutualInformationImageToImageMetricv4.hxx:143:58: error: no match for ?operator>? (operand types are ?itk::MattesMutualInformationImageToImageMetricv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double, itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double> >::PDFValueType {aka double}? and ?const PixelType {aka const itk::Vector}?) this->m_MovingImageTrueMax = (m_MovingImageTrueMax > currValue) ? this->m_MovingImageTrueMax : currValue; ^ In file included from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageGradient/include/itkGradientRecursiveGaussianImageFilter.h:265:0, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkDefaultImageToImageMetricTraitsv4.h:24, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.h:33, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:28, from /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:1: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageGradient/include/itkGradientRecursiveGaussianImageFilter.hxx: In instantiation of ?void itk::GradientRecursiveGaussianImageFilter::GenerateData() [with TInputImage = itk::Image, 2u>; TOutputImage = itk::Image, 2u>, 2u>]?: /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:378:1: required from here /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageGradient/include/itkGradientRecursiveGaussianImageFilter.hxx:313:9: error: no matching function for call to ?itk::ImageRegionIteratorWithIndex, 2u>, 2u>, float> >::Set(itk::GradientRecursiveGaussianImageFilter, 2u>, itk::Image, 2u>, 2u> >::OutputComponentType&)? ot.Set( outValue ); ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageGradient/include/itkGradientRecursiveGaussianImageFilter.hxx:313:9: note: candidate is: In file included from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/DisplacementField/include/itkDisplacementFieldTransform.hxx:25:0, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/DisplacementField/include/itkDisplacementFieldTransform.h:488, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Numerics/Optimizersv4/include/itkObjectToObjectMetric.h:24, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkObjectToObjectMultiMetricv4.h:22, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:26, from /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:1: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkImageRegionIteratorWithIndex.h:106:8: note: void itk::ImageRegionIteratorWithIndex::Set(const PixelType&) const [with TImage = itk::NthElementImageAdaptor, 2u>, 2u>, float>; itk::ImageRegionIteratorWithIndex::PixelType = float] void Set(const PixelType & value) const ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkImageRegionIteratorWithIndex.h:106:8: note: no known conversion for argument 1 from ?itk::GradientRecursiveGaussianImageFilter, 2u>, itk::Image, 2u>, 2u> >::OutputComponentType {aka itk::Vector}? to ?const PixelType& {aka const float&}? In file included from /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:9:0: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageCompare/include/itkSquaredDifferenceImageFilter.h: In instantiation of ?TOutput itk::Functor::SquaredDifference2::operator()(const TInput1&, const TInput2&) const [with TInput1 = itk::Vector; TInput2 = itk::Vector; TOutput = unsigned char]?: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageFilterBase/include/itkBinaryFunctorImageFilter.hxx:238:9: required from ?void itk::BinaryFunctorImageFilter::ThreadedGenerateData(const OutputImageRegionType&, itk::ThreadIdType) [with TInputImage1 = itk::Image, 2u>; TInputImage2 = itk::Image, 2u>; TOutputImage = itk::Image; TFunction = itk::Functor::SquaredDifference2, itk::Vector, unsigned char>; itk::BinaryFunctorImageFilter::OutputImageRegionType = itk::ImageRegion<2u>; itk::ThreadIdType = unsigned int]? /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:378:1: required from here /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageCompare/include/itkSquaredDifferenceImageFilter.h:74:48: error: invalid static_cast from type ?const itk::Vector? to type ?double? const double dA = static_cast< double >( A ); ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageCompare/include/itkSquaredDifferenceImageFilter.h:75:48: error: invalid static_cast from type ?const itk::Vector? to type ?double? const double dB = static_cast< double >( B ); ^ In file included from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageGrid/include/itkBSplineScatteredDataPointSetToImageFilter.hxx:25:0, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageGrid/include/itkBSplineScatteredDataPointSetToImageFilter.h:428, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Numerics/Optimizersv4/include/itkWindowConvergenceMonitoringFunction.hxx:24, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Numerics/Optimizersv4/include/itkWindowConvergenceMonitoringFunction.h:97, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Numerics/Optimizersv4/include/itkGradientDescentOptimizerBasev4.h:22, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Numerics/Optimizersv4/include/itkGradientDescentOptimizerv4.h:21, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.hxx:24, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:518, from /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:1: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageFilterBase/include/itkCastImageFilter.h: In instantiation of ?TOutput itk::Functor::Cast::operator()(const TInput&) const [with TInput = itk::Vector; TOutput = unsigned char]?: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkUnaryFunctorImageFilter.hxx:183:7: required from ?void itk::UnaryFunctorImageFilter::ThreadedGenerateData(const OutputImageRegionType&, itk::ThreadIdType) [with TInputImage = itk::Image, 2u>; TOutputImage = itk::Image; TFunction = itk::Functor::Cast, unsigned char>; itk::UnaryFunctorImageFilter::OutputImageRegionType = itk::ImageRegion<2u>; itk::ThreadIdType = unsigned int]? /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:378:1: required from here /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageFilterBase/include/itkCastImageFilter.h:53:38: error: invalid static_cast from type ?const itk::Vector? to type ?unsigned char? return static_cast< TOutput >( A ); ^ In file included from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/ImageFunction/include/itkCentralDifferenceImageFunction.h:255:0, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkDefaultImageToImageMetricTraitsv4.h:23, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.h:33, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:28, from /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:1: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/ImageFunction/include/itkCentralDifferenceImageFunction.hxx: In instantiation of ?void itk::CentralDifferenceImageFunction::EvaluateSpecialized(const PointType&, itk::CentralDifferenceImageFunction::OutputType&, itk::CentralDifferenceImageFunction::OutputTypeSpecializationStructType::OutputType>) const [with Type = itk::CovariantVector; TInputImage = itk::Image, 2u>; TCoordRep = double; TOutputType = itk::CovariantVector; itk::CentralDifferenceImageFunction::PointType = itk::Point; itk::CentralDifferenceImageFunction::OutputType = itk::CovariantVector; typename itk::ImageFunction::OutputType = itk::CovariantVector]?: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/ImageFunction/include/itkCentralDifferenceImageFunction.hxx:273:22: required from ?itk::CentralDifferenceImageFunction::OutputType itk::CentralDifferenceImageFunction::Evaluate(const PointType&) const [with TInputImage = itk::Image, 2u>; TCoordRep = double; TOutputType = itk::CovariantVector; itk::CentralDifferenceImageFunction::OutputType = itk::CovariantVector; itk::CentralDifferenceImageFunction::PointType = itk::Point]? /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:378:1: required from here /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/ImageFunction/include/itkCentralDifferenceImageFunction.hxx:325:31: error: cannot convert ?itk::Vector::Self {aka itk::Vector}? to ?itk::FixedArray::ValueType {aka double}? in assignment orientedDerivative[dim] = ( this->m_Interpolator->Evaluate( neighPoint2 ) - this->m_Interpolator->Evaluate( neighPoint1 ) ) / delta; ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/ImageFunction/include/itkCentralDifferenceImageFunction.hxx: In instantiation of ?void itk::CentralDifferenceImageFunction::EvaluateAtIndexSpecialized(const IndexType&, itk::CentralDifferenceImageFunction::OutputType&, itk::CentralDifferenceImageFunction::OutputTypeSpecializationStructType::OutputType>) const [with Type = itk::CovariantVector; TInputImage = itk::Image, 2u>; TCoordRep = double; TOutputType = itk::CovariantVector; itk::CentralDifferenceImageFunction::IndexType = itk::Index<2u>; itk::CentralDifferenceImageFunction::OutputType = itk::CovariantVector; typename itk::ImageFunction::OutputType = itk::CovariantVector]?: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/ImageFunction/include/itkCentralDifferenceImageFunction.hxx:117:29: required from ?itk::CentralDifferenceImageFunction::OutputType itk::CentralDifferenceImageFunction::EvaluateAtIndex(const IndexType&) const [with TInputImage = itk::Image, 2u>; TCoordRep = double; TOutputType = itk::CovariantVector; itk::CentralDifferenceImageFunction::OutputType = itk::CovariantVector; itk::CentralDifferenceImageFunction::IndexType = itk::Index<2u>]? /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:378:1: required from here /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/ImageFunction/include/itkCentralDifferenceImageFunction.hxx:158:21: error: cannot convert ?const itk::Vector? to ?itk::FixedArray::ValueType {aka double}? in assignment derivative[dim] = inputImage->GetPixel(neighIndex); ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/ImageFunction/include/itkCentralDifferenceImageFunction.hxx:161:21: error: no match for ?operator-=? (operand types are ?itk::FixedArray::ValueType {aka double}? and ?const itk::Vector?) derivative[dim] -= inputImage->GetPixel(neighIndex); ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/ImageFunction/include/itkCentralDifferenceImageFunction.hxx: In instantiation of ?void itk::CentralDifferenceImageFunction::EvaluateAtContinuousIndexSpecialized(const ContinuousIndexType&, itk::CentralDifferenceImageFunction::OutputType&, itk::CentralDifferenceImageFunction::OutputTypeSpecializationStructType::OutputType>) const [with Type = itk::CovariantVector; TInputImage = itk::Image, 2u>; TCoordRep = double; TOutputType = itk::CovariantVector; itk::CentralDifferenceImageFunction::ContinuousIndexType = itk::ContinuousIndex; itk::CentralDifferenceImageFunction::OutputType = itk::CovariantVector; typename itk::ImageFunction::OutputType = itk::CovariantVector]?: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/ImageFunction/include/itkCentralDifferenceImageFunction.hxx:470:3: required from ?itk::CentralDifferenceImageFunction::OutputType itk::CentralDifferenceImageFunction::EvaluateAtContinuousIndex(const ContinuousIndexType&) const [with TInputImage = itk::Image, 2u>; TCoordRep = double; TOutputType = itk::CovariantVector; itk::CentralDifferenceImageFunction::OutputType = itk::CovariantVector; itk::CentralDifferenceImageFunction::ContinuousIndexType = itk::ContinuousIndex]? /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:378:1: required from here /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/ImageFunction/include/itkCentralDifferenceImageFunction.hxx:511:21: error: cannot convert ?itk::InterpolateImageFunction, 2u>, double>::OutputType {aka itk::Vector}? to ?itk::FixedArray::ValueType {aka double}? in assignment derivative[dim] = this->m_Interpolator->EvaluateAtContinuousIndex(neighIndex); ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/ImageFunction/include/itkCentralDifferenceImageFunction.hxx:514:21: error: no match for ?operator-=? (operand types are ?itk::FixedArray::ValueType {aka double}? and ?itk::InterpolateImageFunction, 2u>, double>::OutputType {aka itk::Vector}?) derivative[dim] -= this->m_Interpolator->EvaluateAtContinuousIndex(neighIndex); ^ In file included from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkNumericTraits.h:1656:0, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkConceptChecking.h:32, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkAtomicInt.h:38, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkLightObject.h:25, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkObject.h:31, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkDataObject.h:31, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkProcessObject.h:31, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:21, from /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:1: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkFixedArray.h: In instantiation of ?itk::FixedArray& itk::FixedArray::operator=(const itk::FixedArray&) [with TFixedArrayValueType = itk::Vector; TValue = double; unsigned int VLength = 2u]?: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkCovariantVector.h:131:27: required from ?itk::CovariantVector::Self& itk::CovariantVector::operator=(const Tt&) [with Tt = itk::CovariantVector, 2u>; T = double; unsigned int NVectorDimension = 2u; itk::CovariantVector::Self = itk::CovariantVector]? /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.hxx:383:14: required from ?void itk::ImageToImageMetricv4::ComputeFixedImageGradientAtPoint(const FixedImagePointType&, itk::ImageToImageMetricv4::FixedImageGradientType&) const [with TFixedImage = itk::Image, 2u>; TMovingImage = itk::Image, 2u>; TVirtualImage = itk::Image, 2u>; TInternalComputationValueType = double; TMetricTraits = itk::DefaultImageToImageMetricTraitsv4, 2u>, itk::Image, 2u>, itk::Image, 2u>, double>; itk::ImageToImageMetricv4::FixedImagePointType = itk::Point; itk::ImageToImageMetricv4::FixedImageGradientType = itk::CovariantVector]? /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:378:1: required from here /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkFixedArray.h:178:14: error: invalid static_cast from type ?const ValueType {aka const itk::Vector}? to type ?double? *i++ = static_cast< TValue >( *input++ ); ^ In file included from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkImageAlgorithm.h:223:0, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkStreamingImageFilter.hxx:22, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkStreamingImageFilter.h:133, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/Smoothing/include/itkDiscreteGaussianImageFilter.hxx:26, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/Smoothing/include/itkDiscreteGaussianImageFilter.h:283, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.hxx:23, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:518, from /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:1: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkImageAlgorithm.hxx: In instantiation of ?static void itk::ImageAlgorithm::DispatchedCopy(const InputImageType*, OutputImageType*, const typename InputImageType::RegionType&, const typename OutputImageType::RegionType&, itk::ImageAlgorithm::FalseType) [with InputImageType = itk::Image, 2u>; OutputImageType = itk::Image; typename InputImageType::RegionType = itk::ImageRegion<2u>; typename OutputImageType::RegionType = itk::ImageRegion<2u>; itk::ImageAlgorithm::FalseType = std::tr1::integral_constant]?: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkImageAlgorithm.h:112:7: required from ?static void itk::ImageAlgorithm::Copy(const itk::Image*, itk::Image*, const typename itk::Image::RegionType&, const typename itk::Image::RegionType&) [with TPixel1 = itk::Vector; TPixel2 = unsigned char; unsigned int VImageDimension = 2u; typename itk::Image::RegionType = itk::ImageRegion<2u>; typename itk::Image::RegionType = itk::ImageRegion<2u>]? /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageFilterBase/include/itkCastImageFilter.hxx:73:90: required from ?void itk::CastImageFilter::ThreadedGenerateData(const OutputImageRegionType&, itk::ThreadIdType) [with TInputImage = itk::Image, 2u>; TOutputImage = itk::Image; itk::CastImageFilter::OutputImageRegionType = itk::ImageRegion<2u>; itk::ThreadIdType = unsigned int]? /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:378:1: required from here /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkImageAlgorithm.hxx:45:9: error: invalid static_cast from type ?itk::ImageConstIterator, 2u> >::PixelType {aka itk::Vector}? to type ?itk::Image::PixelType {aka unsigned char}? ot.Set( static_cast< typename OutputImageType::PixelType >( it.Get() ) ); ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkImageAlgorithm.hxx:60:5: error: invalid static_cast from type ?itk::ImageConstIterator, 2u> >::PixelType {aka itk::Vector}? to type ?itk::Image::PixelType {aka unsigned char}? ot.Set( static_cast< typename OutputImageType::PixelType >( it.Get() ) ); ^ In file included from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageGrid/include/itkBSplineScatteredDataPointSetToImageFilter.hxx:25:0, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageGrid/include/itkBSplineScatteredDataPointSetToImageFilter.h:428, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Numerics/Optimizersv4/include/itkWindowConvergenceMonitoringFunction.hxx:24, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Numerics/Optimizersv4/include/itkWindowConvergenceMonitoringFunction.h:97, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Numerics/Optimizersv4/include/itkGradientDescentOptimizerBasev4.h:22, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Numerics/Optimizersv4/include/itkGradientDescentOptimizerv4.h:21, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.hxx:24, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:518, from /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:1: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageFilterBase/include/itkCastImageFilter.h: In instantiation of ?TOutput itk::Functor::Cast::operator()(const TInput&) const [with TInput = itk::Vector; TOutput = double]?: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkUnaryFunctorImageFilter.hxx:183:7: required from ?void itk::UnaryFunctorImageFilter::ThreadedGenerateData(const OutputImageRegionType&, itk::ThreadIdType) [with TInputImage = itk::Image, 2u>; TOutputImage = itk::Image; TFunction = itk::Functor::Cast, double>; itk::UnaryFunctorImageFilter::OutputImageRegionType = itk::ImageRegion<2u>; itk::ThreadIdType = unsigned int]? /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:378:1: required from here /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageFilterBase/include/itkCastImageFilter.h:53:38: error: invalid static_cast from type ?const itk::Vector? to type ?double? return static_cast< TOutput >( A ); ^ In file included from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkImageAlgorithm.h:223:0, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkStreamingImageFilter.hxx:22, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkStreamingImageFilter.h:133, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/Smoothing/include/itkDiscreteGaussianImageFilter.hxx:26, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/Smoothing/include/itkDiscreteGaussianImageFilter.h:283, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.hxx:23, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:518, from /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:1: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkImageAlgorithm.hxx: In instantiation of ?static void itk::ImageAlgorithm::DispatchedCopy(const InputImageType*, OutputImageType*, const typename InputImageType::RegionType&, const typename OutputImageType::RegionType&, itk::ImageAlgorithm::FalseType) [with InputImageType = itk::Image, 2u>; OutputImageType = itk::Image; typename InputImageType::RegionType = itk::ImageRegion<2u>; typename OutputImageType::RegionType = itk::ImageRegion<2u>; itk::ImageAlgorithm::FalseType = std::tr1::integral_constant]?: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkImageAlgorithm.h:112:7: required from ?static void itk::ImageAlgorithm::Copy(const itk::Image*, itk::Image*, const typename itk::Image::RegionType&, const typename itk::Image::RegionType&) [with TPixel1 = itk::Vector; TPixel2 = double; unsigned int VImageDimension = 2u; typename itk::Image::RegionType = itk::ImageRegion<2u>; typename itk::Image::RegionType = itk::ImageRegion<2u>]? /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageFilterBase/include/itkCastImageFilter.hxx:73:90: required from ?void itk::CastImageFilter::ThreadedGenerateData(const OutputImageRegionType&, itk::ThreadIdType) [with TInputImage = itk::Image, 2u>; TOutputImage = itk::Image; itk::CastImageFilter::OutputImageRegionType = itk::ImageRegion<2u>; itk::ThreadIdType = unsigned int]? /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:378:1: required from here /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkImageAlgorithm.hxx:45:9: error: invalid static_cast from type ?itk::ImageConstIterator, 2u> >::PixelType {aka itk::Vector}? to type ?itk::Image::PixelType {aka double}? ot.Set( static_cast< typename OutputImageType::PixelType >( it.Get() ) ); ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Core/Common/include/itkImageAlgorithm.hxx:60:5: error: invalid static_cast from type ?itk::ImageConstIterator, 2u> >::PixelType {aka itk::Vector}? to type ?itk::Image::PixelType {aka double}? ot.Set( static_cast< typename OutputImageType::PixelType >( it.Get() ) ); ^ In file included from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageGrid/include/itkBSplineScatteredDataPointSetToImageFilter.hxx:25:0, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageGrid/include/itkBSplineScatteredDataPointSetToImageFilter.h:428, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Numerics/Optimizersv4/include/itkWindowConvergenceMonitoringFunction.hxx:24, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Numerics/Optimizersv4/include/itkWindowConvergenceMonitoringFunction.h:97, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Numerics/Optimizersv4/include/itkGradientDescentOptimizerBasev4.h:22, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Numerics/Optimizersv4/include/itkGradientDescentOptimizerv4.h:21, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.hxx:24, from /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Registration/RegistrationMethodsv4/include/itkImageRegistrationMethodv4.h:518, from /home/art/SourceCode/InsightToolkit-4.8.2/Examples/ArtTest/DeformableRegistrationArt.cxx:1: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageFilterBase/include/itkCastImageFilter.h: In member function ?TOutput itk::Functor::Cast::operator()(const TInput&) const [with TInput = itk::Vector; TOutput = double]?: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageFilterBase/include/itkCastImageFilter.h:54:3: warning: control reaches end of non-void function [-Wreturn-type] } ^ /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageFilterBase/include/itkCastImageFilter.h: In member function ?TOutput itk::Functor::Cast::operator()(const TInput&) const [with TInput = itk::Vector; TOutput = unsigned char]?: /home/art/SourceCode/InsightToolkit-4.8.2/Modules/Filtering/ImageFilterBase/include/itkCastImageFilter.h:54:3: warning: control reaches end of non-void function [-Wreturn-type] } ^ make[3]: *** [Examples/ArtTest/CMakeFiles/DeformableRegistrationArt.dir/DeformableRegistrationArt.cxx.o] Error 1 make[2]: *** [Examples/ArtTest/CMakeFiles/DeformableRegistrationArt.dir/all] Error 2 make[1]: *** [Examples/ArtTest/CMakeFiles/DeformableRegistrationArt.dir/rule] Error 2 make: *** [DeformableRegistrationArt] Error 2 -- View this message in context: http://itk-users.7.n7.nabble.com/Deformable-registration-of-RGB-image-tp36786.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Mon Feb 15 01:36:15 2016 From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca) Date: Mon, 15 Feb 2016 07:36:15 +0100 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <84A225AE-400C-4FBA-97FA-6A027CB17208@mail.nih.gov> Message-ID: Hi, Here they are. KR. 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] < ml-node+s2283740n7588490h25 at n2.nabble.com>: > Hi Francisco, > > do you mind attaching the modified files or pointing to your fork of it on > GitHub? > > Regards > > On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden email] > > wrote: > >> Hi Dzenan, >> The original class is here: >> >> >> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >> >> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >> >> I've just added setInput and setMaskImage methods and modify some lines in >> the original class as I indicated in the yesterday mail within this >> thread. >> I'm running it on Windows, and there is no error at all, just a crash. I >> may have to include exceptions management. >> The crash occurs just when calling p3 = maskIter.GetPixel(iter->first) >> >> If you know why it could be or if you need more clarification, please let >> me know. >> Many thanks >> >> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >> [hidden email] >: >> >> > Hi Francisco, >> > >> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the error >> message >> > that goes along with the crash? In which file and line does it crash? >> > >> > Regards >> > >> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca <[hidden >> > email] > wrote: >> > >> >> Hi, >> >> Please, someone that could help me. I'm working in a pre-doctorate >> >> project and I need this class to work. >> >> I've read the chapter 13 in the ITK Software Guide on how to write a >> >> filter and now I see the fact of the threads due to inheritance of >> >> ImageToImageFilter. >> >> But, I keep on without understanding why the code crashes just when >> >> calling >> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >> >> It is just a call to read data, not to write. >> >> >> >> I guess somebody that had worked with creation of filters might see >> >> "easily" the problem, but not me. >> >> >> >> So, again, please, I need someone to help me with this because I'm >> stuck >> >> on this point. >> >> >> >> Thank you very much. >> >> KR. >> >> /Francisco >> >> >> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden email] >> >> >: >> >> >> >>> Hi Bradley again. >> >>> I'm modifying your class in order to be able to set a mask image (a >> >>> binary image) to be used as a limit in the histogram calculations, I >> mean, >> >>> I set an input, a mask and the class should take into account to >> calculate >> >>> the histograms only the voxels that belong to the input and to the >> mask >> >>> image and having the value 1 in the mask image. >> >>> The changes seem to be easy but I don?t know why my tests are not >> >>> working. It seems that 2 threads are working at the same time and >> when I >> >>> added my mask iterator, the code crashes. >> >>> >> >>> *** Consider that the input and mask images are the same origin, >> spacing >> >>> and size. >> >>> >> >>> I attach the main changes I've done, and I would thank you a lot if >> you >> >>> don't mind having a look and help me to find what I'm doing wrong: >> >>> >> >>> template< class TImageType, class TOutputImage > >> >>> void >> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >> >::*SetInput*(InputImageType >> >>> *image) >> >>> { >> >>> // Process object is not const-correct so the const_cast is required >> >>> here >> >>> this->ProcessObject::SetNthInput( 0, >> >>> const_cast< InputImageType * >( >> >>> image ) ); >> >>> } >> >>> >> >>> template< class TImageType, class TOutputImage > >> >>> void >> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >> >::*SetMaskImage*(InputImageType >> >>> *image) >> >>> { >> >>> // Process object is not const-correct so the const_cast is required >> >>> here >> >>> this->ProcessObject::SetNthInput( 1, const_cast< InputImageType * >( >> >>> image ) ); >> >>> >> >>> _maskImage = image; // _maskImage is a private member >> >>> } >> >>> >> >>> In the *ThreadedGenerateData*(const RegionType& outputRegionForThread, >> >>> ThreadIdType threadId ) method: >> >>> { >> >>> >> >>> ... >> >>> >> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >> >>> { >> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, *fit);* >> >>> OutputIterator outIter(output, *fit); >> >>> >> >>> OutputPixelType out; >> >>> NumericTraits::SetLength( out, >> >>> this->GetNumberOfOutputComponents() ); >> >>> >> >>> while( !nIter.IsAtEnd() ) >> >>> { >> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >> >>> >> >>> ... >> >>> >> >>> ++nIter; >> >>> ++outIter; >> >>> * ++maskIter;* >> >>> ... >> >>> >> >>> In the *FillHistogram *method: >> >>> { >> >>> >> >>> ... >> >>> >> >>> while( iter != m_CooccurenceOffsetVector.end() ) >> >>> { >> >>> >> >>> const PixelType p1 = niter.GetPixel(iter->first); >> >>> const PixelType p2 = niter.GetPixel(iter->second); >> >>> std::cout << "Before p3" << std::endl; >> >>> >> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); >> *std::cout >> >>> << "After p3: " << p3 << std::endl; >> >>> >> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >> >>> std::cout << "After p4: " << p4 << std::endl; >> >>> >> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= m_Max >> >>> *&& p3 == _insidePixelValue && p4 == _insidePixelValue* ) >> >>> // The point >> >>> { >> >>> >> >>> ... >> >>> >> >>> >> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >> >>> >> >>> Thank you so much. >> >>> My kind regards. >> >>> /Paco >> >>> >> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca <[hidden >> email] >> >>> >: >> >>> >> >>>> Hello Bradley again. >> >>>> Sorry but I'd like to re-open this issue because I need your class >> but >> >>>> with some modification. >> >>>> I pass to tell you. >> >>>> >> >>>> As my tests with your external class were not good taking into >> account >> >>>> the performance, I wonder if you could create a variant of it, but >> in which >> >>>> I can set a mask image and your class just return the VectorImage >> with all >> >>>> the features for that region (the masked locations) as >> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >> >>>> I mean, to get the vector image with all the features but just >> >>>> calculate it for the regions belonging to the mask image. Positions >> not >> >>>> belonging to the mask region could have a pixel value of 0, for >> instance. >> >>>> >> >>>> I don?t know if it is very costly for you, but I would thank you so >> >>>> much. Otherwise, I could try it but I'd need your suggestions on how >> to do >> >>>> it. >> >>>> >> >>>> Thanks a lot. >> >>>> Best regards. >> >>>> >> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca <[hidden >> email] >> >>>> >: >> >>>> >> >>>>> Hello Bradley again, >> >>>>> I would like to ask you for a couple of favours. In the one hand, >> >>>>> could you please send me your 3D image so that I can test on it? >> And on the >> >>>>> other hand, could you test the example I have referenced in the >> previous >> >>>>> email with your image, not changing anything in the code, such as >> it is, >> >>>>> and tell me if the execution time is normal? >> >>>>> Thank you very much. >> >>>>> Regards, >> >>>>> /Francisco >> >>>>> >> >>>>> PS: All my application trace is printed via standard 'cout' command, >> >>>>> not due to a debugging compilation mode. >> >>>>> >> >>>>> >> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp <[hidden >> >>>>> email] > >> >>>>> escribi?: >> >>>>> >> >>>>>> Hello, >> >>>>>> >> >>>>>> Did you compile TextureFeatureImage in Release mode? >> >>>>>> >> >>>>>> 1) The filter does not scale well with a large radius. And given by >> >>>>>> your initial report of print a very large number of offset you, it >> sounds >> >>>>>> like you are using a large radius with many offsets. I created a >> >>>>>> 224x224x300 unsigned short image and ran with the default offset >> and a >> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this filter is >> was ~10x >> >>>>>> faster than this example... things change though... >> >>>>>> >> >>>>>> >> >>>>>> 2) I sounds like the boundaries/limits of the histogram may be >> >>>>>> clipping you values. I would inspect the co-occurance matrix. >> >>>>>> >> >>>>>> >> >>>>>> HTH, >> >>>>>> Brad >> >>>>>> >> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca <[hidden >> >>>>>> email] > >> >>>>>> wrote: >> >>>>>> >> >>>>>> I've tested with itkTextureFeatureImageFilter, with >> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >> >>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures >> example, >> >>>>>> for a 3D image and here are my comments: >> >>>>>> >> >>>>>> >> >>>>>> 1. I had to interrupt the test after several hours and it kept on >> >>>>>> calculating. And this is for only a 3D image (224x224x300). I need >> to >> >>>>>> process around 35 images. >> >>>>>> 2. The result (texture features: entropy, energy, correlation, LH, >> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, >> 7.83083e+247]. >> >>>>>> These values were not what I expected based on my experience on >> another >> >>>>>> application I developed, but in that case, I calculated the texture >> >>>>>> features for an image as a whole, not voxel by voxel. >> >>>>>> >> >>>>>> Regards. >> >>>>>> >> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >> >>>>>> >: >> >>>>>> >> >>>>>>> i yes i have tried radius = 3; >> >>>>>>> still no luck >> >>>>>>> >> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via ITK >> >>>>>>> Insight >> >>>>>>> Users] <[hidden email] >> >>>>>>> > wrote: >> >>>>>>> >> >>>>>>> > Have you tried with a radius of 3 instead of 1? >> >>>>>>> > >> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >> >>>>>>> > >: >> >>>>>>> > >> >>>>>>> >> hey Matt, >> >>>>>>> >> thanks for ur advice.. it did build successfully... but im not >> >>>>>>> able to run >> >>>>>>> >> the code for 2D png image... i tried to change the dimension >> to 2 >> >>>>>>> and >> >>>>>>> >> build >> >>>>>>> >> it which it did.. but when i run the code using the command >> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png putput.png >> >>>>>>> 1... i see >> >>>>>>> >> this output >> >>>>>>> >> >> >>>>>>> >> offset: [-1, -1] [0, -1] >> >>>>>>> >> offset: [0, -1] [1, -1] >> >>>>>>> >> offset: [-1, 0] [0, 0] >> >>>>>>> >> offset: [0, 0] [1, 0] >> >>>>>>> >> offset: [-1, 1] [0, 1] >> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... if >> pls >> >>>>>>> tel me >> >>>>>>> >> how can i modify this code to work wid 2d image... forgive me >> if >> >>>>>>> my ques >> >>>>>>> >> are really silly im trying to learn something.. >> >>>>>>> >> regards >> >>>>>>> >> Vis >> >>>>>>> >> >> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK >> >>>>>>> Insight Users] >> >>>>>>> >> < >> >>>>>>> >> [hidden email] < >> >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >> >>>>>>> >> wrote: >> >>>>>>> >> >> >>>>>>> >> > Hi, >> >>>>>>> >> > >> >>>>>>> >> > The function: >> >>>>>>> >> > >> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char *argv[]) >> >>>>>>> >> > >> >>>>>>> >> > must be renamed to >> >>>>>>> >> > >> >>>>>>> >> > main(int argc, char* argv[]) >> >>>>>>> >> > >> >>>>>>> >> > HTH, >> >>>>>>> >> > Matt >> >>>>>>> >> > >> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >> >>>>>>> >> > > >> wrote: >> >>>>>>> >> > >> >>>>>>> >> > > hi all, >> >>>>>>> >> > > im trying to build the itkTextureFeatureImageFilterTest.cxx >> >>>>>>> code but >> >>>>>>> >> im >> >>>>>>> >> > not >> >>>>>>> >> > > able to it is showing the following error >> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >> >>>>>>> Configuration: >> >>>>>>> >> Debug >> >>>>>>> >> > x64 >> >>>>>>> >> > > ------ >> >>>>>>> >> > > 1> Checking Build System >> >>>>>>> >> > > 1> CMake does not need to re-run because >> >>>>>>> >> > > >> >>>>>>> >> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >> >>>>>>> >> > is >> >>>>>>> >> > > up-to-date. >> >>>>>>> >> > > 2>------ Rebuild All started: Project: >> >>>>>>> >> itkTextureFeatureImageFilterTest, >> >>>>>>> >> > > Configuration: Debug x64 ------ >> >>>>>>> >> > > 2> Building Custom Rule >> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >> >>>>>>> >> > > 2> CMake does not need to re-run because >> >>>>>>> >> > > >> >>>>>>> >> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >> >>>>>>> >> > is >> >>>>>>> >> > > up-to-date. >> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >> >>>>>>> 'std::_Copy_impl': >> >>>>>>> >> > Function >> >>>>>>> >> > > call with parameters that may be unsafe - this call relies >> on >> >>>>>>> the >> >>>>>>> >> caller >> >>>>>>> >> > to >> >>>>>>> >> > > check that the passed values are correct. To disable this >> >>>>>>> warning, use >> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to use >> >>>>>>> Visual C++ >> >>>>>>> >> > > 'Checked Iterators' >> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >> >>>>>>> 'std::_Copy_impl' >> >>>>>>> >> > > 2> >> >>>>>>> >> > > >> >>>>>>> >> >> >>>>>>> >> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >> >>>>>>> >> > see >> >>>>>>> >> > > reference to function template instantiation '_OutIt >> >>>>>>> std::copy> >>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' being >> >>>>>>> compiled >> >>>>>>> >> > > 2> with >> >>>>>>> >> > > 2> [ >> >>>>>>> >> > > 2> _OutIt=unsigned char *, >> >>>>>>> >> > > 2> _InIt=const unsigned char * >> >>>>>>> >> > > 2> ] >> >>>>>>> >> > > 2> >> >>>>>>> >> > > >> >>>>>>> >> >> >>>>>>> >> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >> >>>>>>> >> > > while compiling class template member function 'void >> >>>>>>> >> > > itk::ImageFileReader::GenerateData(void)' >> >>>>>>> >> > > 2> with >> >>>>>>> >> > > 2> [ >> >>>>>>> >> > > 2> TOutputImage=InputImageType >> >>>>>>> >> > > 2> ] >> >>>>>>> >> > > 2> >> >>>>>>> >> > > >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>> >> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >> >>>>>>> >> > >> >>>>>>> >> > > : see reference to class template instantiation >> >>>>>>> >> > > 'itk::ImageFileReader' being compiled >> >>>>>>> >> > > 2> with >> >>>>>>> >> > > 2> [ >> >>>>>>> >> > > 2> TOutputImage=InputImageType >> >>>>>>> >> > > 2> ] >> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >> >>>>>>> 'std::_Copy_impl' >> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >> >>>>>>> 'std::_Copy_impl' >> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >> >>>>>>> 'std::_Copy_impl' >> >>>>>>> >> > > 2> Creating library >> >>>>>>> >> > > >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>> >> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >> >>>>>>> >> > >> >>>>>>> >> > > and object >> >>>>>>> >> > > >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>> >> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >> >>>>>>> >> > >> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved >> >>>>>>> external symbol >> >>>>>>> >> > main >> >>>>>>> >> > > referenced in function __tmainCRTStartup >> >>>>>>> >> > > >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>> >> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >> >>>>>>> >> > >> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >> >>>>>>> Configuration: Debug >> >>>>>>> >> > x64 >> >>>>>>> >> > > ------ >> >>>>>>> >> > > 3> Building Custom Rule >> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >> >>>>>>> >> > > 3> CMake does not need to re-run because >> >>>>>>> >> > > >> >>>>>>> >> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >> >>>>>>> >> > is >> >>>>>>> >> > > up-to-date. >> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 skipped >> >>>>>>> ========== >> >>>>>>> >> > > im using the follwing CMakeList.txt >> >>>>>>> >> > > # This is the root ITK CMakeLists file. >> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >> >>>>>>> >> > > endif() >> >>>>>>> >> > > >> >>>>>>> >> > > >> >>>>>>> >> > > # This project is designed to be built outside the Insight >> >>>>>>> source >> >>>>>>> >> tree. >> >>>>>>> >> > > project(HelloWorld) >> >>>>>>> >> > > >> >>>>>>> >> > > # Find ITK. >> >>>>>>> >> > > find_package(ITK REQUIRED) >> >>>>>>> >> > > include(${ITK_USE_FILE}) >> >>>>>>> >> > > >> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >> >>>>>>> >> > > >> >>>>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest >> >>>>>>> >> ${ITK_LIBRARIES}) >> >>>>>>> >> > > >> >>>>>>> >> > > please tel me wat the error is?? >> >>>>>>> >> > > >> >>>>>>> >> > > >> >>>>>>> >> > > >> >>>>>>> >> > > -- >> >>>>>>> >> > > View this message in context: >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>> >> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >> >>>>>>> >> > > Sent from the ITK Insight Users mailing list archive at >> >>>>>>> Nabble.com. >> >>>>>>> >> > > _____________________________________ >> >>>>>>> >> > > Powered by www.kitware.com >> >>>>>>> >> > > >> >>>>>>> >> > > Visit other Kitware open-source projects at >> >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >> >>>>>>> >> > > >> >>>>>>> >> > > Kitware offers ITK Training Courses, for more information >> >>>>>>> visit: >> >>>>>>> >> > > http://www.kitware.com/products/protraining.php >> >>>>>>> >> > > >> >>>>>>> >> > > Please keep messages on-topic and check the ITK FAQ at: >> >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >> >>>>>>> >> > > >> >>>>>>> >> > > Follow this link to subscribe/unsubscribe: >> >>>>>>> >> > > http://public.kitware.com/mailman/listinfo/insight-users >> >>>>>>> >> > _____________________________________ >> >>>>>>> >> > Powered by www.kitware.com >> >>>>>>> >> > >> >>>>>>> >> > Visit other Kitware open-source projects at >> >>>>>>> >> > http://www.kitware.com/opensource/opensource.html >> >>>>>>> >> > >> >>>>>>> >> > Kitware offers ITK Training Courses, for more information >> visit: >> >>>>>>> >> > http://www.kitware.com/products/protraining.php >> >>>>>>> >> > >> >>>>>>> >> > Please keep messages on-topic and check 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URL: -------------- next part -------------- /*========================================================================= * * Copyright Bradley Lowekamp * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0.txt * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * *=========================================================================*/ #ifndef __itkTextureFeatureImageFilterV2_hxx #define __itkTextureFeatureImageFilterV2_hxx #include "itkTextureFeatureImageFilterV2.h" #include "vnl/vnl_math.h" #include "itkNeighborhoodAlgorithm.h" #include "itkProgressReporter.h" #include "itkHistogramToTextureFeaturesFilter.h" namespace itk { namespace External { template< class TImageType, class TOutputImage> TextureFeatureImageFilterV2< TImageType, TOutputImage> ::TextureFeatureImageFilterV2() { this->SetNumberOfRequiredInputs(1); this->SetNumberOfRequiredOutputs(1); //this->m_GLCMGenerator = CooccurrenceMatrixFilterType::New(); //this->m_GLCMCalculator = TextureFeaturesFilterType::New(); //this->m_GLCMCalculator->SetInput( this->m_GLCMGenerator->GetOutput() ); this->m_Min = NumericTraits< PixelType >::NonpositiveMin(); this->m_Max = NumericTraits< PixelType >::max(); this->_insidePixelValue = 1; // Default value if not set manually this->m_NumberOfBinsPerAxis = DefaultBinsPerAxis; this->m_Normalize = false; m_WindowSize.Fill( 10 ); _maskImage = NULL; // Set the offset directions to their defaults: half of all the possible // directions 1 pixel away. (The other half is included by symmetry.) // We use a neighborhood iterator to calculate the appropriate offsets. /*typedef Neighborhood< typename InputImageType::PixelType, InputImageType::ImageDimension > NeighborhoodType; NeighborhoodType hood; hood.SetRadius(1); // select all "previous" neighbors that are face+edge+vertex // connected to the current pixel. do not include the center pixel. unsigned int centerIndex = hood.GetCenterNeighborhoodIndex(); OffsetType offset; OffsetVectorPointer offsets = OffsetVector::New(); for ( unsigned int d = 0; d < centerIndex; d++ ) { offset = hood.GetOffset(d); offsets->push_back(offset); } this->SetOffsets(offsets);*/ } template< class TImageType, class TOutputImage> void TextureFeatureImageFilterV2< TImageType, TOutputImage >::SetOffset(const OffsetType &offset) { OffsetVectorType offsetVector; offsetVector.push_back(offset); this->SetOffsets(offsetVector); } template< class TImageType, class TOutputImage> void TextureFeatureImageFilterV2< TImageType, TOutputImage>::SetPixelValueMinMax(PixelType min, PixelType max) { itkDebugMacro("setting Min to " << min << "and Max to " << max); m_Min = min; m_Max = max; //m_GLCMGenerator->SetPixelValueMinMax(min, max); this->Modified(); } template< class TImageType, class TOutputImage > void TextureFeatureImageFilterV2< TImageType, TOutputImage >::SetInput(InputImageType *image) { // Process object is not const-correct so the const_cast is required here this->ProcessObject::SetNthInput( 0, const_cast< InputImageType * >( image ) ); //m_GLCMGenerator->SetInput(image); } template< class TImageType, class TOutputImage > void TextureFeatureImageFilterV2< TImageType, TOutputImage >::SetMaskImage(InputImageType *image) { // Process object is not const-correct so the const_cast is required here this->ProcessObject::SetNthInput( 1, const_cast< InputImageType * >( image ) ); _maskImage = image; //m_GLCMGenerator->SetMaskImage(image); InputImageType *input = (InputImageType*) this->GetInput(); std::cout << "Scalar SubImage Origin: " << input->GetOrigin() << std::endl; std::cout << "Scalar SubImage Spacing: " << input->GetSpacing() << std::endl; std::cout << "Scalar SubImage Size: " << input->GetLargestPossibleRegion().GetSize() << std::endl; std::cout << "Binary SubImage Origin: " << _maskImage->GetOrigin() << std::endl; std::cout << "Binary SubImage Spacing: " << _maskImage->GetSpacing() << std::endl; std::cout << "Binary SubImage Size: " << _maskImage->GetLargestPossibleRegion().GetSize() << std::endl; } /*template< class TImageType, class TOutputImage > const InputImageType * TextureFeatureImageFilterV2< TImageType, TOutputImage >::GetMaskImage() const { return _maskImage; }*/ template< class TImageType, class TOutputImage > void TextureFeatureImageFilterV2< TImageType, TOutputImage >::SetInsidePixelValue(PixelType insidePixelValue) { itkDebugMacro("setting InsidePixelValue to " << insidePixelValue); _insidePixelValue = insidePixelValue; //m_GLCMGenerator->SetInsidePixelValue(insidePixelValue); this->Modified(); } template< class TImageType, class TOutputImage> void TextureFeatureImageFilterV2< TImageType, TOutputImage>::GenerateOutputInformation() { // this methods is overloaded so that if the output image is a // VectorImage then the correct number of components are set. Superclass::GenerateOutputInformation(); OutputImageType* output = this->GetOutput(); if ( !output ) { return; } if ( output->GetNumberOfComponentsPerPixel() != this->GetNumberOfOutputComponents() ) { output->SetNumberOfComponentsPerPixel( this->GetNumberOfOutputComponents() ); } } template< class TImageType, class TOutputImage> void TextureFeatureImageFilterV2< TImageType, TOutputImage>::BeforeThreadedGenerateData( ) { m_CooccurenceOffsetVector.clear(); OffsetType o1; OffsetType o2; // calculate all offsets pairs for( unsigned int i = 0; i < InputImageType::ImageDimension; ++i ) { o1[i] = -m_WindowSize[i]; } // iterate over all point in the window do { typename OffsetVectorType::const_iterator iter; for( iter = this->m_Offsets.begin(); iter != this->m_Offsets.end(); ++iter ) { o2 = o1 + *iter; bool ok = true; for( unsigned int i = 0; i < InputImageType::ImageDimension; ++i ) { if ( vcl_abs(o2[i]) > m_WindowSize[i]) { ok = false; break; } } if ( ok ) { m_CooccurenceOffsetVector.push_back( std::make_pair( o1, o2 ) ); //std::cout << "offset: " << o1 << " " << o2 << std::endl; itkDebugMacro("offset: " << o1 << " " << o2 << std::endl); } } // increment the offset 1 ++o1[0]; for( unsigned int i = 1; i < InputImageType::ImageDimension; ++i ) { if (o1[i-1] > static_cast(m_WindowSize[i-1]) ) { o1[i-1] = -m_WindowSize[i-1]; ++o1[i]; } } } while ( o1[InputImageType::ImageDimension-1] <= static_cast(m_WindowSize[InputImageType::ImageDimension-1]) ); } template< class TImageType, class TOutputImage> void TextureFeatureImageFilterV2< TImageType, TOutputImage> ::ThreadedGenerateData(const RegionType& outputRegionForThread, ThreadIdType threadId ) { InputImageType *input = (InputImageType*) this->GetInput(); if ( _maskImage == NULL ) { _maskImage = input; } std::cout << "input: " << input << std::endl; std::cout << "_maskImage: " << _maskImage << std::endl; OutputImageType *output = this->GetOutput(); // constant for a coocurrence matrix. const unsigned int measurementVectorSize = 2; // // Create Histogram // typename HistogramType::Pointer histogram = HistogramType::New(); histogram->SetMeasurementVectorSize(measurementVectorSize); //initialize parameters MeasurementVectorType lowerBound(measurementVectorSize); MeasurementVectorType upperBound(measurementVectorSize); lowerBound.Fill( this->GetMin() ); upperBound.Fill( this->GetMax() +1 ); // First, create an appropriate histogram with the right number of bins // and mins and maxs correct for the image type. typename HistogramType::SizeType size( histogram->GetMeasurementVectorSize() ); size.Fill(m_NumberOfBinsPerAxis); histogram->Initialize(size, lowerBound, upperBound); typedef Statistics::HistogramToTextureFeaturesFilter FeatureFilterType; typename FeatureFilterType::Pointer featureFilter = FeatureFilterType::New(); // support progress methods/callbacks ProgressReporter progress(this, threadId, outputRegionForThread.GetNumberOfPixels()); typedef ImageRegionIterator OutputIterator; typedef itk::ConstNeighborhoodIterator< InputImageType > NeighborhoodIteratorType; typename NeighborhoodIteratorType::RadiusType radius = m_WindowSize; typedef itk::NeighborhoodAlgorithm::ImageBoundaryFacesCalculator< InputImageType > FaceCalculatorType; FaceCalculatorType faceCalculator; typename FaceCalculatorType::FaceListType faceList; typename FaceCalculatorType::FaceListType::iterator fit; faceList = faceCalculator( input, outputRegionForThread, radius ); for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) { NeighborhoodIteratorType nIter( radius, input, *fit ); NeighborhoodIteratorType maskIter( radius, _maskImage, *fit); OutputIterator outIter(output, *fit); OutputPixelType out; NumericTraits::SetLength( out, this->GetNumberOfOutputComponents() ); while( !nIter.IsAtEnd() ) { this->FillHistogram( *histogram, nIter, maskIter ); featureFilter->SetInput( histogram ); featureFilter->Modified(); featureFilter->Update(); out[0] = featureFilter->GetEnergy(); out[1] = featureFilter->GetEntropy(); out[2] = featureFilter->GetCorrelation(); out[3] = featureFilter->GetInverseDifferenceMoment(); out[4] = featureFilter->GetInertia(); out[5] = featureFilter->GetClusterShade(); out[6] = featureFilter->GetClusterProminence(); out[7] = featureFilter->GetHaralickCorrelation(); outIter.Set( out ); histogram->SetToZero(); ++nIter; ++outIter; ++maskIter; progress.CompletedPixel(); } } } template< class TImageType, class TOutputImage> void TextureFeatureImageFilterV2< TImageType, TOutputImage> ::FillHistogram( HistogramType &histogram, const itk::ConstNeighborhoodIterator< InputImageType > &niter, const itk::ConstNeighborhoodIterator &maskIter) const { MeasurementVectorType cooccur( histogram.GetMeasurementVectorSize() ); typename std::vector >::const_iterator iter = m_CooccurenceOffsetVector.begin(); while( iter != m_CooccurenceOffsetVector.end() ) { std::cout << "iter.first: " << iter->first << " iter.second: " << iter->second << std::endl; std::cout << "niter index: " << niter.GetIndex() << std::endl; std::cout << "maskIter index: " << maskIter.GetIndex() << std::endl; const PixelType p1 = niter.GetPixel(iter->first); const PixelType p2 = niter.GetPixel(iter->second); std::cout << "Before p3" << std::endl; const PixelType p3 = maskIter.GetPixel(iter->first); std::cout << "After p3: " << p3 << std::endl; const PixelType p4 = maskIter.GetPixel(iter->second); std::cout << "After p4: " << p4 << std::endl; /*const PixelType p3 = _insidePixelValue; const PixelType p4 = _insidePixelValue;*/ if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= m_Max && p3 == _insidePixelValue && p4 == _insidePixelValue ) // The point belongs to the mask { cooccur[0] = p1; cooccur[1] = p2; histogram.IncreaseFrequencyOfMeasurement(cooccur, 1.0 ); cooccur[1] = p1; cooccur[0] = p2; histogram.IncreaseFrequencyOfMeasurement(cooccur, 1.0 ); } ++iter; } } template< class TImageType, class TOutputImage> void TextureFeatureImageFilterV2< TImageType, TOutputImage> ::PrintSelf(std::ostream & os, Indent indent) const { Superclass::PrintSelf(os, indent); //fixme // os << indent << "Offsets: " << this->GetOffsets() << std::endl; os << indent << "Min: " << this->GetMin() << std::endl; os << indent << "Max: " << this->GetMax() << std::endl; os << indent << "NumberOfBinsPerAxis: " << this->GetNumberOfBinsPerAxis() << std::endl; os << indent << "Normalize: " << this->GetNormalize() << std::endl; } } // end of namespace External } // end of namespace itk #endif template class itk::External::TextureFeatureImageFilterV2, itk::VectorImage< float, 2 > >; template class itk::External::TextureFeatureImageFilterV2, itk::VectorImage< float, 3 > >; template class itk::External::TextureFeatureImageFilterV2, itk::VectorImage< float, 2 > >; template class itk::External::TextureFeatureImageFilterV2, itk::VectorImage< float, 3 > >; template class itk::External::TextureFeatureImageFilterV2, itk::VectorImage< float, 2 > >; template class itk::External::TextureFeatureImageFilterV2, itk::VectorImage< float, 3 > >; -------------- next part -------------- A non-text attachment was scrubbed... Name: itkTextureFeatureImageFilterv2.h Type: text/x-chdr Size: 7265 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Mon Feb 15 01:36:35 2016 From: franciscolopezdelafranca at gmail.com (=?UTF-8?Q?Francisco_L=C3=B3pez-Franca?=) Date: Sun, 14 Feb 2016 23:36:35 -0700 (MST) Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <84A225AE-400C-4FBA-97FA-6A027CB17208@mail.nih.gov> Message-ID: Hi, Here they are. KR. 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] < ml-node+s2283740n7588490h25 at n2.nabble.com>: > Hi Francisco, > > do you mind attaching the modified files or pointing to your fork of it on > GitHub? > > Regards > > On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden email] > > wrote: > >> Hi Dzenan, >> The original class is here: >> >> >> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >> >> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >> >> I've just added setInput and setMaskImage methods and modify some lines in >> the original class as I indicated in the yesterday mail within this >> thread. >> I'm running it on Windows, and there is no error at all, just a crash. I >> may have to include exceptions management. >> The crash occurs just when calling p3 = maskIter.GetPixel(iter->first) >> >> If you know why it could be or if you need more clarification, please let >> me know. >> Many thanks >> >> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >> [hidden email] >: >> >> > Hi Francisco, >> > >> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the error >> message >> > that goes along with the crash? In which file and line does it crash? >> > >> > Regards >> > >> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca <[hidden >> > email] > wrote: >> > >> >> Hi, >> >> Please, someone that could help me. I'm working in a pre-doctorate >> >> project and I need this class to work. >> >> I've read the chapter 13 in the ITK Software Guide on how to write a >> >> filter and now I see the fact of the threads due to inheritance of >> >> ImageToImageFilter. >> >> But, I keep on without understanding why the code crashes just when >> >> calling >> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >> >> It is just a call to read data, not to write. >> >> >> >> I guess somebody that had worked with creation of filters might see >> >> "easily" the problem, but not me. >> >> >> >> So, again, please, I need someone to help me with this because I'm >> stuck >> >> on this point. >> >> >> >> Thank you very much. >> >> KR. >> >> /Francisco >> >> >> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden email] >> >> >: >> >> >> >>> Hi Bradley again. >> >>> I'm modifying your class in order to be able to set a mask image (a >> >>> binary image) to be used as a limit in the histogram calculations, I >> mean, >> >>> I set an input, a mask and the class should take into account to >> calculate >> >>> the histograms only the voxels that belong to the input and to the >> mask >> >>> image and having the value 1 in the mask image. >> >>> The changes seem to be easy but I don?t know why my tests are not >> >>> working. It seems that 2 threads are working at the same time and >> when I >> >>> added my mask iterator, the code crashes. >> >>> >> >>> *** Consider that the input and mask images are the same origin, >> spacing >> >>> and size. >> >>> >> >>> I attach the main changes I've done, and I would thank you a lot if >> you >> >>> don't mind having a look and help me to find what I'm doing wrong: >> >>> >> >>> template< class TImageType, class TOutputImage > >> >>> void >> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >> >::*SetInput*(InputImageType >> >>> *image) >> >>> { >> >>> // Process object is not const-correct so the const_cast is required >> >>> here >> >>> this->ProcessObject::SetNthInput( 0, >> >>> const_cast< InputImageType * >( >> >>> image ) ); >> >>> } >> >>> >> >>> template< class TImageType, class TOutputImage > >> >>> void >> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >> >::*SetMaskImage*(InputImageType >> >>> *image) >> >>> { >> >>> // Process object is not const-correct so the const_cast is required >> >>> here >> >>> this->ProcessObject::SetNthInput( 1, const_cast< InputImageType * >( >> >>> image ) ); >> >>> >> >>> _maskImage = image; // _maskImage is a private member >> >>> } >> >>> >> >>> In the *ThreadedGenerateData*(const RegionType& outputRegionForThread, >> >>> ThreadIdType threadId ) method: >> >>> { >> >>> >> >>> ... >> >>> >> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >> >>> { >> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, *fit);* >> >>> OutputIterator outIter(output, *fit); >> >>> >> >>> OutputPixelType out; >> >>> NumericTraits::SetLength( out, >> >>> this->GetNumberOfOutputComponents() ); >> >>> >> >>> while( !nIter.IsAtEnd() ) >> >>> { >> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >> >>> >> >>> ... >> >>> >> >>> ++nIter; >> >>> ++outIter; >> >>> * ++maskIter;* >> >>> ... >> >>> >> >>> In the *FillHistogram *method: >> >>> { >> >>> >> >>> ... >> >>> >> >>> while( iter != m_CooccurenceOffsetVector.end() ) >> >>> { >> >>> >> >>> const PixelType p1 = niter.GetPixel(iter->first); >> >>> const PixelType p2 = niter.GetPixel(iter->second); >> >>> std::cout << "Before p3" << std::endl; >> >>> >> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); >> *std::cout >> >>> << "After p3: " << p3 << std::endl; >> >>> >> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >> >>> std::cout << "After p4: " << p4 << std::endl; >> >>> >> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= m_Max >> >>> *&& p3 == _insidePixelValue && p4 == _insidePixelValue* ) >> >>> // The point >> >>> { >> >>> >> >>> ... >> >>> >> >>> >> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >> >>> >> >>> Thank you so much. >> >>> My kind regards. >> >>> /Paco >> >>> >> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca <[hidden >> email] >> >>> >: >> >>> >> >>>> Hello Bradley again. >> >>>> Sorry but I'd like to re-open this issue because I need your class >> but >> >>>> with some modification. >> >>>> I pass to tell you. >> >>>> >> >>>> As my tests with your external class were not good taking into >> account >> >>>> the performance, I wonder if you could create a variant of it, but >> in which >> >>>> I can set a mask image and your class just return the VectorImage >> with all >> >>>> the features for that region (the masked locations) as >> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >> >>>> I mean, to get the vector image with all the features but just >> >>>> calculate it for the regions belonging to the mask image. Positions >> not >> >>>> belonging to the mask region could have a pixel value of 0, for >> instance. >> >>>> >> >>>> I don?t know if it is very costly for you, but I would thank you so >> >>>> much. Otherwise, I could try it but I'd need your suggestions on how >> to do >> >>>> it. >> >>>> >> >>>> Thanks a lot. >> >>>> Best regards. >> >>>> >> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca <[hidden >> email] >> >>>> >: >> >>>> >> >>>>> Hello Bradley again, >> >>>>> I would like to ask you for a couple of favours. In the one hand, >> >>>>> could you please send me your 3D image so that I can test on it? >> And on the >> >>>>> other hand, could you test the example I have referenced in the >> previous >> >>>>> email with your image, not changing anything in the code, such as >> it is, >> >>>>> and tell me if the execution time is normal? >> >>>>> Thank you very much. >> >>>>> Regards, >> >>>>> /Francisco >> >>>>> >> >>>>> PS: All my application trace is printed via standard 'cout' command, >> >>>>> not due to a debugging compilation mode. >> >>>>> >> >>>>> >> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp <[hidden >> >>>>> email] > >> >>>>> escribi?: >> >>>>> >> >>>>>> Hello, >> >>>>>> >> >>>>>> Did you compile TextureFeatureImage in Release mode? >> >>>>>> >> >>>>>> 1) The filter does not scale well with a large radius. And given by >> >>>>>> your initial report of print a very large number of offset you, it >> sounds >> >>>>>> like you are using a large radius with many offsets. I created a >> >>>>>> 224x224x300 unsigned short image and ran with the default offset >> and a >> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this filter is >> was ~10x >> >>>>>> faster than this example... things change though... >> >>>>>> >> >>>>>> >> >>>>>> 2) I sounds like the boundaries/limits of the histogram may be >> >>>>>> clipping you values. I would inspect the co-occurance matrix. >> >>>>>> >> >>>>>> >> >>>>>> HTH, >> >>>>>> Brad >> >>>>>> >> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca <[hidden >> >>>>>> email] > >> >>>>>> wrote: >> >>>>>> >> >>>>>> I've tested with itkTextureFeatureImageFilter, with >> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >> >>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures >> example, >> >>>>>> for a 3D image and here are my comments: >> >>>>>> >> >>>>>> >> >>>>>> 1. I had to interrupt the test after several hours and it kept on >> >>>>>> calculating. And this is for only a 3D image (224x224x300). I need >> to >> >>>>>> process around 35 images. >> >>>>>> 2. The result (texture features: entropy, energy, correlation, LH, >> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, >> 7.83083e+247]. >> >>>>>> These values were not what I expected based on my experience on >> another >> >>>>>> application I developed, but in that case, I calculated the texture >> >>>>>> features for an image as a whole, not voxel by voxel. >> >>>>>> >> >>>>>> Regards. >> >>>>>> >> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >> >>>>>> >: >> >>>>>> >> >>>>>>> i yes i have tried radius = 3; >> >>>>>>> still no luck >> >>>>>>> >> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via ITK >> >>>>>>> Insight >> >>>>>>> Users] <[hidden email] >> >>>>>>> > wrote: >> >>>>>>> >> >>>>>>> > Have you tried with a radius of 3 instead of 1? >> >>>>>>> > >> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >> >>>>>>> > >: >> >>>>>>> > >> >>>>>>> >> hey Matt, >> >>>>>>> >> thanks for ur advice.. it did build successfully... but im not >> >>>>>>> able to run >> >>>>>>> >> the code for 2D png image... i tried to change the dimension >> to 2 >> >>>>>>> and >> >>>>>>> >> build >> >>>>>>> >> it which it did.. but when i run the code using the command >> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png putput.png >> >>>>>>> 1... i see >> >>>>>>> >> this output >> >>>>>>> >> >> >>>>>>> >> offset: [-1, -1] [0, -1] >> >>>>>>> >> offset: [0, -1] [1, -1] >> >>>>>>> >> offset: [-1, 0] [0, 0] >> >>>>>>> >> offset: [0, 0] [1, 0] >> >>>>>>> >> offset: [-1, 1] [0, 1] >> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... if >> pls >> >>>>>>> tel me >> >>>>>>> >> how can i modify this code to work wid 2d image... forgive me >> if >> >>>>>>> my ques >> >>>>>>> >> are really silly im trying to learn something.. >> >>>>>>> >> regards >> >>>>>>> >> Vis >> >>>>>>> >> >> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK >> >>>>>>> Insight Users] >> >>>>>>> >> < >> >>>>>>> >> [hidden email] < >> >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >> >>>>>>> >> wrote: >> >>>>>>> >> >> >>>>>>> >> > Hi, >> >>>>>>> >> > >> >>>>>>> >> > The function: >> >>>>>>> >> > >> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char *argv[]) >> >>>>>>> >> > >> >>>>>>> >> > must be renamed to >> >>>>>>> >> > >> >>>>>>> >> > main(int argc, char* argv[]) >> >>>>>>> >> > >> >>>>>>> >> > HTH, >> >>>>>>> >> > Matt >> >>>>>>> >> > >> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >> >>>>>>> >> > > >> wrote: >> >>>>>>> >> > >> >>>>>>> >> > > hi all, >> >>>>>>> >> > > im trying to build the itkTextureFeatureImageFilterTest.cxx >> >>>>>>> code but >> >>>>>>> >> im >> >>>>>>> >> > not >> >>>>>>> >> > > able to it is showing the following error >> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >> >>>>>>> Configuration: >> >>>>>>> >> Debug >> >>>>>>> >> > x64 >> >>>>>>> >> > > ------ >> >>>>>>> >> > > 1> Checking Build System >> >>>>>>> >> > > 1> CMake does not need to re-run because >> >>>>>>> >> > > >> >>>>>>> >> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >> >>>>>>> >> > is >> >>>>>>> >> > > up-to-date. >> >>>>>>> >> > > 2>------ Rebuild All started: Project: >> >>>>>>> >> itkTextureFeatureImageFilterTest, >> >>>>>>> >> > > Configuration: Debug x64 ------ >> >>>>>>> >> > > 2> Building Custom Rule >> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >> >>>>>>> >> > > 2> CMake does not need to re-run because >> >>>>>>> >> > > >> >>>>>>> >> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >> >>>>>>> >> > is >> >>>>>>> >> > > up-to-date. >> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >> >>>>>>> 'std::_Copy_impl': >> >>>>>>> >> > Function >> >>>>>>> >> > > call with parameters that may be unsafe - this call relies >> on >> >>>>>>> the >> >>>>>>> >> caller >> >>>>>>> >> > to >> >>>>>>> >> > > check that the passed values are correct. To disable this >> >>>>>>> warning, use >> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to use >> >>>>>>> Visual C++ >> >>>>>>> >> > > 'Checked Iterators' >> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >> >>>>>>> 'std::_Copy_impl' >> >>>>>>> >> > > 2> >> >>>>>>> >> > > >> >>>>>>> >> >> >>>>>>> >> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >> >>>>>>> >> > see >> >>>>>>> >> > > reference to function template instantiation '_OutIt >> >>>>>>> std::copy> >>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' being >> >>>>>>> compiled >> >>>>>>> >> > > 2> with >> >>>>>>> >> > > 2> [ >> >>>>>>> >> > > 2> _OutIt=unsigned char *, >> >>>>>>> >> > > 2> _InIt=const unsigned char * >> >>>>>>> >> > > 2> ] >> >>>>>>> >> > > 2> >> >>>>>>> >> > > >> >>>>>>> >> >> >>>>>>> >> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >> >>>>>>> >> > > while compiling class template member function 'void >> >>>>>>> >> > > itk::ImageFileReader::GenerateData(void)' >> >>>>>>> >> > > 2> with >> >>>>>>> >> > > 2> [ >> >>>>>>> >> > > 2> TOutputImage=InputImageType >> >>>>>>> >> > > 2> ] >> >>>>>>> >> > > 2> >> >>>>>>> >> > > >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>> >> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >> >>>>>>> >> > >> >>>>>>> >> > > : see reference to class template instantiation >> >>>>>>> >> > > 'itk::ImageFileReader' being compiled >> >>>>>>> >> > > 2> with >> >>>>>>> >> > > 2> [ >> >>>>>>> >> > > 2> TOutputImage=InputImageType >> >>>>>>> >> > > 2> ] >> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >> >>>>>>> 'std::_Copy_impl' >> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >> >>>>>>> 'std::_Copy_impl' >> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >> >>>>>>> 'std::_Copy_impl' >> >>>>>>> >> > > 2> Creating library >> >>>>>>> >> > > >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>> >> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >> >>>>>>> >> > >> >>>>>>> >> > > and object >> >>>>>>> >> > > >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>> >> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >> >>>>>>> >> > >> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved >> >>>>>>> external symbol >> >>>>>>> >> > main >> >>>>>>> >> > > referenced in function __tmainCRTStartup >> >>>>>>> >> > > >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>> >> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >> >>>>>>> >> > >> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >> >>>>>>> Configuration: Debug >> >>>>>>> >> > x64 >> >>>>>>> >> > > ------ >> >>>>>>> >> > > 3> Building Custom Rule >> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >> >>>>>>> >> > > 3> CMake does not need to re-run because >> >>>>>>> >> > > >> >>>>>>> >> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >> >>>>>>> >> > is >> >>>>>>> >> > > up-to-date. >> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 skipped >> >>>>>>> ========== >> >>>>>>> >> > > im using the follwing CMakeList.txt >> >>>>>>> >> > > # This is the root ITK CMakeLists file. >> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >> >>>>>>> >> > > endif() >> >>>>>>> >> > > >> >>>>>>> >> > > >> >>>>>>> >> > > # This project is designed to be built outside the Insight >> >>>>>>> source >> >>>>>>> >> tree. >> >>>>>>> >> > > project(HelloWorld) >> >>>>>>> >> > > >> >>>>>>> >> > > # Find ITK. >> >>>>>>> >> > > find_package(ITK REQUIRED) >> >>>>>>> >> > > include(${ITK_USE_FILE}) >> >>>>>>> >> > > >> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >> >>>>>>> >> > > >> >>>>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest >> >>>>>>> >> ${ITK_LIBRARIES}) >> >>>>>>> >> > > >> >>>>>>> >> > > please tel me wat the error is?? >> >>>>>>> >> > > >> >>>>>>> >> > > >> >>>>>>> >> > > >> >>>>>>> >> > > -- >> >>>>>>> >> > > View this message in context: >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>> >> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >> >>>>>>> >> > > Sent from the ITK Insight Users mailing list archive at >> >>>>>>> Nabble.com. >> >>>>>>> >> > > _____________________________________ >> >>>>>>> >> > > Powered by www.kitware.com >> >>>>>>> >> > > >> >>>>>>> >> > > Visit other Kitware open-source projects at >> >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >> >>>>>>> >> > > >> >>>>>>> >> > > Kitware offers ITK Training Courses, for more information >> >>>>>>> visit: >> >>>>>>> >> > > http://www.kitware.com/products/protraining.php >> >>>>>>> >> > > >> >>>>>>> >> > > Please keep messages on-topic and check the ITK FAQ at: >> >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >> >>>>>>> >> > > >> >>>>>>> >> > > Follow this link to subscribe/unsubscribe: >> >>>>>>> >> > > http://public.kitware.com/mailman/listinfo/insight-users >> >>>>>>> >> > _____________________________________ >> >>>>>>> >> > Powered by www.kitware.com >> >>>>>>> >> > >> >>>>>>> >> > Visit other Kitware open-source projects at >> >>>>>>> >> > http://www.kitware.com/opensource/opensource.html >> >>>>>>> >> > >> >>>>>>> >> > Kitware offers ITK Training Courses, for more information >> visit: >> >>>>>>> >> > http://www.kitware.com/products/protraining.php >> >>>>>>> >> > >> >>>>>>> >> > Please keep messages on-topic and check the ITK FAQ at: >> >>>>>>> >> > http://www.itk.org/Wiki/ITK_FAQ >> >>>>>>> >> > >> >>>>>>> >> > Follow this link to subscribe/unsubscribe: >> >>>>>>> >> > http://public.kitware.com/mailman/listinfo/insight-users >> >>>>>>> >> > >> >>>>>>> >> > >> >>>>>>> >> > ------------------------------ >> >>>>>>> >> > If you reply to this email, your message will be added to the >> >>>>>>> discussion >> >>>>>>> >> > below: >> >>>>>>> >> > >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>> >> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587952.html >> >>>>>>> >> > To unsubscribe from [ITK-users] Texture pixel by pixel, click >> >>>>>>> here >> >>>>>>> >> > < > . >> >>>>>>> >> > NAML >> >>>>>>> >> > < >> >>>>>>> >> >> >>>>>>> >> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >> >>>>>>> >> > >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>> >> >> >>>>>>> >> >> >>>>>>> >> >> >>>>>>> >> -- >> >>>>>>> >> View this message in context: >> >>>>>>> >> >> >>>>>>> >> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587960.html >> >>>>>>> >> Sent from the ITK Insight Users mailing list archive at >> >>>>>>> Nabble.com. >> >>>>>>> >> _____________________________________ >> >>>>>>> >> Powered by www.kitware.com >> >>>>>>> >> >> >>>>>>> >> Visit other Kitware open-source projects at >> >>>>>>> >> http://www.kitware.com/opensource/opensource.html >> >>>>>>> >> >> >>>>>>> >> Kitware offers ITK Training Courses, for more information >> visit: >> >>>>>>> >> http://www.kitware.com/products/protraining.php >> >>>>>>> >> >> >>>>>>> >> Please keep messages on-topic and check the ITK FAQ at: >> >>>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >> >>>>>>> >> >> >>>>>>> >> Follow this link to subscribe/unsubscribe: >> >>>>>>> >> http://public.kitware.com/mailman/listinfo/insight-users >> >>>>>>> >> >> >>>>>>> > >> >>>>>>> > >> >>>>>>> > _____________________________________ >> >>>>>>> > Powered by www.kitware.com >> >>>>>>> > >> >>>>>>> > Visit other Kitware open-source projects at >> >>>>>>> > http://www.kitware.com/opensource/opensource.html >> >>>>>>> > >> >>>>>>> > Kitware offers ITK Training Courses, for more information visit: >> >>>>>>> > http://www.kitware.com/products/protraining.php >> >>>>>>> > >> >>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >> >>>>>>> > http://www.itk.org/Wiki/ITK_FAQ >> >>>>>>> > >> >>>>>>> > Follow this link to subscribe/unsubscribe: >> >>>>>>> > http://public.kitware.com/mailman/listinfo/insight-users >> >>>>>>> > >> >>>>>>> > >> >>>>>>> > ------------------------------ >> >>>>>>> > If you reply to this email, your message will be added to the >> >>>>>>> discussion >> >>>>>>> > below: >> >>>>>>> > >> >>>>>>> > >> >>>>>>> >> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587961.html >> >>>>>>> > To unsubscribe from [ITK-users] Texture pixel by pixel, click >> here >> >>>>>>> > < > . >> >>>>>>> > NAML >> >>>>>>> > < >> >>>>>>> >> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >> >>>>>>> > >> >>>>>>> > >> >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> -- >> >>>>>>> View this message in context: >> >>>>>>> >> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587963.html >> >>>>>>> Sent from the ITK Insight Users mailing list archive at >> Nabble.com. >> >>>>>>> _____________________________________ >> >>>>>>> Powered by www.kitware.com >> >>>>>>> >> >>>>>>> Visit other Kitware open-source projects at >> >>>>>>> http://www.kitware.com/opensource/opensource.html >> >>>>>>> >> >>>>>>> Kitware offers ITK Training Courses, for more information visit: >> >>>>>>> http://www.kitware.com/products/protraining.php >> >>>>>>> >> >>>>>>> Please keep messages on-topic and check the ITK FAQ at: >> >>>>>>> http://www.itk.org/Wiki/ITK_FAQ >> >>>>>>> >> >>>>>>> Follow this link to subscribe/unsubscribe: >> >>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >> >>>>>>> >> >>>>>> >> >>>>>> _____________________________________ >> >>>>>> Powered by www.kitware.com >> >>>>>> >> >>>>>> Visit other Kitware open-source projects at >> >>>>>> http://www.kitware.com/opensource/opensource.html >> >>>>>> >> >>>>>> Kitware offers ITK Training Courses, for more information visit: >> >>>>>> http://www.kitware.com/products/protraining.php >> >>>>>> >> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >> >>>>>> http://www.itk.org/Wiki/ITK_FAQ >> >>>>>> >> >>>>>> Follow this link to subscribe/unsubscribe: >> >>>>>> 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keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-users >> > >> > >> > ------------------------------ >> > If you reply to this email, your message will be added to the discussion >> > below: >> > >> > >> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588477.html >> > To start a new topic under ITK Insight Users, email >> > [hidden email] >> > To unsubscribe from ITK Insight Users, click here >> > < > . >> > NAML >> > < >> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >> > >> > >> >> >> >> >> -- >> View this message in context: >> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588483.html >> Sent from the ITK Insight Users mailing list archive at Nabble.com. >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588490.html > To start a new topic under ITK Insight Users, email > ml-node+s2283740n2283740h75 at n2.nabble.com > To unsubscribe from ITK Insight Users, click here > > . > NAML > > itkTextureFeatureImageFilterv2.cxx (18K) itkTextureFeatureImageFilterv2.h (9K) -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588494.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From b.naegel at unistra.fr Mon Feb 15 03:24:28 2016 From: b.naegel at unistra.fr (=?UTF-8?Q?Beno=c3=aet_Naegel?=) Date: Mon, 15 Feb 2016 09:24:28 +0100 Subject: [ITK] Post-doc position Message-ID: <56C18B3C.8000207@unistra.fr> Hi, A post-doc position (12 months, starting as soon as possible) is available at ICube Laboratory in University of Strasbourg, France. This position is funded by the ANR project VIVABRAIN (virtual angiography simulation from 3D and 3D+t brain vascular model; http://vivabrain.fr). The VIVABRAIN project aims to develop a full methodological and software pipeline for Magnetic Resonance Angiography (MRA) simulation from real 3D acquisitions. These research works, initiated in 2013, are based on a pluri- and interdisciplinary collaboration between French research labs in Computer Science, Mathematics, Physics and Medicine. They also involve Kitware, the world leader of open-source software for medical imaging. The purpose of this position is to develop innovative methods and tools for tackling the following issues: * 3D angiographic image registration; * vascular atlas generation design; * semi-automated 3D vascular model generation. These works will be carried out in interaction with other PhD students, researchers and developers involved in the project. The recruited candidate must have a PhD in Computer Science (or, alternatively, in Image or Signal Processing). From a methodological point of view, he/she should have a strong expertise in image processing and optimization, especially in medical imaging. He/she should also have high skills in software development, especially in Python, C++ and ITK. The post-doctoral fellowship will start as soon as possible in 2016. Its duration will be 12 months. We invite you to contact Beno?t Naegel (b.naegel at unistra.fr) and Vincent Noblet (vincent.noblet at unistra.fr) for any complementary information. Regards, Beno?t Naegel -- Beno?t Naegel Assistant Professor in Computer Science - Strasbourg University ICube Laboratory UMR 7357, Team "Mod?les, Images et Vision" http://icube-miv.unistra.fr/en/index.php/Beno%C3%AEt_Naegel -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Mon Feb 15 11:14:22 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 15 Feb 2016 11:14:22 -0500 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <84A225AE-400C-4FBA-97FA-6A027CB17208@mail.nih.gov> Message-ID: Hi Francisco, both your code and Brad's code run in debug mode (I did not wait for the end), and both crash in release mode immediately on startup. Here is a sample output: Progress input: 0000000002868970 input: 0000000002868970 _maskImage: 0000000002868970 _maskImage: 0000000002868970 input: 0000000002868970 _maskImage: 0000000002868970 iter.first: iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] [-5, -5, -5] iter.second: [-4, -5, -5] niter index: [5, 5, 210] niter index: [5, 5, 140] maskIter index: [5, 5, 140] maskIter index: [5, 5, 210] Before p3 input: 0000000002868970 _maskImage: 0000000002868970 After p3: | 0niter index: [5, 5, 70] iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] niter index: [5, 5, 5] ? maskIter index: [5, 5, 70] After p4: ? Before p3 Before p3 After p3: ?iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] niter index: [5, 5, 140] maskIter index: [5, 5, 140] maskIter index: [5, 5, 5] Before p3 After p3: ? After p3: ? After p4: ? After p4: ? iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] niter index: [5, 5, 5] maskIter index: [5, 5, 5] iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] Before p3 Before p3 After p4: ? After p3: ? After p4: ? Regards, D?enan On Mon, Feb 15, 2016 at 1:36 AM, Francisco Lopez de la Franca < franciscolopezdelafranca at gmail.com> wrote: > Hi, > Here they are. > KR. > > 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] < > ml-node+s2283740n7588490h25 at n2.nabble.com>: > >> Hi Francisco, >> >> do you mind attaching the modified files or pointing to your fork of it >> on GitHub? >> >> Regards >> >> On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden email] >> > wrote: >> >>> Hi Dzenan, >>> The original class is here: >>> >>> >>> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >>> >>> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >>> >>> I've just added setInput and setMaskImage methods and modify some lines >>> in >>> the original class as I indicated in the yesterday mail within this >>> thread. >>> I'm running it on Windows, and there is no error at all, just a crash. I >>> may have to include exceptions management. >>> The crash occurs just when calling p3 = maskIter.GetPixel(iter->first) >>> >>> If you know why it could be or if you need more clarification, please let >>> me know. >>> Many thanks >>> >>> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >>> [hidden email] >: >>> >>> > Hi Francisco, >>> > >>> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the error >>> message >>> > that goes along with the crash? In which file and line does it crash? >>> > >>> > Regards >>> > >>> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca <[hidden >>> > email] > wrote: >>> > >>> >> Hi, >>> >> Please, someone that could help me. I'm working in a pre-doctorate >>> >> project and I need this class to work. >>> >> I've read the chapter 13 in the ITK Software Guide on how to write a >>> >> filter and now I see the fact of the threads due to inheritance of >>> >> ImageToImageFilter. >>> >> But, I keep on without understanding why the code crashes just when >>> >> calling >>> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >>> >> It is just a call to read data, not to write. >>> >> >>> >> I guess somebody that had worked with creation of filters might see >>> >> "easily" the problem, but not me. >>> >> >>> >> So, again, please, I need someone to help me with this because I'm >>> stuck >>> >> on this point. >>> >> >>> >> Thank you very much. >>> >> KR. >>> >> /Francisco >>> >> >>> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden >>> email] >>> >> >: >>> >> >>> >>> Hi Bradley again. >>> >>> I'm modifying your class in order to be able to set a mask image (a >>> >>> binary image) to be used as a limit in the histogram calculations, I >>> mean, >>> >>> I set an input, a mask and the class should take into account to >>> calculate >>> >>> the histograms only the voxels that belong to the input and to the >>> mask >>> >>> image and having the value 1 in the mask image. >>> >>> The changes seem to be easy but I don?t know why my tests are not >>> >>> working. It seems that 2 threads are working at the same time and >>> when I >>> >>> added my mask iterator, the code crashes. >>> >>> >>> >>> *** Consider that the input and mask images are the same origin, >>> spacing >>> >>> and size. >>> >>> >>> >>> I attach the main changes I've done, and I would thank you a lot if >>> you >>> >>> don't mind having a look and help me to find what I'm doing wrong: >>> >>> >>> >>> template< class TImageType, class TOutputImage > >>> >>> void >>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>> >::*SetInput*(InputImageType >>> >>> *image) >>> >>> { >>> >>> // Process object is not const-correct so the const_cast is >>> required >>> >>> here >>> >>> this->ProcessObject::SetNthInput( 0, >>> >>> const_cast< InputImageType * >( >>> >>> image ) ); >>> >>> } >>> >>> >>> >>> template< class TImageType, class TOutputImage > >>> >>> void >>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>> >::*SetMaskImage*(InputImageType >>> >>> *image) >>> >>> { >>> >>> // Process object is not const-correct so the const_cast is >>> required >>> >>> here >>> >>> this->ProcessObject::SetNthInput( 1, const_cast< InputImageType * >>> >( >>> >>> image ) ); >>> >>> >>> >>> _maskImage = image; // _maskImage is a private member >>> >>> } >>> >>> >>> >>> In the *ThreadedGenerateData*(const RegionType& >>> outputRegionForThread, >>> >>> ThreadIdType threadId ) method: >>> >>> { >>> >>> >>> >>> ... >>> >>> >>> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >>> >>> { >>> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >>> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, *fit);* >>> >>> OutputIterator outIter(output, *fit); >>> >>> >>> >>> OutputPixelType out; >>> >>> NumericTraits::SetLength( out, >>> >>> this->GetNumberOfOutputComponents() ); >>> >>> >>> >>> while( !nIter.IsAtEnd() ) >>> >>> { >>> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >>> >>> >>> >>> ... >>> >>> >>> >>> ++nIter; >>> >>> ++outIter; >>> >>> * ++maskIter;* >>> >>> ... >>> >>> >>> >>> In the *FillHistogram *method: >>> >>> { >>> >>> >>> >>> ... >>> >>> >>> >>> while( iter != m_CooccurenceOffsetVector.end() ) >>> >>> { >>> >>> >>> >>> const PixelType p1 = niter.GetPixel(iter->first); >>> >>> const PixelType p2 = niter.GetPixel(iter->second); >>> >>> std::cout << "Before p3" << std::endl; >>> >>> >>> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); >>> *std::cout >>> >>> << "After p3: " << p3 << std::endl; >>> >>> >>> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >>> >>> std::cout << "After p4: " << p4 << std::endl; >>> >>> >>> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= m_Max >>> >>> *&& p3 == _insidePixelValue && p4 == _insidePixelValue* ) >>> >>> // The point >>> >>> { >>> >>> >>> >>> ... >>> >>> >>> >>> >>> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >>> >>> >>> >>> Thank you so much. >>> >>> My kind regards. >>> >>> /Paco >>> >>> >>> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca <[hidden >>> email] >>> >>> >: >>> >>> >>> >>>> Hello Bradley again. >>> >>>> Sorry but I'd like to re-open this issue because I need your class >>> but >>> >>>> with some modification. >>> >>>> I pass to tell you. >>> >>>> >>> >>>> As my tests with your external class were not good taking into >>> account >>> >>>> the performance, I wonder if you could create a variant of it, but >>> in which >>> >>>> I can set a mask image and your class just return the VectorImage >>> with all >>> >>>> the features for that region (the masked locations) as >>> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >>> >>>> I mean, to get the vector image with all the features but just >>> >>>> calculate it for the regions belonging to the mask image. Positions >>> not >>> >>>> belonging to the mask region could have a pixel value of 0, for >>> instance. >>> >>>> >>> >>>> I don?t know if it is very costly for you, but I would thank you so >>> >>>> much. Otherwise, I could try it but I'd need your suggestions on >>> how to do >>> >>>> it. >>> >>>> >>> >>>> Thanks a lot. >>> >>>> Best regards. >>> >>>> >>> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca <[hidden >>> email] >>> >>>> >: >>> >>>> >>> >>>>> Hello Bradley again, >>> >>>>> I would like to ask you for a couple of favours. In the one hand, >>> >>>>> could you please send me your 3D image so that I can test on it? >>> And on the >>> >>>>> other hand, could you test the example I have referenced in the >>> previous >>> >>>>> email with your image, not changing anything in the code, such as >>> it is, >>> >>>>> and tell me if the execution time is normal? >>> >>>>> Thank you very much. >>> >>>>> Regards, >>> >>>>> /Francisco >>> >>>>> >>> >>>>> PS: All my application trace is printed via standard 'cout' >>> command, >>> >>>>> not due to a debugging compilation mode. >>> >>>>> >>> >>>>> >>> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp <[hidden >>> >>>>> email] > >>> >>>>> escribi?: >>> >>>>> >>> >>>>>> Hello, >>> >>>>>> >>> >>>>>> Did you compile TextureFeatureImage in Release mode? >>> >>>>>> >>> >>>>>> 1) The filter does not scale well with a large radius. And given >>> by >>> >>>>>> your initial report of print a very large number of offset you, >>> it sounds >>> >>>>>> like you are using a large radius with many offsets. I created a >>> >>>>>> 224x224x300 unsigned short image and ran with the default offset >>> and a >>> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this filter >>> is was ~10x >>> >>>>>> faster than this example... things change though... >>> >>>>>> >>> >>>>>> >>> >>>>>> 2) I sounds like the boundaries/limits of the histogram may be >>> >>>>>> clipping you values. I would inspect the co-occurance matrix. >>> >>>>>> >>> >>>>>> >>> >>>>>> HTH, >>> >>>>>> Brad >>> >>>>>> >>> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca <[hidden >>> >>>>>> email] > >>> >>>>>> wrote: >>> >>>>>> >>> >>>>>> I've tested with itkTextureFeatureImageFilter, with >>> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>> >>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures >>> example, >>> >>>>>> for a 3D image and here are my comments: >>> >>>>>> >>> >>>>>> >>> >>>>>> 1. I had to interrupt the test after several hours and it kept on >>> >>>>>> calculating. And this is for only a 3D image (224x224x300). I >>> need to >>> >>>>>> process around 35 images. >>> >>>>>> 2. The result (texture features: entropy, energy, correlation, LH, >>> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, >>> 7.83083e+247]. >>> >>>>>> These values were not what I expected based on my experience on >>> another >>> >>>>>> application I developed, but in that case, I calculated the >>> texture >>> >>>>>> features for an image as a whole, not voxel by voxel. >>> >>>>>> >>> >>>>>> Regards. >>> >>>>>> >>> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >>> >>>>>> >: >>> >>>>>> >>> >>>>>>> i yes i have tried radius = 3; >>> >>>>>>> still no luck >>> >>>>>>> >>> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via ITK >>> >>>>>>> Insight >>> >>>>>>> Users] <[hidden email] >>> >>>>>>> > wrote: >>> >>>>>>> >>> >>>>>>> > Have you tried with a radius of 3 instead of 1? >>> >>>>>>> > >>> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>> >>>>>>> > >: >>> >>>>>>> > >>> >>>>>>> >> hey Matt, >>> >>>>>>> >> thanks for ur advice.. it did build successfully... but im not >>> >>>>>>> able to run >>> >>>>>>> >> the code for 2D png image... i tried to change the dimension >>> to 2 >>> >>>>>>> and >>> >>>>>>> >> build >>> >>>>>>> >> it which it did.. but when i run the code using the command >>> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png >>> putput.png >>> >>>>>>> 1... i see >>> >>>>>>> >> this output >>> >>>>>>> >> >>> >>>>>>> >> offset: [-1, -1] [0, -1] >>> >>>>>>> >> offset: [0, -1] [1, -1] >>> >>>>>>> >> offset: [-1, 0] [0, 0] >>> >>>>>>> >> offset: [0, 0] [1, 0] >>> >>>>>>> >> offset: [-1, 1] [0, 1] >>> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... if >>> pls >>> >>>>>>> tel me >>> >>>>>>> >> how can i modify this code to work wid 2d image... forgive me >>> if >>> >>>>>>> my ques >>> >>>>>>> >> are really silly im trying to learn something.. >>> >>>>>>> >> regards >>> >>>>>>> >> Vis >>> >>>>>>> >> >>> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK >>> >>>>>>> Insight Users] >>> >>>>>>> >> < >>> >>>>>>> >> [hidden email] < >>> >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>> >>>>>>> >> wrote: >>> >>>>>>> >> >>> >>>>>>> >> > Hi, >>> >>>>>>> >> > >>> >>>>>>> >> > The function: >>> >>>>>>> >> > >>> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char *argv[]) >>> >>>>>>> >> > >>> >>>>>>> >> > must be renamed to >>> >>>>>>> >> > >>> >>>>>>> >> > main(int argc, char* argv[]) >>> >>>>>>> >> > >>> >>>>>>> >> > HTH, >>> >>>>>>> >> > Matt >>> >>>>>>> >> > >>> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>> >>>>>>> >> > > >>> wrote: >>> >>>>>>> >> > >>> >>>>>>> >> > > hi all, >>> >>>>>>> >> > > im trying to build the >>> itkTextureFeatureImageFilterTest.cxx >>> >>>>>>> code but >>> >>>>>>> >> im >>> >>>>>>> >> > not >>> >>>>>>> >> > > able to it is showing the following error >>> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>> >>>>>>> Configuration: >>> >>>>>>> >> Debug >>> >>>>>>> >> > x64 >>> >>>>>>> >> > > ------ >>> >>>>>>> >> > > 1> Checking Build System >>> >>>>>>> >> > > 1> CMake does not need to re-run because >>> >>>>>>> >> > > >>> >>>>>>> >>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>> >>>>>>> >> > is >>> >>>>>>> >> > > up-to-date. >>> >>>>>>> >> > > 2>------ Rebuild All started: Project: >>> >>>>>>> >> itkTextureFeatureImageFilterTest, >>> >>>>>>> >> > > Configuration: Debug x64 ------ >>> >>>>>>> >> > > 2> Building Custom Rule >>> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>> >>>>>>> >> > > 2> CMake does not need to re-run because >>> >>>>>>> >> > > >>> >>>>>>> >>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>> >>>>>>> >> > is >>> >>>>>>> >> > > up-to-date. >>> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>> >>>>>>> 'std::_Copy_impl': >>> >>>>>>> >> > Function >>> >>>>>>> >> > > call with parameters that may be unsafe - this call >>> relies on >>> >>>>>>> the >>> >>>>>>> >> caller >>> >>>>>>> >> > to >>> >>>>>>> >> > > check that the passed values are correct. To disable this >>> >>>>>>> warning, use >>> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to use >>> >>>>>>> Visual C++ >>> >>>>>>> >> > > 'Checked Iterators' >>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>> >>>>>>> 'std::_Copy_impl' >>> >>>>>>> >> > > 2> >>> >>>>>>> >> > > >>> >>>>>>> >> >>> >>>>>>> >>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>> >>>>>>> >> > see >>> >>>>>>> >> > > reference to function template instantiation '_OutIt >>> >>>>>>> std::copy>> >>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' being >>> >>>>>>> compiled >>> >>>>>>> >> > > 2> with >>> >>>>>>> >> > > 2> [ >>> >>>>>>> >> > > 2> _OutIt=unsigned char *, >>> >>>>>>> >> > > 2> _InIt=const unsigned char * >>> >>>>>>> >> > > 2> ] >>> >>>>>>> >> > > 2> >>> >>>>>>> >> > > >>> >>>>>>> >> >>> >>>>>>> >>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>> >>>>>>> >> > > while compiling class template member function 'void >>> >>>>>>> >> > > itk::ImageFileReader::GenerateData(void)' >>> >>>>>>> >> > > 2> with >>> >>>>>>> >> > > 2> [ >>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>> >>>>>>> >> > > 2> ] >>> >>>>>>> >> > > 2> >>> >>>>>>> >> > > >>> >>>>>>> >> > >>> >>>>>>> >> >>> >>>>>>> >>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>> >>>>>>> >> > >>> >>>>>>> >> > > : see reference to class template instantiation >>> >>>>>>> >> > > 'itk::ImageFileReader' being compiled >>> >>>>>>> >> > > 2> with >>> >>>>>>> >> > > 2> [ >>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>> >>>>>>> >> > > 2> ] >>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>> >>>>>>> 'std::_Copy_impl' >>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>> >>>>>>> 'std::_Copy_impl' >>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>> >>>>>>> 'std::_Copy_impl' >>> >>>>>>> >> > > 2> Creating library >>> >>>>>>> >> > > >>> >>>>>>> >> > >>> >>>>>>> >> >>> >>>>>>> >>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>> >>>>>>> >> > >>> >>>>>>> >> > > and object >>> >>>>>>> >> > > >>> >>>>>>> >> > >>> >>>>>>> >> >>> >>>>>>> >>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>> >>>>>>> >> > >>> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved >>> >>>>>>> external symbol >>> >>>>>>> >> > main >>> >>>>>>> >> > > referenced in function __tmainCRTStartup >>> >>>>>>> >> > > >>> >>>>>>> >> > >>> >>>>>>> >> >>> >>>>>>> >>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>> >>>>>>> >> > >>> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>> >>>>>>> Configuration: Debug >>> >>>>>>> >> > x64 >>> >>>>>>> >> > > ------ >>> >>>>>>> >> > > 3> Building Custom Rule >>> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>> >>>>>>> >> > > 3> CMake does not need to re-run because >>> >>>>>>> >> > > >>> >>>>>>> >>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>> >>>>>>> >> > is >>> >>>>>>> >> > > up-to-date. >>> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 skipped >>> >>>>>>> ========== >>> >>>>>>> >> > > im using the follwing CMakeList.txt >>> >>>>>>> >> > > # This is the root ITK CMakeLists file. >>> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >>> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>> >>>>>>> >> > > endif() >>> >>>>>>> >> > > >>> >>>>>>> >> > > >>> >>>>>>> >> > > # This project is designed to be built outside the Insight >>> >>>>>>> source >>> >>>>>>> >> tree. >>> >>>>>>> >> > > project(HelloWorld) >>> >>>>>>> >> > > >>> >>>>>>> >> > > # Find ITK. >>> >>>>>>> >> > > find_package(ITK REQUIRED) >>> >>>>>>> >> > > include(${ITK_USE_FILE}) >>> >>>>>>> >> > > >>> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>> >>>>>>> >> > > >>> >>>>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest >>> >>>>>>> >> ${ITK_LIBRARIES}) >>> >>>>>>> >> > > >>> >>>>>>> >> > > please tel me wat the error is?? >>> >>>>>>> >> > > >>> >>>>>>> >> > > >>> >>>>>>> >> > > >>> >>>>>>> >> > > -- >>> >>>>>>> >> > > View this message in context: >>> >>>>>>> >> > >>> >>>>>>> >> >>> >>>>>>> >>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>> >>>>>>> >> > > Sent from the ITK Insight Users mailing list archive at >>> >>>>>>> Nabble.com. >>> >>>>>>> >> > > _____________________________________ >>> >>>>>>> >> > > Powered 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http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> ------------------------------ >> If you reply to this email, your message will be added to the discussion >> below: >> >> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588490.html >> To start a new topic under ITK Insight Users, email >> ml-node+s2283740n2283740h75 at n2.nabble.com >> To unsubscribe from ITK Insight Users, click here >> >> . >> NAML >> >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From kolin9105 at gmail.com Mon Feb 15 12:05:30 2016 From: kolin9105 at gmail.com (meikolin saimara) Date: Tue, 16 Feb 2016 00:05:30 +0700 Subject: [ITK] [ITK-users] (no subject) Message-ID: hello every one. I am beginner in ITK. I have a Question. I had a image (threshold) and then I want to know the black pixel of the image before that I have processed using confidence connected. can you give the source code how to get value of black pixel ?? pleas help me. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Mon Feb 15 12:59:55 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 15 Feb 2016 12:59:55 -0500 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: Hi Saimara, did you take a look at the wiki example ? Or other examples referenced in the documentation ? Regards, D?enan On Mon, Feb 15, 2016 at 12:05 PM, meikolin saimara wrote: > hello every one. > I am beginner in ITK. > I have a Question. > I had a image (threshold) and then I want to know the black pixel of the > image before that I have processed using confidence connected. > can you give the source code how to get value of black pixel ?? > pleas help me. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From kolin9105 at gmail.com Tue Feb 16 00:37:21 2016 From: kolin9105 at gmail.com (meikolin saimara) Date: Tue, 16 Feb 2016 12:37:21 +0700 Subject: [ITK] [ITK-users] (no subject) Message-ID: hello guys. I am beginner in itk. in RGBImage we can found red pixel but how we can get black pixel value of image. I have a image with view black and white. but I just need black pixel value.. Pleas help me guys. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Tue Feb 16 01:52:02 2016 From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca) Date: Tue, 16 Feb 2016 07:52:02 +0100 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <84A225AE-400C-4FBA-97FA-6A027CB17208@mail.nih.gov> Message-ID: Excuse me Dzenanz, but that's not completely true, because I've tested Brad's class and it works right. The problem seems to be that when you add a new neighbor iterator to include just the mask points in the "histogram" then it is when the application crashes, and I donot understand why. If you just comment the 'maskIter' references you'll see that the application works. I've created a single threaded class based on the Brad's code and it works but it is twice slower, that is why I'm interesting on Brad's class (multi-threaded) to make it work. 2016-02-15 17:15 GMT+01:00 dzenanz [via ITK Insight Users] < ml-node+s2283740n7588495h80 at n2.nabble.com>: > Hi Francisco, > > both your code and Brad's code run in debug mode (I did not wait for the > end), and both crash in release mode immediately on startup. Here is a > sample output: > > Progress input: 0000000002868970 > input: 0000000002868970 > _maskImage: 0000000002868970 > _maskImage: 0000000002868970 > input: 0000000002868970 > _maskImage: 0000000002868970 > iter.first: iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] > iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] > [-5, -5, -5] iter.second: [-4, -5, -5] > niter index: [5, 5, 210] > niter index: [5, 5, 140] > maskIter index: [5, 5, 140] > maskIter index: [5, 5, 210] > Before p3 > input: 0000000002868970 > _maskImage: 0000000002868970 > After p3: | 0niter index: [5, 5, 70] > iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] > niter index: [5, 5, 5] > ? > maskIter index: [5, 5, 70] > After p4: ? > Before p3 > Before p3 > After p3: ?iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] > niter index: [5, 5, 140] > maskIter index: [5, 5, 140] > maskIter index: [5, 5, 5] > Before p3 > After p3: ? > After p3: ? > After p4: ? > After p4: ? > iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] > niter index: [5, 5, 5] > maskIter index: [5, 5, 5] > > iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] > Before p3 > Before p3 > After p4: ? > After p3: ? > After p4: ? > > Regards, > D?enan > > On Mon, Feb 15, 2016 at 1:36 AM, Francisco Lopez de la Franca <[hidden > email] > wrote: > >> Hi, >> Here they are. >> KR. >> >> 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >> email] >: >> >>> Hi Francisco, >>> >>> do you mind attaching the modified files or pointing to your fork of it >>> on GitHub? >>> >>> Regards >>> >>> On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden email] >>> > wrote: >>> >>>> Hi Dzenan, >>>> The original class is here: >>>> >>>> >>>> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >>>> >>>> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >>>> >>>> I've just added setInput and setMaskImage methods and modify some lines >>>> in >>>> the original class as I indicated in the yesterday mail within this >>>> thread. >>>> I'm running it on Windows, and there is no error at all, just a crash. I >>>> may have to include exceptions management. >>>> The crash occurs just when calling p3 = maskIter.GetPixel(iter->first) >>>> >>>> If you know why it could be or if you need more clarification, please >>>> let >>>> me know. >>>> Many thanks >>>> >>>> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >>>> [hidden email] >>>> >: >>>> >>>> > Hi Francisco, >>>> > >>>> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the error >>>> message >>>> > that goes along with the crash? In which file and line does it crash? >>>> > >>>> > Regards >>>> > >>>> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca <[hidden >>>> > email] > >>>> wrote: >>>> > >>>> >> Hi, >>>> >> Please, someone that could help me. I'm working in a pre-doctorate >>>> >> project and I need this class to work. >>>> >> I've read the chapter 13 in the ITK Software Guide on how to write a >>>> >> filter and now I see the fact of the threads due to inheritance of >>>> >> ImageToImageFilter. >>>> >> But, I keep on without understanding why the code crashes just when >>>> >> calling >>>> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >>>> >> It is just a call to read data, not to write. >>>> >> >>>> >> I guess somebody that had worked with creation of filters might see >>>> >> "easily" the problem, but not me. >>>> >> >>>> >> So, again, please, I need someone to help me with this because I'm >>>> stuck >>>> >> on this point. >>>> >> >>>> >> Thank you very much. >>>> >> KR. >>>> >> /Francisco >>>> >> >>>> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden >>>> email] >>>> >> >: >>>> >> >>>> >>> Hi Bradley again. >>>> >>> I'm modifying your class in order to be able to set a mask image (a >>>> >>> binary image) to be used as a limit in the histogram calculations, >>>> I mean, >>>> >>> I set an input, a mask and the class should take into account to >>>> calculate >>>> >>> the histograms only the voxels that belong to the input and to the >>>> mask >>>> >>> image and having the value 1 in the mask image. >>>> >>> The changes seem to be easy but I don?t know why my tests are not >>>> >>> working. It seems that 2 threads are working at the same time and >>>> when I >>>> >>> added my mask iterator, the code crashes. >>>> >>> >>>> >>> *** Consider that the input and mask images are the same origin, >>>> spacing >>>> >>> and size. >>>> >>> >>>> >>> I attach the main changes I've done, and I would thank you a lot if >>>> you >>>> >>> don't mind having a look and help me to find what I'm doing wrong: >>>> >>> >>>> >>> template< class TImageType, class TOutputImage > >>>> >>> void >>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>> >::*SetInput*(InputImageType >>>> >>> *image) >>>> >>> { >>>> >>> // Process object is not const-correct so the const_cast is >>>> required >>>> >>> here >>>> >>> this->ProcessObject::SetNthInput( 0, >>>> >>> const_cast< InputImageType * >( >>>> >>> image ) ); >>>> >>> } >>>> >>> >>>> >>> template< class TImageType, class TOutputImage > >>>> >>> void >>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>> >::*SetMaskImage*(InputImageType >>>> >>> *image) >>>> >>> { >>>> >>> // Process object is not const-correct so the const_cast is >>>> required >>>> >>> here >>>> >>> this->ProcessObject::SetNthInput( 1, const_cast< InputImageType * >>>> >( >>>> >>> image ) ); >>>> >>> >>>> >>> _maskImage = image; // _maskImage is a private member >>>> >>> } >>>> >>> >>>> >>> In the *ThreadedGenerateData*(const RegionType& >>>> outputRegionForThread, >>>> >>> ThreadIdType threadId ) method: >>>> >>> { >>>> >>> >>>> >>> ... >>>> >>> >>>> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >>>> >>> { >>>> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >>>> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, *fit);* >>>> >>> OutputIterator outIter(output, *fit); >>>> >>> >>>> >>> OutputPixelType out; >>>> >>> NumericTraits::SetLength( out, >>>> >>> this->GetNumberOfOutputComponents() ); >>>> >>> >>>> >>> while( !nIter.IsAtEnd() ) >>>> >>> { >>>> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >>>> >>> >>>> >>> ... >>>> >>> >>>> >>> ++nIter; >>>> >>> ++outIter; >>>> >>> * ++maskIter;* >>>> >>> ... >>>> >>> >>>> >>> In the *FillHistogram *method: >>>> >>> { >>>> >>> >>>> >>> ... >>>> >>> >>>> >>> while( iter != m_CooccurenceOffsetVector.end() ) >>>> >>> { >>>> >>> >>>> >>> const PixelType p1 = niter.GetPixel(iter->first); >>>> >>> const PixelType p2 = niter.GetPixel(iter->second); >>>> >>> std::cout << "Before p3" << std::endl; >>>> >>> >>>> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); >>>> *std::cout >>>> >>> << "After p3: " << p3 << std::endl; >>>> >>> >>>> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >>>> >>> std::cout << "After p4: " << p4 << std::endl; >>>> >>> >>>> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= m_Max >>>> >>> *&& p3 == _insidePixelValue && p4 == _insidePixelValue* >>>> ) >>>> >>> // The point >>>> >>> { >>>> >>> >>>> >>> ... >>>> >>> >>>> >>> >>>> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >>>> >>> >>>> >>> Thank you so much. >>>> >>> My kind regards. >>>> >>> /Paco >>>> >>> >>>> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca <[hidden >>>> email] >>>> >>> >: >>>> >>> >>>> >>>> Hello Bradley again. >>>> >>>> Sorry but I'd like to re-open this issue because I need your class >>>> but >>>> >>>> with some modification. >>>> >>>> I pass to tell you. >>>> >>>> >>>> >>>> As my tests with your external class were not good taking into >>>> account >>>> >>>> the performance, I wonder if you could create a variant of it, but >>>> in which >>>> >>>> I can set a mask image and your class just return the VectorImage >>>> with all >>>> >>>> the features for that region (the masked locations) as >>>> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >>>> >>>> I mean, to get the vector image with all the features but just >>>> >>>> calculate it for the regions belonging to the mask image. >>>> Positions not >>>> >>>> belonging to the mask region could have a pixel value of 0, for >>>> instance. >>>> >>>> >>>> >>>> I don?t know if it is very costly for you, but I would thank you >>>> so >>>> >>>> much. Otherwise, I could try it but I'd need your suggestions on >>>> how to do >>>> >>>> it. >>>> >>>> >>>> >>>> Thanks a lot. >>>> >>>> Best regards. >>>> >>>> >>>> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca <[hidden >>>> email] >>>> >>>> >: >>>> >>>> >>>> >>>>> Hello Bradley again, >>>> >>>>> I would like to ask you for a couple of favours. In the one hand, >>>> >>>>> could you please send me your 3D image so that I can test on it? >>>> And on the >>>> >>>>> other hand, could you test the example I have referenced in the >>>> previous >>>> >>>>> email with your image, not changing anything in the code, such as >>>> it is, >>>> >>>>> and tell me if the execution time is normal? >>>> >>>>> Thank you very much. >>>> >>>>> Regards, >>>> >>>>> /Francisco >>>> >>>>> >>>> >>>>> PS: All my application trace is printed via standard 'cout' >>>> command, >>>> >>>>> not due to a debugging compilation mode. >>>> >>>>> >>>> >>>>> >>>> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp <[hidden >>>> >>>>> email] > >>>> >>>>> escribi?: >>>> >>>>> >>>> >>>>>> Hello, >>>> >>>>>> >>>> >>>>>> Did you compile TextureFeatureImage in Release mode? >>>> >>>>>> >>>> >>>>>> 1) The filter does not scale well with a large radius. And given >>>> by >>>> >>>>>> your initial report of print a very large number of offset you, >>>> it sounds >>>> >>>>>> like you are using a large radius with many offsets. I created a >>>> >>>>>> 224x224x300 unsigned short image and ran with the default offset >>>> and a >>>> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this filter >>>> is was ~10x >>>> >>>>>> faster than this example... things change though... >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> 2) I sounds like the boundaries/limits of the histogram may be >>>> >>>>>> clipping you values. I would inspect the co-occurance matrix. >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> HTH, >>>> >>>>>> Brad >>>> >>>>>> >>>> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca >>>> <[hidden >>>> >>>>>> email] > >>>> >>>>>> wrote: >>>> >>>>>> >>>> >>>>>> I've tested with itkTextureFeatureImageFilter, with >>>> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>> >>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures >>>> example, >>>> >>>>>> for a 3D image and here are my comments: >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> 1. I had to interrupt the test after several hours and it kept on >>>> >>>>>> calculating. And this is for only a 3D image (224x224x300). I >>>> need to >>>> >>>>>> process around 35 images. >>>> >>>>>> 2. The result (texture features: entropy, energy, correlation, >>>> LH, >>>> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, >>>> 7.83083e+247]. >>>> >>>>>> These values were not what I expected based on my experience on >>>> another >>>> >>>>>> application I developed, but in that case, I calculated the >>>> texture >>>> >>>>>> features for an image as a whole, not voxel by voxel. >>>> >>>>>> >>>> >>>>>> Regards. >>>> >>>>>> >>>> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >>>> >>>>>> >: >>>> >>>>>> >>>> >>>>>>> i yes i have tried radius = 3; >>>> >>>>>>> still no luck >>>> >>>>>>> >>>> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via >>>> ITK >>>> >>>>>>> Insight >>>> >>>>>>> Users] <[hidden email] >>>> >>>>>>> > wrote: >>>> >>>>>>> >>>> >>>>>>> > Have you tried with a radius of 3 instead of 1? >>>> >>>>>>> > >>>> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>> >>>>>>> > >: >>>> >>>>>>> > >>>> >>>>>>> >> hey Matt, >>>> >>>>>>> >> thanks for ur advice.. it did build successfully... but im >>>> not >>>> >>>>>>> able to run >>>> >>>>>>> >> the code for 2D png image... i tried to change the dimension >>>> to 2 >>>> >>>>>>> and >>>> >>>>>>> >> build >>>> >>>>>>> >> it which it did.. but when i run the code using the command >>>> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png >>>> putput.png >>>> >>>>>>> 1... i see >>>> >>>>>>> >> this output >>>> >>>>>>> >> >>>> >>>>>>> >> offset: [-1, -1] [0, -1] >>>> >>>>>>> >> offset: [0, -1] [1, -1] >>>> >>>>>>> >> offset: [-1, 0] [0, 0] >>>> >>>>>>> >> offset: [0, 0] [1, 0] >>>> >>>>>>> >> offset: [-1, 1] [0, 1] >>>> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... >>>> if pls >>>> >>>>>>> tel me >>>> >>>>>>> >> how can i modify this code to work wid 2d image... forgive >>>> me if >>>> >>>>>>> my ques >>>> >>>>>>> >> are really silly im trying to learn something.. >>>> >>>>>>> >> regards >>>> >>>>>>> >> Vis >>>> >>>>>>> >> >>>> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK >>>> >>>>>>> Insight Users] >>>> >>>>>>> >> < >>>> >>>>>>> >> [hidden email] < >>>> >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>>> >>>>>>> >> wrote: >>>> >>>>>>> >> >>>> >>>>>>> >> > Hi, >>>> >>>>>>> >> > >>>> >>>>>>> >> > The function: >>>> >>>>>>> >> > >>>> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char *argv[]) >>>> >>>>>>> >> > >>>> >>>>>>> >> > must be renamed to >>>> >>>>>>> >> > >>>> >>>>>>> >> > main(int argc, char* argv[]) >>>> >>>>>>> >> > >>>> >>>>>>> >> > HTH, >>>> >>>>>>> >> > Matt >>>> >>>>>>> >> > >>>> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>> >>>>>>> >> > > >>>> wrote: >>>> >>>>>>> >> > >>>> >>>>>>> >> > > hi all, >>>> >>>>>>> >> > > im trying to build the >>>> itkTextureFeatureImageFilterTest.cxx >>>> >>>>>>> code but >>>> >>>>>>> >> im >>>> >>>>>>> >> > not >>>> >>>>>>> >> > > able to it is showing the following error >>>> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>> >>>>>>> Configuration: >>>> >>>>>>> >> Debug >>>> >>>>>>> >> > x64 >>>> >>>>>>> >> > > ------ >>>> >>>>>>> >> > > 1> Checking Build System >>>> >>>>>>> >> > > 1> CMake does not need to re-run because >>>> >>>>>>> >> > > >>>> >>>>>>> >>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>> >>>>>>> >> > is >>>> >>>>>>> >> > > up-to-date. >>>> >>>>>>> >> > > 2>------ Rebuild All started: Project: >>>> >>>>>>> >> itkTextureFeatureImageFilterTest, >>>> >>>>>>> >> > > Configuration: Debug x64 ------ >>>> >>>>>>> >> > > 2> Building Custom Rule >>>> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>> >>>>>>> >> > > 2> CMake does not need to re-run because >>>> >>>>>>> >> > > >>>> >>>>>>> >>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>> >>>>>>> >> > is >>>> >>>>>>> >> > > up-to-date. >>>> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>> >>>>>>> 'std::_Copy_impl': >>>> >>>>>>> >> > Function >>>> >>>>>>> >> > > call with parameters that may be unsafe - this call >>>> relies on >>>> >>>>>>> the >>>> >>>>>>> >> caller >>>> >>>>>>> >> > to >>>> >>>>>>> >> > > check that the passed values are correct. To disable this >>>> >>>>>>> warning, use >>>> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to >>>> use >>>> >>>>>>> Visual C++ >>>> >>>>>>> >> > > 'Checked Iterators' >>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>> Studio >>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>> >>>>>>> 'std::_Copy_impl' >>>> >>>>>>> >> > > 2> >>>> >>>>>>> >> > > >>>> >>>>>>> >> >>>> >>>>>>> >>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>> >>>>>>> >> > see >>>> >>>>>>> >> > > reference to function template instantiation '_OutIt >>>> >>>>>>> std::copy>>> >>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' being >>>> >>>>>>> compiled >>>> >>>>>>> >> > > 2> with >>>> >>>>>>> >> > > 2> [ >>>> >>>>>>> >> > > 2> _OutIt=unsigned char *, >>>> >>>>>>> >> > > 2> _InIt=const unsigned char * >>>> >>>>>>> >> > > 2> ] >>>> >>>>>>> >> > > 2> >>>> >>>>>>> >> > > >>>> >>>>>>> >> >>>> >>>>>>> >>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>> >>>>>>> >> > > while compiling class template member function 'void >>>> >>>>>>> >> > > itk::ImageFileReader::GenerateData(void)' >>>> >>>>>>> >> > > 2> with >>>> >>>>>>> >> > > 2> [ >>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>> >>>>>>> >> > > 2> ] >>>> >>>>>>> >> > > 2> >>>> >>>>>>> >> > > >>>> >>>>>>> >> > >>>> >>>>>>> >> >>>> >>>>>>> >>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>> >>>>>>> >> > >>>> >>>>>>> >> > > : see reference to class template instantiation >>>> >>>>>>> >> > > 'itk::ImageFileReader' being compiled >>>> >>>>>>> >> > > 2> with >>>> >>>>>>> >> > > 2> [ >>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>> >>>>>>> >> > > 2> ] >>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>> Studio >>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>> >>>>>>> 'std::_Copy_impl' >>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>> Studio >>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>> >>>>>>> 'std::_Copy_impl' >>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>> Studio >>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>> >>>>>>> 'std::_Copy_impl' >>>> >>>>>>> >> > > 2> Creating library >>>> >>>>>>> >> > > >>>> >>>>>>> >> > >>>> >>>>>>> >> >>>> >>>>>>> >>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>> >>>>>>> >> > >>>> >>>>>>> >> > > and object >>>> >>>>>>> >> > > >>>> >>>>>>> >> > >>>> >>>>>>> >> >>>> >>>>>>> >>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>> >>>>>>> >> > >>>> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved >>>> >>>>>>> external symbol >>>> >>>>>>> >> > main >>>> >>>>>>> >> > > referenced in function __tmainCRTStartup >>>> >>>>>>> >> > > >>>> >>>>>>> >> > >>>> >>>>>>> >> >>>> >>>>>>> >>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>> >>>>>>> >> > >>>> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>> >>>>>>> Configuration: Debug >>>> >>>>>>> >> > x64 >>>> >>>>>>> >> > > ------ >>>> >>>>>>> >> > > 3> Building Custom Rule >>>> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>> >>>>>>> >> > > 3> CMake does not need to re-run because >>>> >>>>>>> >> > > >>>> >>>>>>> >>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>> >>>>>>> >> > is >>>> >>>>>>> >> > > up-to-date. >>>> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 skipped >>>> >>>>>>> ========== >>>> >>>>>>> >> > > im using the follwing CMakeList.txt >>>> >>>>>>> >> > > # This is the root ITK CMakeLists file. >>>> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >>>> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>> >>>>>>> >> > > endif() >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > # This project is designed to be built outside the >>>> Insight >>>> >>>>>>> source >>>> >>>>>>> >> tree. >>>> >>>>>>> >> > > project(HelloWorld) >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > # Find ITK. >>>> >>>>>>> >> > > find_package(ITK REQUIRED) >>>> >>>>>>> >> > > include(${ITK_USE_FILE}) >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest >>>> >>>>>>> >> ${ITK_LIBRARIES}) >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > please tel me wat the error is?? >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > -- >>>> >>>>>>> >> > > View this message in context: >>>> >>>>>>> >> > >>>> >>>>>>> >> >>>> >>>>>>> >>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>> >>>>>>> >> > > Sent from the ITK Insight Users mailing list archive at >>>> >>>>>>> Nabble.com. >>>> >>>>>>> >> > > _____________________________________ >>>> >>>>>>> >> > > Powered by www.kitware.com >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > Visit other Kitware open-source projects at >>>> >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > Kitware offers ITK Training Courses, for more information >>>> >>>>>>> visit: >>>> >>>>>>> >> > > http://www.kitware.com/products/protraining.php >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > Please keep messages on-topic and check the ITK FAQ at: >>>> >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > Follow this link to subscribe/unsubscribe: >>>> >>>>>>> >> > > http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>>>>> >> > _____________________________________ >>>> >>>>>>> >> > Powered by www.kitware.com >>>> >>>>>>> >> > >>>> >>>>>>> >> > Visit other Kitware open-source projects at 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Kitware offers ITK Training Courses, for more information >>>> visit: >>>> >>>>>>> > http://www.kitware.com/products/protraining.php >>>> >>>>>>> > >>>> >>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>> >>>>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>> >>>>>>> > >>>> >>>>>>> > Follow this link to subscribe/unsubscribe: >>>> >>>>>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>>>>> > >>>> >>>>>>> > >>>> >>>>>>> > ------------------------------ >>>> >>>>>>> > If you reply to this email, your message will be added to the >>>> >>>>>>> discussion >>>> >>>>>>> > below: >>>> >>>>>>> > >>>> >>>>>>> > >>>> >>>>>>> >>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587961.html >>>> >>>>>>> > To unsubscribe from [ITK-users] Texture pixel by pixel, click >>>> here >>>> >>>>>>> > < > . >>>> >>>>>>> > NAML >>>> >>>>>>> > < >>>> >>>>>>> >>>> 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offers ITK Training Courses, for more information visit: >>>> > http://www.kitware.com/products/protraining.php >>>> > >>>> > Please keep messages on-topic and check the ITK FAQ at: >>>> > http://www.itk.org/Wiki/ITK_FAQ >>>> > >>>> > Follow this link to subscribe/unsubscribe: >>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>> > >>>> > >>>> > ------------------------------ >>>> > If you reply to this email, your message will be added to the >>>> discussion >>>> > below: >>>> > >>>> > >>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588477.html >>>> > To start a new topic under ITK Insight Users, email >>>> > [hidden email] >>>> >>>> > To unsubscribe from ITK Insight Users, click here >>>> > < > . >>>> > NAML >>>> > < >>>> 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in context: >>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588483.html >>>> Sent from the ITK Insight Users mailing list archive at Nabble.com. >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>> ------------------------------ >>> If you reply to this email, your message will be added to the discussion >>> below: >>> >>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588490.html >>> To start a new topic under ITK Insight Users, email [hidden email] >>> >>> To unsubscribe from ITK Insight Users, click here. >>> NAML >>> >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588495.html > To start a new topic under ITK Insight Users, email > ml-node+s2283740n2283740h75 at n2.nabble.com > To unsubscribe from ITK Insight Users, click here > > . > NAML > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Tue Feb 16 01:52:21 2016 From: franciscolopezdelafranca at gmail.com (=?UTF-8?Q?Francisco_L=C3=B3pez-Franca?=) Date: Mon, 15 Feb 2016 23:52:21 -0700 (MST) Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <84A225AE-400C-4FBA-97FA-6A027CB17208@mail.nih.gov> Message-ID: Excuse me Dzenanz, but that's not completely true, because I've tested Brad's class and it works right. The problem seems to be that when you add a new neighbor iterator to include just the mask points in the "histogram" then it is when the application crashes, and I donot understand why. If you just comment the 'maskIter' references you'll see that the application works. I've created a single threaded class based on the Brad's code and it works but it is twice slower, that is why I'm interesting on Brad's class (multi-threaded) to make it work. 2016-02-15 17:15 GMT+01:00 dzenanz [via ITK Insight Users] < ml-node+s2283740n7588495h80 at n2.nabble.com>: > Hi Francisco, > > both your code and Brad's code run in debug mode (I did not wait for the > end), and both crash in release mode immediately on startup. Here is a > sample output: > > Progress input: 0000000002868970 > input: 0000000002868970 > _maskImage: 0000000002868970 > _maskImage: 0000000002868970 > input: 0000000002868970 > _maskImage: 0000000002868970 > iter.first: iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] > iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] > [-5, -5, -5] iter.second: [-4, -5, -5] > niter index: [5, 5, 210] > niter index: [5, 5, 140] > maskIter index: [5, 5, 140] > maskIter index: [5, 5, 210] > Before p3 > input: 0000000002868970 > _maskImage: 0000000002868970 > After p3: | 0niter index: [5, 5, 70] > iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] > niter index: [5, 5, 5] > ? > maskIter index: [5, 5, 70] > After p4: ? > Before p3 > Before p3 > After p3: ?iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] > niter index: [5, 5, 140] > maskIter index: [5, 5, 140] > maskIter index: [5, 5, 5] > Before p3 > After p3: ? > After p3: ? > After p4: ? > After p4: ? > iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] > niter index: [5, 5, 5] > maskIter index: [5, 5, 5] > > iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] > Before p3 > Before p3 > After p4: ? > After p3: ? > After p4: ? > > Regards, > D?enan > > On Mon, Feb 15, 2016 at 1:36 AM, Francisco Lopez de la Franca <[hidden > email] > wrote: > >> Hi, >> Here they are. >> KR. >> >> 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >> email] >: >> >>> Hi Francisco, >>> >>> do you mind attaching the modified files or pointing to your fork of it >>> on GitHub? >>> >>> Regards >>> >>> On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden email] >>> > wrote: >>> >>>> Hi Dzenan, >>>> The original class is here: >>>> >>>> >>>> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >>>> >>>> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >>>> >>>> I've just added setInput and setMaskImage methods and modify some lines >>>> in >>>> the original class as I indicated in the yesterday mail within this >>>> thread. >>>> I'm running it on Windows, and there is no error at all, just a crash. I >>>> may have to include exceptions management. >>>> The crash occurs just when calling p3 = maskIter.GetPixel(iter->first) >>>> >>>> If you know why it could be or if you need more clarification, please >>>> let >>>> me know. >>>> Many thanks >>>> >>>> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >>>> [hidden email] >>>> >: >>>> >>>> > Hi Francisco, >>>> > >>>> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the error >>>> message >>>> > that goes along with the crash? In which file and line does it crash? >>>> > >>>> > Regards >>>> > >>>> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca <[hidden >>>> > email] > >>>> wrote: >>>> > >>>> >> Hi, >>>> >> Please, someone that could help me. I'm working in a pre-doctorate >>>> >> project and I need this class to work. >>>> >> I've read the chapter 13 in the ITK Software Guide on how to write a >>>> >> filter and now I see the fact of the threads due to inheritance of >>>> >> ImageToImageFilter. >>>> >> But, I keep on without understanding why the code crashes just when >>>> >> calling >>>> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >>>> >> It is just a call to read data, not to write. >>>> >> >>>> >> I guess somebody that had worked with creation of filters might see >>>> >> "easily" the problem, but not me. >>>> >> >>>> >> So, again, please, I need someone to help me with this because I'm >>>> stuck >>>> >> on this point. >>>> >> >>>> >> Thank you very much. >>>> >> KR. >>>> >> /Francisco >>>> >> >>>> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden >>>> email] >>>> >> >: >>>> >> >>>> >>> Hi Bradley again. >>>> >>> I'm modifying your class in order to be able to set a mask image (a >>>> >>> binary image) to be used as a limit in the histogram calculations, >>>> I mean, >>>> >>> I set an input, a mask and the class should take into account to >>>> calculate >>>> >>> the histograms only the voxels that belong to the input and to the >>>> mask >>>> >>> image and having the value 1 in the mask image. >>>> >>> The changes seem to be easy but I don?t know why my tests are not >>>> >>> working. It seems that 2 threads are working at the same time and >>>> when I >>>> >>> added my mask iterator, the code crashes. >>>> >>> >>>> >>> *** Consider that the input and mask images are the same origin, >>>> spacing >>>> >>> and size. >>>> >>> >>>> >>> I attach the main changes I've done, and I would thank you a lot if >>>> you >>>> >>> don't mind having a look and help me to find what I'm doing wrong: >>>> >>> >>>> >>> template< class TImageType, class TOutputImage > >>>> >>> void >>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>> >::*SetInput*(InputImageType >>>> >>> *image) >>>> >>> { >>>> >>> // Process object is not const-correct so the const_cast is >>>> required >>>> >>> here >>>> >>> this->ProcessObject::SetNthInput( 0, >>>> >>> const_cast< InputImageType * >( >>>> >>> image ) ); >>>> >>> } >>>> >>> >>>> >>> template< class TImageType, class TOutputImage > >>>> >>> void >>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>> >::*SetMaskImage*(InputImageType >>>> >>> *image) >>>> >>> { >>>> >>> // Process object is not const-correct so the const_cast is >>>> required >>>> >>> here >>>> >>> this->ProcessObject::SetNthInput( 1, const_cast< InputImageType * >>>> >( >>>> >>> image ) ); >>>> >>> >>>> >>> _maskImage = image; // _maskImage is a private member >>>> >>> } >>>> >>> >>>> >>> In the *ThreadedGenerateData*(const RegionType& >>>> outputRegionForThread, >>>> >>> ThreadIdType threadId ) method: >>>> >>> { >>>> >>> >>>> >>> ... >>>> >>> >>>> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >>>> >>> { >>>> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >>>> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, *fit);* >>>> >>> OutputIterator outIter(output, *fit); >>>> >>> >>>> >>> OutputPixelType out; >>>> >>> NumericTraits::SetLength( out, >>>> >>> this->GetNumberOfOutputComponents() ); >>>> >>> >>>> >>> while( !nIter.IsAtEnd() ) >>>> >>> { >>>> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >>>> >>> >>>> >>> ... >>>> >>> >>>> >>> ++nIter; >>>> >>> ++outIter; >>>> >>> * ++maskIter;* >>>> >>> ... >>>> >>> >>>> >>> In the *FillHistogram *method: >>>> >>> { >>>> >>> >>>> >>> ... >>>> >>> >>>> >>> while( iter != m_CooccurenceOffsetVector.end() ) >>>> >>> { >>>> >>> >>>> >>> const PixelType p1 = niter.GetPixel(iter->first); >>>> >>> const PixelType p2 = niter.GetPixel(iter->second); >>>> >>> std::cout << "Before p3" << std::endl; >>>> >>> >>>> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); >>>> *std::cout >>>> >>> << "After p3: " << p3 << std::endl; >>>> >>> >>>> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >>>> >>> std::cout << "After p4: " << p4 << std::endl; >>>> >>> >>>> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= m_Max >>>> >>> *&& p3 == _insidePixelValue && p4 == _insidePixelValue* >>>> ) >>>> >>> // The point >>>> >>> { >>>> >>> >>>> >>> ... >>>> >>> >>>> >>> >>>> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >>>> >>> >>>> >>> Thank you so much. >>>> >>> My kind regards. >>>> >>> /Paco >>>> >>> >>>> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca <[hidden >>>> email] >>>> >>> >: >>>> >>> >>>> >>>> Hello Bradley again. >>>> >>>> Sorry but I'd like to re-open this issue because I need your class >>>> but >>>> >>>> with some modification. >>>> >>>> I pass to tell you. >>>> >>>> >>>> >>>> As my tests with your external class were not good taking into >>>> account >>>> >>>> the performance, I wonder if you could create a variant of it, but >>>> in which >>>> >>>> I can set a mask image and your class just return the VectorImage >>>> with all >>>> >>>> the features for that region (the masked locations) as >>>> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >>>> >>>> I mean, to get the vector image with all the features but just >>>> >>>> calculate it for the regions belonging to the mask image. >>>> Positions not >>>> >>>> belonging to the mask region could have a pixel value of 0, for >>>> instance. >>>> >>>> >>>> >>>> I don?t know if it is very costly for you, but I would thank you >>>> so >>>> >>>> much. Otherwise, I could try it but I'd need your suggestions on >>>> how to do >>>> >>>> it. >>>> >>>> >>>> >>>> Thanks a lot. >>>> >>>> Best regards. >>>> >>>> >>>> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca <[hidden >>>> email] >>>> >>>> >: >>>> >>>> >>>> >>>>> Hello Bradley again, >>>> >>>>> I would like to ask you for a couple of favours. In the one hand, >>>> >>>>> could you please send me your 3D image so that I can test on it? >>>> And on the >>>> >>>>> other hand, could you test the example I have referenced in the >>>> previous >>>> >>>>> email with your image, not changing anything in the code, such as >>>> it is, >>>> >>>>> and tell me if the execution time is normal? >>>> >>>>> Thank you very much. >>>> >>>>> Regards, >>>> >>>>> /Francisco >>>> >>>>> >>>> >>>>> PS: All my application trace is printed via standard 'cout' >>>> command, >>>> >>>>> not due to a debugging compilation mode. >>>> >>>>> >>>> >>>>> >>>> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp <[hidden >>>> >>>>> email] > >>>> >>>>> escribi?: >>>> >>>>> >>>> >>>>>> Hello, >>>> >>>>>> >>>> >>>>>> Did you compile TextureFeatureImage in Release mode? >>>> >>>>>> >>>> >>>>>> 1) The filter does not scale well with a large radius. And given >>>> by >>>> >>>>>> your initial report of print a very large number of offset you, >>>> it sounds >>>> >>>>>> like you are using a large radius with many offsets. I created a >>>> >>>>>> 224x224x300 unsigned short image and ran with the default offset >>>> and a >>>> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this filter >>>> is was ~10x >>>> >>>>>> faster than this example... things change though... >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> 2) I sounds like the boundaries/limits of the histogram may be >>>> >>>>>> clipping you values. I would inspect the co-occurance matrix. >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> HTH, >>>> >>>>>> Brad >>>> >>>>>> >>>> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca >>>> <[hidden >>>> >>>>>> email] > >>>> >>>>>> wrote: >>>> >>>>>> >>>> >>>>>> I've tested with itkTextureFeatureImageFilter, with >>>> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>> >>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures >>>> example, >>>> >>>>>> for a 3D image and here are my comments: >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> 1. I had to interrupt the test after several hours and it kept on >>>> >>>>>> calculating. And this is for only a 3D image (224x224x300). I >>>> need to >>>> >>>>>> process around 35 images. >>>> >>>>>> 2. The result (texture features: entropy, energy, correlation, >>>> LH, >>>> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, >>>> 7.83083e+247]. >>>> >>>>>> These values were not what I expected based on my experience on >>>> another >>>> >>>>>> application I developed, but in that case, I calculated the >>>> texture >>>> >>>>>> features for an image as a whole, not voxel by voxel. >>>> >>>>>> >>>> >>>>>> Regards. >>>> >>>>>> >>>> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >>>> >>>>>> >: >>>> >>>>>> >>>> >>>>>>> i yes i have tried radius = 3; >>>> >>>>>>> still no luck >>>> >>>>>>> >>>> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via >>>> ITK >>>> >>>>>>> Insight >>>> >>>>>>> Users] <[hidden email] >>>> >>>>>>> > wrote: >>>> >>>>>>> >>>> >>>>>>> > Have you tried with a radius of 3 instead of 1? >>>> >>>>>>> > >>>> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>> >>>>>>> > >: >>>> >>>>>>> > >>>> >>>>>>> >> hey Matt, >>>> >>>>>>> >> thanks for ur advice.. it did build successfully... but im >>>> not >>>> >>>>>>> able to run >>>> >>>>>>> >> the code for 2D png image... i tried to change the dimension >>>> to 2 >>>> >>>>>>> and >>>> >>>>>>> >> build >>>> >>>>>>> >> it which it did.. but when i run the code using the command >>>> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png >>>> putput.png >>>> >>>>>>> 1... i see >>>> >>>>>>> >> this output >>>> >>>>>>> >> >>>> >>>>>>> >> offset: [-1, -1] [0, -1] >>>> >>>>>>> >> offset: [0, -1] [1, -1] >>>> >>>>>>> >> offset: [-1, 0] [0, 0] >>>> >>>>>>> >> offset: [0, 0] [1, 0] >>>> >>>>>>> >> offset: [-1, 1] [0, 1] >>>> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... >>>> if pls >>>> >>>>>>> tel me >>>> >>>>>>> >> how can i modify this code to work wid 2d image... forgive >>>> me if >>>> >>>>>>> my ques >>>> >>>>>>> >> are really silly im trying to learn something.. >>>> >>>>>>> >> regards >>>> >>>>>>> >> Vis >>>> >>>>>>> >> >>>> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK >>>> >>>>>>> Insight Users] >>>> >>>>>>> >> < >>>> >>>>>>> >> [hidden email] < >>>> >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>>> >>>>>>> >> wrote: >>>> >>>>>>> >> >>>> >>>>>>> >> > Hi, >>>> >>>>>>> >> > >>>> >>>>>>> >> > The function: >>>> >>>>>>> >> > >>>> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char *argv[]) >>>> >>>>>>> >> > >>>> >>>>>>> >> > must be renamed to >>>> >>>>>>> >> > >>>> >>>>>>> >> > main(int argc, char* argv[]) >>>> >>>>>>> >> > >>>> >>>>>>> >> > HTH, >>>> >>>>>>> >> > Matt >>>> >>>>>>> >> > >>>> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>> >>>>>>> >> > > >>>> wrote: >>>> >>>>>>> >> > >>>> >>>>>>> >> > > hi all, >>>> >>>>>>> >> > > im trying to build the >>>> itkTextureFeatureImageFilterTest.cxx >>>> >>>>>>> code but >>>> >>>>>>> >> im >>>> >>>>>>> >> > not >>>> >>>>>>> >> > > able to it is showing the following error >>>> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>> >>>>>>> Configuration: >>>> >>>>>>> >> Debug >>>> >>>>>>> >> > x64 >>>> >>>>>>> >> > > ------ >>>> >>>>>>> >> > > 1> Checking Build System >>>> >>>>>>> >> > > 1> CMake does not need to re-run because >>>> >>>>>>> >> > > >>>> >>>>>>> >>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>> >>>>>>> >> > is >>>> >>>>>>> >> > > up-to-date. >>>> >>>>>>> >> > > 2>------ Rebuild All started: Project: >>>> >>>>>>> >> itkTextureFeatureImageFilterTest, >>>> >>>>>>> >> > > Configuration: Debug x64 ------ >>>> >>>>>>> >> > > 2> Building Custom Rule >>>> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>> >>>>>>> >> > > 2> CMake does not need to re-run because >>>> >>>>>>> >> > > >>>> >>>>>>> >>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>> >>>>>>> >> > is >>>> >>>>>>> >> > > up-to-date. >>>> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>> >>>>>>> 'std::_Copy_impl': >>>> >>>>>>> >> > Function >>>> >>>>>>> >> > > call with parameters that may be unsafe - this call >>>> relies on >>>> >>>>>>> the >>>> >>>>>>> >> caller >>>> >>>>>>> >> > to >>>> >>>>>>> >> > > check that the passed values are correct. To disable this >>>> >>>>>>> warning, use >>>> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to >>>> use >>>> >>>>>>> Visual C++ >>>> >>>>>>> >> > > 'Checked Iterators' >>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>> Studio >>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>> >>>>>>> 'std::_Copy_impl' >>>> >>>>>>> >> > > 2> >>>> >>>>>>> >> > > >>>> >>>>>>> >> >>>> >>>>>>> >>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>> >>>>>>> >> > see >>>> >>>>>>> >> > > reference to function template instantiation '_OutIt >>>> >>>>>>> std::copy>>> >>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' being >>>> >>>>>>> compiled >>>> >>>>>>> >> > > 2> with >>>> >>>>>>> >> > > 2> [ >>>> >>>>>>> >> > > 2> _OutIt=unsigned char *, >>>> >>>>>>> >> > > 2> _InIt=const unsigned char * >>>> >>>>>>> >> > > 2> ] >>>> >>>>>>> >> > > 2> >>>> >>>>>>> >> > > >>>> >>>>>>> >> >>>> >>>>>>> >>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>> >>>>>>> >> > > while compiling class template member function 'void >>>> >>>>>>> >> > > itk::ImageFileReader::GenerateData(void)' >>>> >>>>>>> >> > > 2> with >>>> >>>>>>> >> > > 2> [ >>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>> >>>>>>> >> > > 2> ] >>>> >>>>>>> >> > > 2> >>>> >>>>>>> >> > > >>>> >>>>>>> >> > >>>> >>>>>>> >> >>>> >>>>>>> >>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>> >>>>>>> >> > >>>> >>>>>>> >> > > : see reference to class template instantiation >>>> >>>>>>> >> > > 'itk::ImageFileReader' being compiled >>>> >>>>>>> >> > > 2> with >>>> >>>>>>> >> > > 2> [ >>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>> >>>>>>> >> > > 2> ] >>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>> Studio >>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>> >>>>>>> 'std::_Copy_impl' >>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>> Studio >>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>> >>>>>>> 'std::_Copy_impl' >>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>> Studio >>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>> >>>>>>> 'std::_Copy_impl' >>>> >>>>>>> >> > > 2> Creating library >>>> >>>>>>> >> > > >>>> >>>>>>> >> > >>>> >>>>>>> >> >>>> >>>>>>> >>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>> >>>>>>> >> > >>>> >>>>>>> >> > > and object >>>> >>>>>>> >> > > >>>> >>>>>>> >> > >>>> >>>>>>> >> >>>> >>>>>>> >>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>> >>>>>>> >> > >>>> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved >>>> >>>>>>> external symbol >>>> >>>>>>> >> > main >>>> >>>>>>> >> > > referenced in function __tmainCRTStartup >>>> >>>>>>> >> > > >>>> >>>>>>> >> > >>>> >>>>>>> >> >>>> >>>>>>> >>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>> >>>>>>> >> > >>>> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>> >>>>>>> Configuration: Debug >>>> >>>>>>> >> > x64 >>>> >>>>>>> >> > > ------ >>>> >>>>>>> >> > > 3> Building Custom Rule >>>> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>> >>>>>>> >> > > 3> CMake does not need to re-run because >>>> >>>>>>> >> > > >>>> >>>>>>> >>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>> >>>>>>> >> > is >>>> >>>>>>> >> > > up-to-date. >>>> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 skipped >>>> >>>>>>> ========== >>>> >>>>>>> >> > > im using the follwing CMakeList.txt >>>> >>>>>>> >> > > # This is the root ITK CMakeLists file. >>>> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >>>> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>> >>>>>>> >> > > endif() >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > # This project is designed to be built outside the >>>> Insight >>>> >>>>>>> source >>>> >>>>>>> >> tree. >>>> >>>>>>> >> > > project(HelloWorld) >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > # Find ITK. >>>> >>>>>>> >> > > find_package(ITK REQUIRED) >>>> >>>>>>> >> > > include(${ITK_USE_FILE}) >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest >>>> >>>>>>> >> ${ITK_LIBRARIES}) >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > please tel me wat the error is?? >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > -- >>>> >>>>>>> >> > > View this message in context: >>>> >>>>>>> >> > >>>> >>>>>>> >> >>>> >>>>>>> >>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>> >>>>>>> >> > > Sent from the ITK Insight Users mailing list archive at >>>> >>>>>>> Nabble.com. >>>> >>>>>>> >> > > _____________________________________ >>>> >>>>>>> >> > > Powered by www.kitware.com >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > Visit other Kitware open-source projects at >>>> >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > Kitware offers ITK Training Courses, for more information >>>> >>>>>>> visit: >>>> >>>>>>> >> > > http://www.kitware.com/products/protraining.php >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > Please keep messages on-topic and check the ITK FAQ at: >>>> >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >>>> >>>>>>> >> > > >>>> >>>>>>> >> > > Follow this link to subscribe/unsubscribe: >>>> >>>>>>> >> > > http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>>>>> >> > _____________________________________ >>>> >>>>>>> >> > Powered by www.kitware.com >>>> >>>>>>> >> > >>>> >>>>>>> >> > Visit other Kitware open-source projects at 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in context: >>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588483.html >>>> Sent from the ITK Insight Users mailing list archive at Nabble.com. >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>> ------------------------------ >>> If you reply to this email, your message will be added to the discussion >>> below: >>> >>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588490.html >>> To start a new topic under ITK Insight Users, email [hidden email] >>> >>> To unsubscribe from ITK Insight Users, click here. >>> NAML >>> >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588495.html > To start a new topic under ITK Insight Users, email > ml-node+s2283740n2283740h75 at n2.nabble.com > To unsubscribe from ITK Insight Users, click here > > . > NAML > > -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588500.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Tue Feb 16 10:16:22 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 16 Feb 2016 10:16:22 -0500 Subject: [ITK] [ITK-users] Issue with Seed points in Geodesic Active contour In-Reply-To: References: Message-ID: Hi Naik, with directions being identity matrix and Size: [240, 240, 155] Spacing: [1, 1, 1] Origin: [0, -239, 0] the physical extent of your image is x: -0.5 to 239.5, y: -239.5 to 0.5 and z: -0.5 to 154.5 (all millimeters). In other words, x and z are positive, while y is negative. HTH, D?enan On Tue, Feb 16, 2016 at 7:40 AM, Gunjan Naik wrote: > Hi D?enan > > > > I am using T1 weighted brain tumor image from BRATS challenge. > > > > The meta information is as follows: > > Image (00000000193D62F0) > > RTTI typeinfo: class itk::Image > > Reference Count: 1 > > Modified Time: 1194 > > Debug: Off > > Object Name: > > Observers: > > none > > Source: (none) > > Source output name: (none) > > Release Data: Off > > Data Released: False > > Global Release Data: Off > > PipelineMTime: 1034 > > UpdateMTime: 1193 > > RealTimeStamp: 0 seconds > > LargestPossibleRegion: > > Dimension: 3 > > Index: [0, 0, 0] > > Size: [240, 240, 155] > > BufferedRegion: > > Dimension: 3 > > Index: [0, 0, 0] > > Size: [240, 240, 155] > > RequestedRegion: > > Dimension: 3 > > Index: [0, 0, 0] > > Size: [240, 240, 155] > > Spacing: [1, 1, 1] > > Origin: [0, -239, 0] > > Direction: > > 1 0 0 > > 0 1 0 > > 0 0 1 > > > > IndexToPointMatrix: > > 1 0 0 > > 0 1 0 > > 0 0 1 > > > > PointToIndexMatrix: > > 1 0 0 > > 0 1 0 > > 0 0 1 > > > > Inverse Direction: > > 1 0 0 > > 0 1 0 > > 0 0 1 > > > > PixelContainer: > > ImportImageContainer (000000001917BD50) > > RTTI typeinfo: class itk::ImportImageContainer __int64,short> > > Reference Count: 1 > > Modified Time: 1190 > > Debug: Off > > Object Name: > > Observers: > > none > > Pointer: 000000001B8E0040 > > Container manages memory: true > > Size: 8928000 > > Capacity: 8928000 > > > > I am passing co-ordinate to tumor region using Opencv. > > > > Thanks and Regards, > > Gunjan Naik > > > > *Gunjan G. Naik **|** Persistent LABS | PhD Student ? University of Pune* > > *gunjan_naik at persistent.com * *|** Cell: > +91-8087996979 <%2B91-8087996979> **| **Tel: +91-20-670 34878* > > *Persistent Systems Ltd. | **Partners in Innovation **| * > *www.persistent.com* > > > > *From:* D?enan Zuki? [mailto:dzenanz at gmail.com] > *Sent:* Tuesday, February 09, 2016 8:53 PM > *To:* Gunjan Naik > *Cc:* insight-users at itk.org > *Subject:* Re: [ITK-users] Issue with Seed points in Geodesic Active > contour > > > > Hi Naik, > > > > you should provide your image's meta-information e.g. by: > > std::cout< > as well as coordinates of the point which you try to pass. Then we will be > able to tell you what is wrong. > > > > Regards, > > D?enan > > > > On Tue, Feb 9, 2016 at 1:12 AM, Gunjan Naik > wrote: > > Hi All, > > > > I am using geodesic active contour for brain tumor segmentation. > > > > In that, I have to give seed points for creating level set. > > > > I have calculated seed points using opencv, but when I input these points > using ?TransformPhysicalPointToIndex? it throws error stating that index > out of bounds. > > > > It works for only points [(0,0)]. > > > > Please provide me directions. > > > > Thanks and Regards, > > Gunjan Naik > > > > > > *Gunjan G. Naik **|** Persistent LABS | PhD Student ? University of Pune* > > *gunjan_naik at persistent.com * *|** Cell: > +91-8087996979 <%2B91-8087996979> **| **Tel: +91-20-670 34878* > > *Persistent Systems Ltd. | **Partners in Innovation **| * > *www.persistent.com* > > > > DISCLAIMER ========== This e-mail may contain privileged and confidential > information which is the property of Persistent Systems Ltd. It is intended > only for the use of the individual or entity to which it is addressed. If > you are not the intended recipient, you are not authorized to read, retain, > copy, print, distribute or use this message. If you have received this > communication in error, please notify the sender and delete all copies of > this message. Persistent Systems Ltd. does not accept any liability for > virus infected mails. > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > > DISCLAIMER ========== This e-mail may contain privileged and confidential > information which is the property of Persistent Systems Ltd. It is intended > only for the use of the individual or entity to which it is addressed. If > you are not the intended recipient, you are not authorized to read, retain, > copy, print, distribute or use this message. If you have received this > communication in error, please notify the sender and delete all copies of > this message. Persistent Systems Ltd. does not accept any liability for > virus infected mails. > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Tue Feb 16 10:27:46 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 16 Feb 2016 10:27:46 -0500 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: Maybe you want to use one of the threshold filters: http://www.itk.org/Doxygen/html/classitk_1_1BinaryThresholdImageFilter.html http://www.itk.org/Doxygen/html/classitk_1_1ThresholdImageFilter.html HTH On Tue, Feb 16, 2016 at 12:37 AM, meikolin saimara wrote: > hello guys. > > I am beginner in itk. > in RGBImage we can found red pixel but > how we can get black pixel value of image. > I have a image with view black and white. > but I just need black pixel value.. > Pleas help me guys. > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Tue Feb 16 10:35:29 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 16 Feb 2016 10:35:29 -0500 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <84A225AE-400C-4FBA-97FA-6A027CB17208@mail.nih.gov> Message-ID: I have set up a project using one of the tests from Brad's repository (attached), and it works in debug mode both with his original code and with your modified class, and crashes in release mode both with his original code and with your modified class. I will now compile ITK in RelWithDebInfo in an attempt to figure out where is the crash occurring. Regards, D?enan On Tue, Feb 16, 2016 at 1:52 AM, Francisco Lopez de la Franca < franciscolopezdelafranca at gmail.com> wrote: > Excuse me Dzenanz, but that's not completely true, because I've tested > Brad's class and it works right. > The problem seems to be that when you add a new neighbor iterator to > include just the mask points in the "histogram" then it is when the > application crashes, and I donot understand why. > If you just comment the 'maskIter' references you'll see that the > application works. > I've created a single threaded class based on the Brad's code and it works > but it is twice slower, that is why I'm interesting on Brad's class > (multi-threaded) to make it work. > > > 2016-02-15 17:15 GMT+01:00 dzenanz [via ITK Insight Users] < > ml-node+s2283740n7588495h80 at n2.nabble.com>: > >> Hi Francisco, >> >> both your code and Brad's code run in debug mode (I did not wait for the >> end), and both crash in release mode immediately on startup. Here is a >> sample output: >> >> Progress input: 0000000002868970 >> input: 0000000002868970 >> _maskImage: 0000000002868970 >> _maskImage: 0000000002868970 >> input: 0000000002868970 >> _maskImage: 0000000002868970 >> iter.first: iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >> [-5, -5, -5] iter.second: [-4, -5, -5] >> niter index: [5, 5, 210] >> niter index: [5, 5, 140] >> maskIter index: [5, 5, 140] >> maskIter index: [5, 5, 210] >> Before p3 >> input: 0000000002868970 >> _maskImage: 0000000002868970 >> After p3: | 0niter index: [5, 5, 70] >> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >> niter index: [5, 5, 5] >> ? >> maskIter index: [5, 5, 70] >> After p4: ? >> Before p3 >> Before p3 >> After p3: ?iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >> niter index: [5, 5, 140] >> maskIter index: [5, 5, 140] >> maskIter index: [5, 5, 5] >> Before p3 >> After p3: ? >> After p3: ? >> After p4: ? >> After p4: ? >> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >> niter index: [5, 5, 5] >> maskIter index: [5, 5, 5] >> >> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >> Before p3 >> Before p3 >> After p4: ? >> After p3: ? >> After p4: ? >> >> Regards, >> D?enan >> >> On Mon, Feb 15, 2016 at 1:36 AM, Francisco Lopez de la Franca <[hidden >> email] > wrote: >> >>> Hi, >>> Here they are. >>> KR. >>> >>> 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>> email] >: >>> >>>> Hi Francisco, >>>> >>>> do you mind attaching the modified files or pointing to your fork of it >>>> on GitHub? >>>> >>>> Regards >>>> >>>> On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden >>>> email] > wrote: >>>> >>>>> Hi Dzenan, >>>>> The original class is here: >>>>> >>>>> >>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >>>>> >>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >>>>> >>>>> I've just added setInput and setMaskImage methods and modify some >>>>> lines in >>>>> the original class as I indicated in the yesterday mail within this >>>>> thread. >>>>> I'm running it on Windows, and there is no error at all, just a crash. >>>>> I >>>>> may have to include exceptions management. >>>>> The crash occurs just when calling p3 = maskIter.GetPixel(iter->first) >>>>> >>>>> If you know why it could be or if you need more clarification, please >>>>> let >>>>> me know. >>>>> Many thanks >>>>> >>>>> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >>>>> [hidden email] >>>>> >: >>>>> >>>>> > Hi Francisco, >>>>> > >>>>> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the error >>>>> message >>>>> > that goes along with the crash? In which file and line does it crash? >>>>> > >>>>> > Regards >>>>> > >>>>> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca >>>>> <[hidden >>>>> > email] > >>>>> wrote: >>>>> > >>>>> >> Hi, >>>>> >> Please, someone that could help me. I'm working in a pre-doctorate >>>>> >> project and I need this class to work. >>>>> >> I've read the chapter 13 in the ITK Software Guide on how to write a >>>>> >> filter and now I see the fact of the threads due to inheritance of >>>>> >> ImageToImageFilter. >>>>> >> But, I keep on without understanding why the code crashes just when >>>>> >> calling >>>>> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >>>>> >> It is just a call to read data, not to write. >>>>> >> >>>>> >> I guess somebody that had worked with creation of filters might see >>>>> >> "easily" the problem, but not me. >>>>> >> >>>>> >> So, again, please, I need someone to help me with this because I'm >>>>> stuck >>>>> >> on this point. >>>>> >> >>>>> >> Thank you very much. >>>>> >> KR. >>>>> >> /Francisco >>>>> >> >>>>> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden >>>>> email] >>>>> >> >: >>>>> >> >>>>> >>> Hi Bradley again. >>>>> >>> I'm modifying your class in order to be able to set a mask image (a >>>>> >>> binary image) to be used as a limit in the histogram calculations, >>>>> I mean, >>>>> >>> I set an input, a mask and the class should take into account to >>>>> calculate >>>>> >>> the histograms only the voxels that belong to the input and to the >>>>> mask >>>>> >>> image and having the value 1 in the mask image. >>>>> >>> The changes seem to be easy but I don?t know why my tests are not >>>>> >>> working. It seems that 2 threads are working at the same time and >>>>> when I >>>>> >>> added my mask iterator, the code crashes. >>>>> >>> >>>>> >>> *** Consider that the input and mask images are the same origin, >>>>> spacing >>>>> >>> and size. >>>>> >>> >>>>> >>> I attach the main changes I've done, and I would thank you a lot >>>>> if you >>>>> >>> don't mind having a look and help me to find what I'm doing wrong: >>>>> >>> >>>>> >>> template< class TImageType, class TOutputImage > >>>>> >>> void >>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>> >::*SetInput*(InputImageType >>>>> >>> *image) >>>>> >>> { >>>>> >>> // Process object is not const-correct so the const_cast is >>>>> required >>>>> >>> here >>>>> >>> this->ProcessObject::SetNthInput( 0, >>>>> >>> const_cast< InputImageType * >( >>>>> >>> image ) ); >>>>> >>> } >>>>> >>> >>>>> >>> template< class TImageType, class TOutputImage > >>>>> >>> void >>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>> >::*SetMaskImage*(InputImageType >>>>> >>> *image) >>>>> >>> { >>>>> >>> // Process object is not const-correct so the const_cast is >>>>> required >>>>> >>> here >>>>> >>> this->ProcessObject::SetNthInput( 1, const_cast< InputImageType >>>>> * >( >>>>> >>> image ) ); >>>>> >>> >>>>> >>> _maskImage = image; // _maskImage is a private member >>>>> >>> } >>>>> >>> >>>>> >>> In the *ThreadedGenerateData*(const RegionType& >>>>> outputRegionForThread, >>>>> >>> ThreadIdType threadId ) method: >>>>> >>> { >>>>> >>> >>>>> >>> ... >>>>> >>> >>>>> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >>>>> >>> { >>>>> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >>>>> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, *fit);* >>>>> >>> OutputIterator outIter(output, *fit); >>>>> >>> >>>>> >>> OutputPixelType out; >>>>> >>> NumericTraits::SetLength( out, >>>>> >>> this->GetNumberOfOutputComponents() ); >>>>> >>> >>>>> >>> while( !nIter.IsAtEnd() ) >>>>> >>> { >>>>> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >>>>> >>> >>>>> >>> ... >>>>> >>> >>>>> >>> ++nIter; >>>>> >>> ++outIter; >>>>> >>> * ++maskIter;* >>>>> >>> ... >>>>> >>> >>>>> >>> In the *FillHistogram *method: >>>>> >>> { >>>>> >>> >>>>> >>> ... >>>>> >>> >>>>> >>> while( iter != m_CooccurenceOffsetVector.end() ) >>>>> >>> { >>>>> >>> >>>>> >>> const PixelType p1 = niter.GetPixel(iter->first); >>>>> >>> const PixelType p2 = niter.GetPixel(iter->second); >>>>> >>> std::cout << "Before p3" << std::endl; >>>>> >>> >>>>> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); >>>>> *std::cout >>>>> >>> << "After p3: " << p3 << std::endl; >>>>> >>> >>>>> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >>>>> >>> std::cout << "After p4: " << p4 << std::endl; >>>>> >>> >>>>> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= >>>>> m_Max >>>>> >>> *&& p3 == _insidePixelValue && p4 == >>>>> _insidePixelValue* ) >>>>> >>> // The point >>>>> >>> { >>>>> >>> >>>>> >>> ... >>>>> >>> >>>>> >>> >>>>> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >>>>> >>> >>>>> >>> Thank you so much. >>>>> >>> My kind regards. >>>>> >>> /Paco >>>>> >>> >>>>> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca <[hidden >>>>> email] >>>>> >>> >: >>>>> >>> >>>>> >>>> Hello Bradley again. >>>>> >>>> Sorry but I'd like to re-open this issue because I need your >>>>> class but >>>>> >>>> with some modification. >>>>> >>>> I pass to tell you. >>>>> >>>> >>>>> >>>> As my tests with your external class were not good taking into >>>>> account >>>>> >>>> the performance, I wonder if you could create a variant of it, >>>>> but in which >>>>> >>>> I can set a mask image and your class just return the VectorImage >>>>> with all >>>>> >>>> the features for that region (the masked locations) as >>>>> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >>>>> >>>> I mean, to get the vector image with all the features but just >>>>> >>>> calculate it for the regions belonging to the mask image. >>>>> Positions not >>>>> >>>> belonging to the mask region could have a pixel value of 0, for >>>>> instance. >>>>> >>>> >>>>> >>>> I don?t know if it is very costly for you, but I would thank you >>>>> so >>>>> >>>> much. Otherwise, I could try it but I'd need your suggestions on >>>>> how to do >>>>> >>>> it. >>>>> >>>> >>>>> >>>> Thanks a lot. >>>>> >>>> Best regards. >>>>> >>>> >>>>> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca <[hidden >>>>> email] >>>>> >>>> >: >>>>> >>>> >>>>> >>>>> Hello Bradley again, >>>>> >>>>> I would like to ask you for a couple of favours. In the one hand, >>>>> >>>>> could you please send me your 3D image so that I can test on it? >>>>> And on the >>>>> >>>>> other hand, could you test the example I have referenced in the >>>>> previous >>>>> >>>>> email with your image, not changing anything in the code, such >>>>> as it is, >>>>> >>>>> and tell me if the execution time is normal? >>>>> >>>>> Thank you very much. >>>>> >>>>> Regards, >>>>> >>>>> /Francisco >>>>> >>>>> >>>>> >>>>> PS: All my application trace is printed via standard 'cout' >>>>> command, >>>>> >>>>> not due to a debugging compilation mode. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp <[hidden >>>>> >>>>> email] > >>>>> >>>>> escribi?: >>>>> >>>>> >>>>> >>>>>> Hello, >>>>> >>>>>> >>>>> >>>>>> Did you compile TextureFeatureImage in Release mode? >>>>> >>>>>> >>>>> >>>>>> 1) The filter does not scale well with a large radius. And >>>>> given by >>>>> >>>>>> your initial report of print a very large number of offset you, >>>>> it sounds >>>>> >>>>>> like you are using a large radius with many offsets. I created a >>>>> >>>>>> 224x224x300 unsigned short image and ran with the default >>>>> offset and a >>>>> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this filter >>>>> is was ~10x >>>>> >>>>>> faster than this example... things change though... >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>>>> 2) I sounds like the boundaries/limits of the histogram may be >>>>> >>>>>> clipping you values. I would inspect the co-occurance matrix. >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>>>> HTH, >>>>> >>>>>> Brad >>>>> >>>>>> >>>>> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca >>>>> <[hidden >>>>> >>>>>> email] > >>>>> >>>>>> wrote: >>>>> >>>>>> >>>>> >>>>>> I've tested with itkTextureFeatureImageFilter, with >>>>> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>>> >>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures >>>>> example, >>>>> >>>>>> for a 3D image and here are my comments: >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>>>> 1. I had to interrupt the test after several hours and it kept >>>>> on >>>>> >>>>>> calculating. And this is for only a 3D image (224x224x300). I >>>>> need to >>>>> >>>>>> process around 35 images. >>>>> >>>>>> 2. The result (texture features: entropy, energy, correlation, >>>>> LH, >>>>> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, >>>>> 7.83083e+247]. >>>>> >>>>>> These values were not what I expected based on my experience on >>>>> another >>>>> >>>>>> application I developed, but in that case, I calculated the >>>>> texture >>>>> >>>>>> features for an image as a whole, not voxel by voxel. >>>>> >>>>>> >>>>> >>>>>> Regards. >>>>> >>>>>> >>>>> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >>>>> >>>>>> >: >>>>> >>>>>> >>>>> >>>>>>> i yes i have tried radius = 3; >>>>> >>>>>>> still no luck >>>>> >>>>>>> >>>>> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via >>>>> ITK >>>>> >>>>>>> Insight >>>>> >>>>>>> Users] <[hidden email] >>>>> >>>>>>> > >>>>> wrote: >>>>> >>>>>>> >>>>> >>>>>>> > Have you tried with a radius of 3 instead of 1? >>>>> >>>>>>> > >>>>> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>>> >>>>>>> > >: >>>>> >>>>>>> > >>>>> >>>>>>> >> hey Matt, >>>>> >>>>>>> >> thanks for ur advice.. it did build successfully... but im >>>>> not >>>>> >>>>>>> able to run >>>>> >>>>>>> >> the code for 2D png image... i tried to change the >>>>> dimension to 2 >>>>> >>>>>>> and >>>>> >>>>>>> >> build >>>>> >>>>>>> >> it which it did.. but when i run the code using the command >>>>> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png >>>>> putput.png >>>>> >>>>>>> 1... i see >>>>> >>>>>>> >> this output >>>>> >>>>>>> >> >>>>> >>>>>>> >> offset: [-1, -1] [0, -1] >>>>> >>>>>>> >> offset: [0, -1] [1, -1] >>>>> >>>>>>> >> offset: [-1, 0] [0, 0] >>>>> >>>>>>> >> offset: [0, 0] [1, 0] >>>>> >>>>>>> >> offset: [-1, 1] [0, 1] >>>>> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... >>>>> if pls >>>>> >>>>>>> tel me >>>>> >>>>>>> >> how can i modify this code to work wid 2d image... forgive >>>>> me if >>>>> >>>>>>> my ques >>>>> >>>>>>> >> are really silly im trying to learn something.. >>>>> >>>>>>> >> regards >>>>> >>>>>>> >> Vis >>>>> >>>>>>> >> >>>>> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK >>>>> >>>>>>> Insight Users] >>>>> >>>>>>> >> < >>>>> >>>>>>> >> [hidden email] < >>>>> >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>>>> >>>>>>> >> wrote: >>>>> >>>>>>> >> >>>>> >>>>>>> >> > Hi, >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > The function: >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char *argv[]) >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > must be renamed to >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > main(int argc, char* argv[]) >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > HTH, >>>>> >>>>>>> >> > Matt >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>>> >>>>>>> >> > > >>>>> wrote: >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > > hi all, >>>>> >>>>>>> >> > > im trying to build the >>>>> itkTextureFeatureImageFilterTest.cxx >>>>> >>>>>>> code but >>>>> >>>>>>> >> im >>>>> >>>>>>> >> > not >>>>> >>>>>>> >> > > able to it is showing the following error >>>>> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>>> >>>>>>> Configuration: >>>>> >>>>>>> >> Debug >>>>> >>>>>>> >> > x64 >>>>> >>>>>>> >> > > ------ >>>>> >>>>>>> >> > > 1> Checking Build System >>>>> >>>>>>> >> > > 1> CMake does not need to re-run because >>>>> >>>>>>> >> > > >>>>> >>>>>>> >>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>>> >>>>>>> >> > is >>>>> >>>>>>> >> > > up-to-date. >>>>> >>>>>>> >> > > 2>------ Rebuild All started: Project: >>>>> >>>>>>> >> itkTextureFeatureImageFilterTest, >>>>> >>>>>>> >> > > Configuration: Debug x64 ------ >>>>> >>>>>>> >> > > 2> Building Custom Rule >>>>> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>> >>>>>>> >> > > 2> CMake does not need to re-run because >>>>> >>>>>>> >> > > >>>>> >>>>>>> >>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>> >>>>>>> >> > is >>>>> >>>>>>> >> > > up-to-date. >>>>> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>>> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>>> >>>>>>> 'std::_Copy_impl': >>>>> >>>>>>> >> > Function >>>>> >>>>>>> >> > > call with parameters that may be unsafe - this call >>>>> relies on >>>>> >>>>>>> the >>>>> >>>>>>> >> caller >>>>> >>>>>>> >> > to >>>>> >>>>>>> >> > > check that the passed values are correct. To disable >>>>> this >>>>> >>>>>>> warning, use >>>>> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to >>>>> use >>>>> >>>>>>> Visual C++ >>>>> >>>>>>> >> > > 'Checked Iterators' >>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>> Studio >>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>> >>>>>>> 'std::_Copy_impl' >>>>> >>>>>>> >> > > 2> >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> >>>>> >>>>>>> >>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>>> >>>>>>> >> > see >>>>> >>>>>>> >> > > reference to function template instantiation '_OutIt >>>>> >>>>>>> std::copy>>>> >>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' >>>>> being >>>>> >>>>>>> compiled >>>>> >>>>>>> >> > > 2> with >>>>> >>>>>>> >> > > 2> [ >>>>> >>>>>>> >> > > 2> _OutIt=unsigned char *, >>>>> >>>>>>> >> > > 2> _InIt=const unsigned char * >>>>> >>>>>>> >> > > 2> ] >>>>> >>>>>>> >> > > 2> >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> >>>>> >>>>>>> >>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>>> >>>>>>> >> > > while compiling class template member function 'void >>>>> >>>>>>> >> > > itk::ImageFileReader::GenerateData(void)' >>>>> >>>>>>> >> > > 2> with >>>>> >>>>>>> >> > > 2> [ >>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>> >>>>>>> >> > > 2> ] >>>>> >>>>>>> >> > > 2> >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > >>>>> >>>>>>> >> >>>>> >>>>>>> >>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > > : see reference to class template instantiation >>>>> >>>>>>> >> > > 'itk::ImageFileReader' being compiled >>>>> >>>>>>> >> > > 2> with >>>>> >>>>>>> >> > > 2> [ >>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>> >>>>>>> >> > > 2> ] >>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>> Studio >>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>> >>>>>>> 'std::_Copy_impl' >>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>> Studio >>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>> >>>>>>> 'std::_Copy_impl' >>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>> Studio >>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>> >>>>>>> 'std::_Copy_impl' >>>>> >>>>>>> >> > > 2> Creating library >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > >>>>> >>>>>>> >> >>>>> >>>>>>> >>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > > and object >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > >>>>> >>>>>>> >> >>>>> >>>>>>> >>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved >>>>> >>>>>>> external symbol >>>>> >>>>>>> >> > main >>>>> >>>>>>> >> > > referenced in function __tmainCRTStartup >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > >>>>> >>>>>>> >> >>>>> >>>>>>> >>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>>> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>>> >>>>>>> Configuration: Debug >>>>> >>>>>>> >> > x64 >>>>> >>>>>>> >> > > ------ >>>>> >>>>>>> >> > > 3> Building Custom Rule >>>>> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>> >>>>>>> >> > > 3> CMake does not need to re-run because >>>>> >>>>>>> >> > > >>>>> >>>>>>> >>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>> >>>>>>> >> > is >>>>> >>>>>>> >> > > up-to-date. >>>>> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 skipped >>>>> >>>>>>> ========== >>>>> >>>>>>> >> > > im using the follwing CMakeList.txt >>>>> >>>>>>> >> > > # This is the root ITK CMakeLists file. >>>>> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>>> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >>>>> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>>> >>>>>>> >> > > endif() >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > > # This project is designed to be built outside the >>>>> Insight >>>>> >>>>>>> source >>>>> >>>>>>> >> tree. >>>>> >>>>>>> >> > > project(HelloWorld) >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > > # Find ITK. >>>>> >>>>>>> >> > > find_package(ITK REQUIRED) >>>>> >>>>>>> >> > > include(${ITK_USE_FILE}) >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>>> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest >>>>> >>>>>>> >> ${ITK_LIBRARIES}) >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > > please tel me wat the error is?? >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > > -- >>>>> >>>>>>> >> > > View this message in context: >>>>> >>>>>>> >> > >>>>> >>>>>>> >> >>>>> >>>>>>> >>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>>> >>>>>>> >> > > Sent from the ITK Insight Users mailing list archive at >>>>> >>>>>>> Nabble.com. >>>>> >>>>>>> >> > > _____________________________________ >>>>> >>>>>>> >> > > Powered by www.kitware.com >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > > Visit other Kitware open-source projects at >>>>> >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > > Kitware offers ITK Training Courses, for more >>>>> information >>>>> >>>>>>> visit: >>>>> >>>>>>> >> > > http://www.kitware.com/products/protraining.php >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > > Please keep messages on-topic and check the ITK FAQ at: >>>>> >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>>>> >> > > >>>>> >>>>>>> >> > > Follow this link to subscribe/unsubscribe: >>>>> >>>>>>> >> > > >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>>>>> >> > _____________________________________ >>>>> >>>>>>> >> > Powered by www.kitware.com >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > Visit other Kitware open-source projects at >>>>> >>>>>>> >> > http://www.kitware.com/opensource/opensource.html >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > Kitware offers ITK Training Courses, for more information >>>>> visit: >>>>> >>>>>>> >> > http://www.kitware.com/products/protraining.php >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > Please keep messages on-topic and check the ITK FAQ at: >>>>> >>>>>>> >> > http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > Follow this link to subscribe/unsubscribe: >>>>> >>>>>>> >> > http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > >>>>> >>>>>>> >> > ------------------------------ >>>>> >>>>>>> >> > If you reply to this email, your message will be added to >>>>> the >>>>> >>>>>>> discussion >>>>> 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>>>>> >>>>>>> >> View this message in context: >>>>> >>>>>>> >> >>>>> >>>>>>> >>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587960.html >>>>> >>>>>>> >> Sent from the ITK Insight Users mailing list archive at >>>>> >>>>>>> Nabble.com. >>>>> >>>>>>> >> _____________________________________ >>>>> >>>>>>> >> Powered by www.kitware.com >>>>> >>>>>>> >> >>>>> >>>>>>> >> Visit other Kitware open-source projects at >>>>> >>>>>>> >> http://www.kitware.com/opensource/opensource.html >>>>> >>>>>>> >> >>>>> >>>>>>> >> Kitware offers ITK Training Courses, for more information >>>>> visit: >>>>> >>>>>>> >> http://www.kitware.com/products/protraining.php >>>>> >>>>>>> >> >>>>> >>>>>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>> >>>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>>>> >> >>>>> >>>>>>> >> Follow this link to subscribe/unsubscribe: >>>>> >>>>>>> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>>>>> >> >>>>> >>>>>>> > >>>>> >>>>>>> > >>>>> >>>>>>> > _____________________________________ >>>>> >>>>>>> > Powered by www.kitware.com >>>>> >>>>>>> > >>>>> >>>>>>> > Visit other Kitware open-source projects at >>>>> >>>>>>> > http://www.kitware.com/opensource/opensource.html >>>>> >>>>>>> > >>>>> >>>>>>> > Kitware offers ITK Training Courses, for more information >>>>> visit: >>>>> >>>>>>> > http://www.kitware.com/products/protraining.php >>>>> >>>>>>> > >>>>> >>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>> >>>>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>>>> > >>>>> >>>>>>> > Follow this link to subscribe/unsubscribe: >>>>> >>>>>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>>>>> > >>>>> >>>>>>> > >>>>> >>>>>>> > ------------------------------ >>>>> >>>>>>> > If you reply to this email, your message will be added to the >>>>> >>>>>>> discussion >>>>> >>>>>>> > below: >>>>> >>>>>>> > >>>>> >>>>>>> > >>>>> >>>>>>> >>>>> 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http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587963.html >>>>> >>>>>>> Sent from the ITK Insight Users mailing list archive at >>>>> Nabble.com. >>>>> >>>>>>> _____________________________________ >>>>> >>>>>>> Powered by www.kitware.com >>>>> >>>>>>> >>>>> >>>>>>> Visit other Kitware open-source projects at >>>>> >>>>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>>>> >>>>> >>>>>>> Kitware offers ITK Training Courses, for more information >>>>> visit: >>>>> >>>>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>>>> >>>>> >>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> >>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>>>> >>>>> >>>>>>> Follow this link to subscribe/unsubscribe: >>>>> >>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>>>>> >>>>> >>>>>> >>>>> >>>>>> _____________________________________ >>>>> >>>>>> Powered by www.kitware.com >>>>> >>>>>> >>>>> >>>>>> Visit other Kitware open-source projects at >>>>> >>>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>>> >>>>> >>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> >>>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>>> >>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>>> >>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>> >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>> >>>>> >>> >>>>> >> >>>>> >> _____________________________________ >>>>> >> Powered by www.kitware.com >>>>> >> >>>>> >> Visit other Kitware open-source projects at >>>>> >> http://www.kitware.com/opensource/opensource.html >>>>> >> >>>>> >> Kitware offers ITK Training Courses, for more information visit: >>>>> >> http://www.kitware.com/products/protraining.php >>>>> >> >>>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>> >> >>>>> >> Follow this link to subscribe/unsubscribe: >>>>> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >> >>>>> >> >>>>> > >>>>> > _____________________________________ >>>>> > Powered by www.kitware.com >>>>> > >>>>> > Visit other Kitware open-source projects at >>>>> > http://www.kitware.com/opensource/opensource.html >>>>> > >>>>> > Kitware offers ITK Training Courses, for more information visit: >>>>> > http://www.kitware.com/products/protraining.php >>>>> > >>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>> > >>>>> > Follow this link to subscribe/unsubscribe: >>>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>> > >>>>> > >>>>> > ------------------------------ >>>>> > If you reply to this email, your message will be added to the >>>>> discussion >>>>> > below: >>>>> > >>>>> > >>>>> 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URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: tester.cpp Type: text/x-c++src Size: 1765 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Feb 16 12:52:45 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 16 Feb 2016 12:52:45 -0500 Subject: [ITK] Insight Journal down today for maintenance Message-ID: Hi folks, The Insight Journal will be down today for maintenance from 5:30 - 6:00 PM EST. Matt From blowekamp at mail.nih.gov Tue Feb 16 16:03:45 2016 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 16 Feb 2016 16:03:45 -0500 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <84A225AE-400C-4FBA-97FA-6A027CB17208@mail.nih.gov> Message-ID: <3F877AC4-BCD1-43FF-B8B3-7B30F9B6D30B@mail.nih.gov> Hello, Please take a look at these changes: https://github.com/blowekamp/itkTextureAnalysis/commit/9654d74ea1d09f0677f1d1b93242cc94340591bf Brad > On Feb 16, 2016, at 10:35 AM, D?enan Zuki? wrote: > > I have set up a project using one of the tests from Brad's repository (attached), and it works in debug mode both with his original code and with your modified class, and crashes in release mode both with his original code and with your modified class. I will now compile ITK in RelWithDebInfo in an attempt to figure out where is the crash occurring. > > Regards, > D?enan > > On Tue, Feb 16, 2016 at 1:52 AM, Francisco Lopez de la Franca > wrote: > Excuse me Dzenanz, but that's not completely true, because I've tested Brad's class and it works right. > The problem seems to be that when you add a new neighbor iterator to include just the mask points in the "histogram" then it is when the application crashes, and I donot understand why. > If you just comment the 'maskIter' references you'll see that the application works. > I've created a single threaded class based on the Brad's code and it works but it is twice slower, that is why I'm interesting on Brad's class (multi-threaded) to make it work. > > > 2016-02-15 17:15 GMT+01:00 dzenanz [via ITK Insight Users] >: > Hi Francisco, > > both your code and Brad's code run in debug mode (I did not wait for the end), and both crash in release mode immediately on startup. Here is a sample output: > > Progress input: 0000000002868970 > input: 0000000002868970 > _maskImage: 0000000002868970 > _maskImage: 0000000002868970 > input: 0000000002868970 > _maskImage: 0000000002868970 > iter.first: iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] > iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] > [-5, -5, -5] iter.second: [-4, -5, -5] > niter index: [5, 5, 210] > niter index: [5, 5, 140] > maskIter index: [5, 5, 140] > maskIter index: [5, 5, 210] > Before p3 > input: 0000000002868970 > _maskImage: 0000000002868970 > After p3: | 0niter index: [5, 5, 70] > iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] > niter index: [5, 5, 5] > ? > maskIter index: [5, 5, 70] > After p4: ? > Before p3 > Before p3 > After p3: ?iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] > niter index: [5, 5, 140] > maskIter index: [5, 5, 140] > maskIter index: [5, 5, 5] > Before p3 > After p3: ? > After p3: ? > After p4: ? > After p4: ? > iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] > niter index: [5, 5, 5] > maskIter index: [5, 5, 5] > > iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] > Before p3 > Before p3 > After p4: ? > After p3: ? > After p4: ? > > Regards, > D?enan > > On Mon, Feb 15, 2016 at 1:36 AM, Francisco Lopez de la Franca <[hidden email] > wrote: > Hi, > Here they are. > KR. > > 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden email] >: > Hi Francisco, > > do you mind attaching the modified files or pointing to your fork of it on GitHub? > > Regards > > On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden email] > wrote: > Hi Dzenan, > The original class is here: > > https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h > https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx > > I've just added setInput and setMaskImage methods and modify some lines in > the original class as I indicated in the yesterday mail within this thread. > I'm running it on Windows, and there is no error at all, just a crash. I > may have to include exceptions management. > The crash occurs just when calling p3 = maskIter.GetPixel(iter->first) > > If you know why it could be or if you need more clarification, please let > me know. > Many thanks > > 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < > [hidden email] >: > > > Hi Francisco, > > > > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the error message > > that goes along with the crash? In which file and line does it crash? > > > > Regards > > > > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca <[hidden > > email] > wrote: > > > >> Hi, > >> Please, someone that could help me. I'm working in a pre-doctorate > >> project and I need this class to work. > >> I've read the chapter 13 in the ITK Software Guide on how to write a > >> filter and now I see the fact of the threads due to inheritance of > >> ImageToImageFilter. > >> But, I keep on without understanding why the code crashes just when > >> calling > >> *const PixelType p3 = maskIter.GetPixel(iter->first);* > >> It is just a call to read data, not to write. > >> > >> I guess somebody that had worked with creation of filters might see > >> "easily" the problem, but not me. > >> > >> So, again, please, I need someone to help me with this because I'm stuck > >> on this point. > >> > >> Thank you very much. > >> KR. > >> /Francisco > >> > >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden email] > >> >: > >> > >>> Hi Bradley again. > >>> I'm modifying your class in order to be able to set a mask image (a > >>> binary image) to be used as a limit in the histogram calculations, I mean, > >>> I set an input, a mask and the class should take into account to calculate > >>> the histograms only the voxels that belong to the input and to the mask > >>> image and having the value 1 in the mask image. > >>> The changes seem to be easy but I don?t know why my tests are not > >>> working. It seems that 2 threads are working at the same time and when I > >>> added my mask iterator, the code crashes. > >>> > >>> *** Consider that the input and mask images are the same origin, spacing > >>> and size. > >>> > >>> I attach the main changes I've done, and I would thank you a lot if you > >>> don't mind having a look and help me to find what I'm doing wrong: > >>> > >>> template< class TImageType, class TOutputImage > > >>> void > >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >::*SetInput*(InputImageType > >>> *image) > >>> { > >>> // Process object is not const-correct so the const_cast is required > >>> here > >>> this->ProcessObject::SetNthInput( 0, > >>> const_cast< InputImageType * >( > >>> image ) ); > >>> } > >>> > >>> template< class TImageType, class TOutputImage > > >>> void > >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >::*SetMaskImage*(InputImageType > >>> *image) > >>> { > >>> // Process object is not const-correct so the const_cast is required > >>> here > >>> this->ProcessObject::SetNthInput( 1, const_cast< InputImageType * >( > >>> image ) ); > >>> > >>> _maskImage = image; // _maskImage is a private member > >>> } > >>> > >>> In the *ThreadedGenerateData*(const RegionType& outputRegionForThread, > >>> ThreadIdType threadId ) method: > >>> { > >>> > >>> ... > >>> > >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) > >>> { > >>> NeighborhoodIteratorType nIter( radius, input, *fit ); > >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, *fit);* > >>> OutputIterator outIter(output, *fit); > >>> > >>> OutputPixelType out; > >>> NumericTraits::SetLength( out, > >>> this->GetNumberOfOutputComponents() ); > >>> > >>> while( !nIter.IsAtEnd() ) > >>> { > >>> this->FillHistogram( *histogram, nIter, *maskIter *); > >>> > >>> ... > >>> > >>> ++nIter; > >>> ++outIter; > >>> * ++maskIter;* > >>> ... > >>> > >>> In the *FillHistogram *method: > >>> { > >>> > >>> ... > >>> > >>> while( iter != m_CooccurenceOffsetVector.end() ) > >>> { > >>> > >>> const PixelType p1 = niter.GetPixel(iter->first); > >>> const PixelType p2 = niter.GetPixel(iter->second); > >>> std::cout << "Before p3" << std::endl; > >>> > >>> * const PixelType p3 = maskIter.GetPixel(iter->first); *std::cout > >>> << "After p3: " << p3 << std::endl; > >>> > >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * > >>> std::cout << "After p4: " << p4 << std::endl; > >>> > >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= m_Max > >>> *&& p3 == _insidePixelValue && p4 == _insidePixelValue* ) > >>> // The point > >>> { > >>> > >>> ... > >>> > >>> > >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* > >>> > >>> Thank you so much. > >>> My kind regards. > >>> /Paco > >>> > >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca <[hidden email] > >>> >: > >>> > >>>> Hello Bradley again. > >>>> Sorry but I'd like to re-open this issue because I need your class but > >>>> with some modification. > >>>> I pass to tell you. > >>>> > >>>> As my tests with your external class were not good taking into account > >>>> the performance, I wonder if you could create a variant of it, but in which > >>>> I can set a mask image and your class just return the VectorImage with all > >>>> the features for that region (the masked locations) as > >>>> itk::ScalarImageToTextureFeaturesFilter class does. > >>>> I mean, to get the vector image with all the features but just > >>>> calculate it for the regions belonging to the mask image. Positions not > >>>> belonging to the mask region could have a pixel value of 0, for instance. > >>>> > >>>> I don?t know if it is very costly for you, but I would thank you so > >>>> much. Otherwise, I could try it but I'd need your suggestions on how to do > >>>> it. > >>>> > >>>> Thanks a lot. > >>>> Best regards. > >>>> > >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca <[hidden email] > >>>> >: > >>>> > >>>>> Hello Bradley again, > >>>>> I would like to ask you for a couple of favours. In the one hand, > >>>>> could you please send me your 3D image so that I can test on it? And on the > >>>>> other hand, could you test the example I have referenced in the previous > >>>>> email with your image, not changing anything in the code, such as it is, > >>>>> and tell me if the execution time is normal? > >>>>> Thank you very much. > >>>>> Regards, > >>>>> /Francisco > >>>>> > >>>>> PS: All my application trace is printed via standard 'cout' command, > >>>>> not due to a debugging compilation mode. > >>>>> > >>>>> > >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp <[hidden > >>>>> email] > > >>>>> escribi?: > >>>>> > >>>>>> Hello, > >>>>>> > >>>>>> Did you compile TextureFeatureImage in Release mode? > >>>>>> > >>>>>> 1) The filter does not scale well with a large radius. And given by > >>>>>> your initial report of print a very large number of offset you, it sounds > >>>>>> like you are using a large radius with many offsets. I created a > >>>>>> 224x224x300 unsigned short image and ran with the default offset and a > >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this filter is was ~10x > >>>>>> faster than this example... things change though... > >>>>>> > >>>>>> > >>>>>> 2) I sounds like the boundaries/limits of the histogram may be > >>>>>> clipping you values. I would inspect the co-occurance matrix. > >>>>>> > >>>>>> > >>>>>> HTH, > >>>>>> Brad > >>>>>> > >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca <[hidden > >>>>>> email] > > >>>>>> wrote: > >>>>>> > >>>>>> I've tested with itkTextureFeatureImageFilter, with > >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the > >>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures example, > >>>>>> for a 3D image and here are my comments: > >>>>>> > >>>>>> > >>>>>> 1. I had to interrupt the test after several hours and it kept on > >>>>>> calculating. And this is for only a 3D image (224x224x300). I need to > >>>>>> process around 35 images. > >>>>>> 2. The result (texture features: entropy, energy, correlation, LH, > >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, 7.83083e+247]. > >>>>>> These values were not what I expected based on my experience on another > >>>>>> application I developed, but in that case, I calculated the texture > >>>>>> features for an image as a whole, not voxel by voxel. > >>>>>> > >>>>>> Regards. > >>>>>> > >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] > >>>>>> >: > >>>>>> > >>>>>>> i yes i have tried radius = 3; > >>>>>>> still no luck > >>>>>>> > >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via ITK > >>>>>>> Insight > >>>>>>> Users] <[hidden email] > >>>>>>> > wrote: > >>>>>>> > >>>>>>> > Have you tried with a radius of 3 instead of 1? > >>>>>>> > > >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] > >>>>>>> > >: > >>>>>>> > > >>>>>>> >> hey Matt, > >>>>>>> >> thanks for ur advice.. it did build successfully... but im not > >>>>>>> able to run > >>>>>>> >> the code for 2D png image... i tried to change the dimension to 2 > >>>>>>> and > >>>>>>> >> build > >>>>>>> >> it which it did.. but when i run the code using the command > >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png putput.png > >>>>>>> 1... i see > >>>>>>> >> this output > >>>>>>> >> > >>>>>>> >> offset: [-1, -1] [0, -1] > >>>>>>> >> offset: [0, -1] [1, -1] > >>>>>>> >> offset: [-1, 0] [0, 0] > >>>>>>> >> offset: [0, 0] [1, 0] > >>>>>>> >> offset: [-1, 1] [0, 1] > >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... if pls > >>>>>>> tel me > >>>>>>> >> how can i modify this code to work wid 2d image... forgive me if > >>>>>>> my ques > >>>>>>> >> are really silly im trying to learn something.. > >>>>>>> >> regards > >>>>>>> >> Vis > >>>>>>> >> > >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK > >>>>>>> Insight Users] > >>>>>>> >> < > >>>>>>> >> [hidden email] < > >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> > >>>>>>> >> wrote: > >>>>>>> >> > >>>>>>> >> > Hi, > >>>>>>> >> > > >>>>>>> >> > The function: > >>>>>>> >> > > >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char *argv[]) > >>>>>>> >> > > >>>>>>> >> > must be renamed to > >>>>>>> >> > > >>>>>>> >> > main(int argc, char* argv[]) > >>>>>>> >> > > >>>>>>> >> > HTH, > >>>>>>> >> > Matt > >>>>>>> >> > > >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] > >>>>>>> >> > > wrote: > >>>>>>> >> > > >>>>>>> >> > > hi all, > >>>>>>> >> > > im trying to build the itkTextureFeatureImageFilterTest.cxx > >>>>>>> code but > >>>>>>> >> im > >>>>>>> >> > not > >>>>>>> >> > > able to it is showing the following error > >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, > >>>>>>> Configuration: > >>>>>>> >> Debug > >>>>>>> >> > x64 > >>>>>>> >> > > ------ > >>>>>>> >> > > 1> Checking Build System > >>>>>>> >> > > 1> CMake does not need to re-run because > >>>>>>> >> > > > >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp > >>>>>>> >> > is > >>>>>>> >> > > up-to-date. > >>>>>>> >> > > 2>------ Rebuild All started: Project: > >>>>>>> >> itkTextureFeatureImageFilterTest, > >>>>>>> >> > > Configuration: Debug x64 ------ > >>>>>>> >> > > 2> Building Custom Rule > >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt > >>>>>>> >> > > 2> CMake does not need to re-run because > >>>>>>> >> > > > >>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp > >>>>>>> >> > is > >>>>>>> >> > > up-to-date. > >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx > >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio > >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: > >>>>>>> 'std::_Copy_impl': > >>>>>>> >> > Function > >>>>>>> >> > > call with parameters that may be unsafe - this call relies on > >>>>>>> the > >>>>>>> >> caller > >>>>>>> >> > to > >>>>>>> >> > > check that the passed values are correct. To disable this > >>>>>>> warning, use > >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to use > >>>>>>> Visual C++ > >>>>>>> >> > > 'Checked Iterators' > >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio > >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of > >>>>>>> 'std::_Copy_impl' > >>>>>>> >> > > 2> > >>>>>>> >> > > > >>>>>>> >> > >>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : > >>>>>>> >> > see > >>>>>>> >> > > reference to function template instantiation '_OutIt > >>>>>>> std::copy >>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' being > >>>>>>> compiled > >>>>>>> >> > > 2> with > >>>>>>> >> > > 2> [ > >>>>>>> >> > > 2> _OutIt=unsigned char *, > >>>>>>> >> > > 2> _InIt=const unsigned char * > >>>>>>> >> > > 2> ] > >>>>>>> >> > > 2> > >>>>>>> >> > > > >>>>>>> >> > >>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : > >>>>>>> >> > > while compiling class template member function 'void > >>>>>>> >> > > itk::ImageFileReader::GenerateData(void)' > >>>>>>> >> > > 2> with > >>>>>>> >> > > 2> [ > >>>>>>> >> > > 2> TOutputImage=InputImageType > >>>>>>> >> > > 2> ] > >>>>>>> >> > > 2> > >>>>>>> >> > > > >>>>>>> >> > > >>>>>>> >> > >>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) > >>>>>>> >> > > >>>>>>> >> > > : see reference to class template instantiation > >>>>>>> >> > > 'itk::ImageFileReader' being compiled > >>>>>>> >> > > 2> with > >>>>>>> >> > > 2> [ > >>>>>>> >> > > 2> TOutputImage=InputImageType > >>>>>>> >> > > 2> ] > >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio > >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of > >>>>>>> 'std::_Copy_impl' > >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio > >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of > >>>>>>> 'std::_Copy_impl' > >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio > >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of > >>>>>>> 'std::_Copy_impl' > >>>>>>> >> > > 2> Creating library > >>>>>>> >> > > > >>>>>>> >> > > >>>>>>> >> > >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib > >>>>>>> >> > > >>>>>>> >> > > and object > >>>>>>> >> > > > >>>>>>> >> > > >>>>>>> >> > >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp > >>>>>>> >> > > >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved > >>>>>>> external symbol > >>>>>>> >> > main > >>>>>>> >> > > referenced in function __tmainCRTStartup > >>>>>>> >> > > > >>>>>>> >> > > >>>>>>> >> > >>>>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe > >>>>>>> >> > > >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals > >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, > >>>>>>> Configuration: Debug > >>>>>>> >> > x64 > >>>>>>> >> > > ------ > >>>>>>> >> > > 3> Building Custom Rule > >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt > >>>>>>> >> > > 3> CMake does not need to re-run because > >>>>>>> >> > > > >>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp > >>>>>>> >> > is > >>>>>>> >> > > up-to-date. > >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 skipped > >>>>>>> ========== > >>>>>>> >> > > im using the follwing CMakeList.txt > >>>>>>> >> > > # This is the root ITK CMakeLists file. > >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) > >>>>>>> >> > > if(COMMAND CMAKE_POLICY) > >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) > >>>>>>> >> > > endif() > >>>>>>> >> > > > >>>>>>> >> > > > >>>>>>> >> > > # This project is designed to be built outside the Insight > >>>>>>> source > >>>>>>> >> tree. > >>>>>>> >> > > project(HelloWorld) > >>>>>>> >> > > > >>>>>>> >> > > # Find ITK. > >>>>>>> >> > > find_package(ITK REQUIRED) > >>>>>>> >> > > include(${ITK_USE_FILE}) > >>>>>>> >> > > > >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest > >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) > >>>>>>> >> > > > >>>>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest > >>>>>>> >> ${ITK_LIBRARIES}) > >>>>>>> >> > > > >>>>>>> >> > > please tel me wat the error is?? > >>>>>>> >> > > > >>>>>>> >> > > > >>>>>>> >> > > > >>>>>>> >> > > -- > >>>>>>> >> > > View this message in context: > >>>>>>> >> > > >>>>>>> >> > >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html > >>>>>>> >> > > Sent from the ITK Insight Users mailing list archive at > >>>>>>> Nabble.com. > >>>>>>> >> > > _____________________________________ > >>>>>>> >> > > Powered by www.kitware.com > >>>>>>> >> > > > >>>>>>> >> > > Visit other Kitware open-source projects at > >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html > >>>>>>> >> > > > >>>>>>> >> > > Kitware offers ITK Training Courses, for more information > >>>>>>> visit: > >>>>>>> >> > > http://www.kitware.com/products/protraining.php > >>>>>>> >> > > > >>>>>>> >> > > Please keep messages on-topic and check the ITK FAQ at: > >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ > >>>>>>> >> > > > >>>>>>> >> > > Follow this link to subscribe/unsubscribe: > >>>>>>> >> > > http://public.kitware.com/mailman/listinfo/insight-users > >>>>>>> >> > _____________________________________ > >>>>>>> >> > Powered by www.kitware.com > >>>>>>> >> > > >>>>>>> >> > Visit other Kitware open-source projects at > >>>>>>> >> > http://www.kitware.com/opensource/opensource.html > >>>>>>> >> > > >>>>>>> >> > Kitware offers ITK Training Courses, for more information visit: > >>>>>>> >> > http://www.kitware.com/products/protraining.php > >>>>>>> >> > > >>>>>>> >> > Please keep messages on-topic and check the ITK FAQ at: > >>>>>>> >> > http://www.itk.org/Wiki/ITK_FAQ > >>>>>>> >> > > >>>>>>> >> > Follow this link to subscribe/unsubscribe: > >>>>>>> >> > http://public.kitware.com/mailman/listinfo/insight-users > >>>>>>> >> > > >>>>>>> >> > > >>>>>>> >> > ------------------------------ > >>>>>>> >> > If you reply to this email, your message will be added to the > >>>>>>> discussion > >>>>>>> >> > below: > >>>>>>> >> > > >>>>>>> >> > > >>>>>>> >> > >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587952.html > >>>>>>> >> > To unsubscribe from [ITK-users] Texture pixel by pixel, click > >>>>>>> here > >>>>>>> >> > < > . > >>>>>>> >> > NAML > >>>>>>> >> > < > >>>>>>> >> > >>>>>>> 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>>>>>>> > > >>>>>>> > Follow this link to subscribe/unsubscribe: > >>>>>>> > http://public.kitware.com/mailman/listinfo/insight-users > >>>>>>> > > >>>>>>> > > >>>>>>> > ------------------------------ > >>>>>>> > If you reply to this email, your message will be added to the > >>>>>>> discussion > >>>>>>> > below: > >>>>>>> > > >>>>>>> > > >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587961.html > >>>>>>> > To unsubscribe from [ITK-users] Texture pixel by pixel, click here > >>>>>>> > < > . > >>>>>>> > NAML > >>>>>>> > < > >>>>>>> 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Kitware offers ITK Training Courses, for more information visit: > >>>>>>> http://www.kitware.com/products/protraining.php > >>>>>>> > >>>>>>> Please keep messages on-topic and check the ITK FAQ at: > >>>>>>> http://www.itk.org/Wiki/ITK_FAQ > >>>>>>> > >>>>>>> Follow this link to subscribe/unsubscribe: > >>>>>>> http://public.kitware.com/mailman/listinfo/insight-users > >>>>>>> > >>>>>> > >>>>>> _____________________________________ > >>>>>> Powered by www.kitware.com > >>>>>> > >>>>>> Visit other Kitware open-source projects at > >>>>>> http://www.kitware.com/opensource/opensource.html > >>>>>> > >>>>>> Kitware offers ITK Training Courses, for more information visit: > >>>>>> http://www.kitware.com/products/protraining.php > >>>>>> > >>>>>> Please keep messages on-topic and check the ITK FAQ at: > >>>>>> http://www.itk.org/Wiki/ITK_FAQ > >>>>>> > >>>>>> Follow this link to subscribe/unsubscribe: > >>>>>> http://public.kitware.com/mailman/listinfo/insight-users > >>>>>> > >>>>>> > >>>>>> > >>>> > >>> > >> > >> _____________________________________ > >> Powered by www.kitware.com > >> > >> Visit other Kitware open-source projects at > >> http://www.kitware.com/opensource/opensource.html > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> http://www.kitware.com/products/protraining.php > >> > >> Please keep messages on-topic and check the ITK FAQ at: > >> http://www.itk.org/Wiki/ITK_FAQ > >> > >> Follow this link to subscribe/unsubscribe: > >> http://public.kitware.com/mailman/listinfo/insight-users > >> > >> > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to 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<>http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml > > > > > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588483.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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_____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > If you reply to this email, your message will be added to the discussion below: > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588495.html > To start a new topic under ITK Insight Users, email ml-node+s2283740n2283740h75 at n2.nabble.com > To unsubscribe from ITK Insight Users, click here . > NAML > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From davis.vigneault at gmail.com Wed Feb 17 07:37:58 2016 From: davis.vigneault at gmail.com (DVigneault) Date: Wed, 17 Feb 2016 05:37:58 -0700 (MST) Subject: [ITK] [ITK-users] Pulling VNL function into ITK? Message-ID: <1455712678409-7588506.post@n2.nabble.com> All-- There is a function called "double angle_minuspi_to_pi(double angle);" in Insight's vxl branch [1], which hasn't yet made it into the ITK source tree [2]. It looks like this is the commit where the function was added [3]. Would it be possible to pull this into ITK? Best, and thanks, --Davis [1] https://github.com/InsightSoftwareConsortium/vxl/blob/master/core/vnl/vnl_math.h [2] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_math.h [3] https://github.com/InsightSoftwareConsortium/vxl/commit/47460747604cb4058b53d831c3e73da6fa0d7835 -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Pulling-VNL-function-into-ITK-tp7588506.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Feb 17 10:39:23 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 17 Feb 2016 10:39:23 -0500 Subject: [ITK] [ITK-users] Pulling VNL function into ITK? In-Reply-To: <1455712678409-7588506.post@n2.nabble.com> References: <1455712678409-7588506.post@n2.nabble.com> Message-ID: Hi Davis, Hans lead some amazing work at updating VNL recently in preparation of a major update for ITK recently. This will enable maintenance and evolution of VNL in ITK. @Hans, is it a good time to pull the trigger and do the initial subtree merge? Thanks, Matt On Wed, Feb 17, 2016 at 7:37 AM, DVigneault wrote: > All-- > > There is a function called "double angle_minuspi_to_pi(double angle);" in > Insight's vxl branch [1], which hasn't yet made it into the ITK source tree > [2]. It looks like this is the commit where the function was added [3]. > Would it be possible to pull this into ITK? > > Best, and thanks, > > --Davis > > [1] > https://github.com/InsightSoftwareConsortium/vxl/blob/master/core/vnl/vnl_math.h > [2] > https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_math.h > [3] > https://github.com/InsightSoftwareConsortium/vxl/commit/47460747604cb4058b53d831c3e73da6fa0d7835 > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Pulling-VNL-function-into-ITK-tp7588506.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From kolin9105 at gmail.com Wed Feb 17 10:46:25 2016 From: kolin9105 at gmail.com (meikolin saimara) Date: Wed, 17 Feb 2016 22:46:25 +0700 Subject: [ITK] [ITK-users] (no subject) Message-ID: hello guys, anyone can help me?? I need a program in itk how to apply a number of black pixel value on image in cmd. when we input this image in cmd(command promt) and then the output is a number of black pixel value. pleas help me. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: OutPutIM-0001-0009.dcm Type: application/octet-stream Size: 83974 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From hans-johnson at uiowa.edu Wed Feb 17 10:54:37 2016 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Wed, 17 Feb 2016 15:54:37 +0000 Subject: [ITK] [ITK-users] Pulling VNL function into ITK? In-Reply-To: References: <1455712678409-7588506.post@n2.nabble.com> Message-ID: Matt, I have been doing sub-tree merges in private branches, identifying custimizations for VXL in the ITK environmnet, and then making changes in the VXL tree so that there is no need for customizations. I am hoping to make another pass this weekend and then, hopefully, quit working on VXL for a while. Alexander Leinoff has been working through clang static analysis and valgrind analysis trying to clean up compiler warnings and errors. I am mostly concerned about library linking, library installation, and library naming through the ITK install directory right now. It seems that the ITK version of VXL had many customizations to get VXL installed so that external projects could link against them. This issue is one that really scares me: https://github.com/vxl/vxl/issues/127 I?m not quite sure how to attack modernizing this in such a way that it is compatible with ITK ask well. Hans -- On 2/17/16, 9:39 AM, "Matt McCormick" wrote: >Hi Davis, > >Hans lead some amazing work at updating VNL recently in preparation of >a major update for ITK recently. This will enable maintenance and >evolution of VNL in ITK. > >@Hans, is it a good time to pull the trigger and do the initial subtree merge? > >Thanks, >Matt > >On Wed, Feb 17, 2016 at 7:37 AM, DVigneault wrote: >> All-- >> >> There is a function called "double angle_minuspi_to_pi(double angle);" in >> Insight's vxl branch [1], which hasn't yet made it into the ITK source tree >> [2]. It looks like this is the commit where the function was added [3]. >> Would it be possible to pull this into ITK? >> >> Best, and thanks, >> >> --Davis >> >> [1] >> https://github.com/InsightSoftwareConsortium/vxl/blob/master/core/vnl/vnl_math.h >> [2] >> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/ThirdParty/VNL/src/vxl/core/vnl/vnl_math.h >> [3] >> https://github.com/InsightSoftwareConsortium/vxl/commit/47460747604cb4058b53d831c3e73da6fa0d7835 >> >> >> >> -- >> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Pulling-VNL-function-into-ITK-tp7588506.html >> Sent from the ITK Insight Users mailing list archive at Nabble.com. >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From jmatuteflores at gmail.com Wed Feb 17 11:42:14 2016 From: jmatuteflores at gmail.com (jose alejandro matute flores) Date: Wed, 17 Feb 2016 17:42:14 +0100 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: Hi, Take a look at using a histogram [1] or simply iterate throughout the image using fx. a const iterator [2] and aggregate whenever you find the desired pixel value. [1] http://itk.org/Wiki/ITK/Examples/Statistics/HistogramToImageFilterGrayscale [2] http://www.itk.org/Doxygen/html/classitk_1_1ImageConstIterator.html Best, Jose On Wed, Feb 17, 2016 at 4:46 PM, meikolin saimara wrote: > hello guys, anyone can help me?? > I need a program in itk how to apply a number of black pixel value on > image in cmd. when we input this image in cmd(command promt) and then the > output is a number of black pixel value. > pleas help me. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Thu Feb 18 06:37:10 2016 From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca) Date: Thu, 18 Feb 2016 12:37:10 +0100 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: <3F877AC4-BCD1-43FF-B8B3-7B30F9B6D30B@mail.nih.gov> References: <3F877AC4-BCD1-43FF-B8B3-7B30F9B6D30B@mail.nih.gov> Message-ID: Hi again, I've got ITK version 4.5.1 (a little bit old, I know), and after making the changes suggested by Dzenanz and recompiling ITK, the problem continues, that is, my code crashes at the same point. Then, I've downloaded the latest stable ITK version, ITK 4.9.0 and compiled from scratch and I get the following error: [ 98%] Building CXX object Modules/IO/TransformBase/src/CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.obj C:/MINGW/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: too many sections (33106) C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Assembler messages: C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Fatal error: can't write CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: File too big After doing some "googling" and follow some of the instructions referred on the web, I've been unable to solve this. Has anyone met this problem and solved it? Thanks. KR. /Francisco 2016-02-16 22:13 GMT+01:00 Bradley Lowekamp [via ITK Insight Users] < ml-node+s2283740n7588505h90 at n2.nabble.com>: > Hello, > > Please take a look at these changes: > > https://github.com/blowekamp/itkTextureAnalysis/commit/9654d74ea1d09f0677f1d1b93242cc94340591bf > > Brad > > On Feb 16, 2016, at 10:35 AM, D?enan Zuki? <[hidden email] > > wrote: > > I have set up a project using one of the tests from Brad's repository > (attached), and it works in debug mode both with his original code and with > your modified class, and crashes in release mode both with his original > code and with your modified class. I will now compile ITK in RelWithDebInfo > in an attempt to figure out where is the crash occurring. > > Regards, > D?enan > > On Tue, Feb 16, 2016 at 1:52 AM, Francisco Lopez de la Franca <[hidden > email] > wrote: > >> Excuse me Dzenanz, but that's not completely true, because I've tested >> Brad's class and it works right. >> The problem seems to be that when you add a new neighbor iterator to >> include just the mask points in the "histogram" then it is when the >> application crashes, and I donot understand why. >> If you just comment the 'maskIter' references you'll see that the >> application works. >> I've created a single threaded class based on the Brad's code and it >> works but it is twice slower, that is why I'm interesting on Brad's class >> (multi-threaded) to make it work. >> >> >> 2016-02-15 17:15 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >> email] >: >> >>> Hi Francisco, >>> >>> both your code and Brad's code run in debug mode (I did not wait for the >>> end), and both crash in release mode immediately on startup. Here is a >>> sample output: >>> >>> Progress input: 0000000002868970 >>> input: 0000000002868970 >>> _maskImage: 0000000002868970 >>> _maskImage: 0000000002868970 >>> input: 0000000002868970 >>> _maskImage: 0000000002868970 >>> iter.first: iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>> [-5, -5, -5] iter.second: [-4, -5, -5] >>> niter index: [5, 5, 210] >>> niter index: [5, 5, 140] >>> maskIter index: [5, 5, 140] >>> maskIter index: [5, 5, 210] >>> Before p3 >>> input: 0000000002868970 >>> _maskImage: 0000000002868970 >>> After p3: | 0niter index: [5, 5, 70] >>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>> niter index: [5, 5, 5] >>> ? >>> maskIter index: [5, 5, 70] >>> After p4: ? >>> Before p3 >>> Before p3 >>> After p3: ?iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>> niter index: [5, 5, 140] >>> maskIter index: [5, 5, 140] >>> maskIter index: [5, 5, 5] >>> Before p3 >>> After p3: ? >>> After p3: ? >>> After p4: ? >>> After p4: ? >>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>> niter index: [5, 5, 5] >>> maskIter index: [5, 5, 5] >>> >>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>> Before p3 >>> Before p3 >>> After p4: ? >>> After p3: ? >>> After p4: ? >>> >>> Regards, >>> D?enan >>> >>> On Mon, Feb 15, 2016 at 1:36 AM, Francisco Lopez de la Franca <[hidden >>> email] > wrote: >>> >>>> Hi, >>>> Here they are. >>>> KR. >>>> >>>> 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>> email] >: >>>> >>>>> Hi Francisco, >>>>> >>>>> do you mind attaching the modified files or pointing to your fork of >>>>> it on GitHub? >>>>> >>>>> Regards >>>>> >>>>> On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden >>>>> email] > wrote: >>>>> >>>>>> Hi Dzenan, >>>>>> The original class is here: >>>>>> >>>>>> >>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >>>>>> >>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >>>>>> >>>>>> I've just added setInput and setMaskImage methods and modify some >>>>>> lines in >>>>>> the original class as I indicated in the yesterday mail within this >>>>>> thread. >>>>>> I'm running it on Windows, and there is no error at all, just a >>>>>> crash. I >>>>>> may have to include exceptions management. >>>>>> The crash occurs just when calling p3 = maskIter.GetPixel(iter->first) >>>>>> >>>>>> If you know why it could be or if you need more clarification, please >>>>>> let >>>>>> me know. >>>>>> Many thanks >>>>>> >>>>>> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >>>>>> [hidden email] >>>>>> >: >>>>>> >>>>>> > Hi Francisco, >>>>>> > >>>>>> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the error >>>>>> message >>>>>> > that goes along with the crash? In which file and line does it >>>>>> crash? >>>>>> > >>>>>> > Regards >>>>>> > >>>>>> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca >>>>>> <[hidden >>>>>> > email] > >>>>>> wrote: >>>>>> > >>>>>> >> Hi, >>>>>> >> Please, someone that could help me. I'm working in a pre-doctorate >>>>>> >> project and I need this class to work. >>>>>> >> I've read the chapter 13 in the ITK Software Guide on how to write >>>>>> a >>>>>> >> filter and now I see the fact of the threads due to inheritance of >>>>>> >> ImageToImageFilter. >>>>>> >> But, I keep on without understanding why the code crashes just when >>>>>> >> calling >>>>>> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >>>>>> >> It is just a call to read data, not to write. >>>>>> >> >>>>>> >> I guess somebody that had worked with creation of filters might see >>>>>> >> "easily" the problem, but not me. >>>>>> >> >>>>>> >> So, again, please, I need someone to help me with this because I'm >>>>>> stuck >>>>>> >> on this point. >>>>>> >> >>>>>> >> Thank you very much. >>>>>> >> KR. >>>>>> >> /Francisco >>>>>> >> >>>>>> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden >>>>>> email] >>>>>> >> >: >>>>>> >> >>>>>> >>> Hi Bradley again. >>>>>> >>> I'm modifying your class in order to be able to set a mask image >>>>>> (a >>>>>> >>> binary image) to be used as a limit in the histogram >>>>>> calculations, I mean, >>>>>> >>> I set an input, a mask and the class should take into account to >>>>>> calculate >>>>>> >>> the histograms only the voxels that belong to the input and to >>>>>> the mask >>>>>> >>> image and having the value 1 in the mask image. >>>>>> >>> The changes seem to be easy but I don?t know why my tests are not >>>>>> >>> working. It seems that 2 threads are working at the same time and >>>>>> when I >>>>>> >>> added my mask iterator, the code crashes. >>>>>> >>> >>>>>> >>> *** Consider that the input and mask images are the same origin, >>>>>> spacing >>>>>> >>> and size. >>>>>> >>> >>>>>> >>> I attach the main changes I've done, and I would thank you a lot >>>>>> if you >>>>>> >>> don't mind having a look and help me to find what I'm doing wrong: >>>>>> >>> >>>>>> >>> template< class TImageType, class TOutputImage > >>>>>> >>> void >>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>> >::*SetInput*(InputImageType >>>>>> >>> *image) >>>>>> >>> { >>>>>> >>> // Process object is not const-correct so the const_cast is >>>>>> required >>>>>> >>> here >>>>>> >>> this->ProcessObject::SetNthInput( 0, >>>>>> >>> const_cast< InputImageType * >>>>>> >( >>>>>> >>> image ) ); >>>>>> >>> } >>>>>> >>> >>>>>> >>> template< class TImageType, class TOutputImage > >>>>>> >>> void >>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>> >::*SetMaskImage*(InputImageType >>>>>> >>> *image) >>>>>> >>> { >>>>>> >>> // Process object is not const-correct so the const_cast is >>>>>> required >>>>>> >>> here >>>>>> >>> this->ProcessObject::SetNthInput( 1, const_cast< InputImageType >>>>>> * >( >>>>>> >>> image ) ); >>>>>> >>> >>>>>> >>> _maskImage = image; // _maskImage is a private member >>>>>> >>> } >>>>>> >>> >>>>>> >>> In the *ThreadedGenerateData*(const RegionType& >>>>>> outputRegionForThread, >>>>>> >>> ThreadIdType threadId ) method: >>>>>> >>> { >>>>>> >>> >>>>>> >>> ... >>>>>> >>> >>>>>> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >>>>>> >>> { >>>>>> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >>>>>> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, >>>>>> *fit);* >>>>>> >>> OutputIterator outIter(output, *fit); >>>>>> >>> >>>>>> >>> OutputPixelType out; >>>>>> >>> NumericTraits::SetLength( out, >>>>>> >>> this->GetNumberOfOutputComponents() ); >>>>>> >>> >>>>>> >>> while( !nIter.IsAtEnd() ) >>>>>> >>> { >>>>>> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >>>>>> >>> >>>>>> >>> ... >>>>>> >>> >>>>>> >>> ++nIter; >>>>>> >>> ++outIter; >>>>>> >>> * ++maskIter;* >>>>>> >>> ... >>>>>> >>> >>>>>> >>> In the *FillHistogram *method: >>>>>> >>> { >>>>>> >>> >>>>>> >>> ... >>>>>> >>> >>>>>> >>> while( iter != m_CooccurenceOffsetVector.end() ) >>>>>> >>> { >>>>>> >>> >>>>>> >>> const PixelType p1 = niter.GetPixel(iter->first); >>>>>> >>> const PixelType p2 = niter.GetPixel(iter->second); >>>>>> >>> std::cout << "Before p3" << std::endl; >>>>>> >>> >>>>>> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); >>>>>> *std::cout >>>>>> >>> << "After p3: " << p3 << std::endl; >>>>>> >>> >>>>>> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >>>>>> >>> std::cout << "After p4: " << p4 << std::endl; >>>>>> >>> >>>>>> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= >>>>>> m_Max >>>>>> >>> *&& p3 == _insidePixelValue && p4 == >>>>>> _insidePixelValue* ) >>>>>> >>> // The point >>>>>> >>> { >>>>>> >>> >>>>>> >>> ... >>>>>> >>> >>>>>> >>> >>>>>> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >>>>>> >>> >>>>>> >>> Thank you so much. >>>>>> >>> My kind regards. >>>>>> >>> /Paco >>>>>> >>> >>>>>> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca <[hidden >>>>>> email] >>>>>> >>> >: >>>>>> >>> >>>>>> >>>> Hello Bradley again. >>>>>> >>>> Sorry but I'd like to re-open this issue because I need your >>>>>> class but >>>>>> >>>> with some modification. >>>>>> >>>> I pass to tell you. >>>>>> >>>> >>>>>> >>>> As my tests with your external class were not good taking into >>>>>> account >>>>>> >>>> the performance, I wonder if you could create a variant of it, >>>>>> but in which >>>>>> >>>> I can set a mask image and your class just return the >>>>>> VectorImage with all >>>>>> >>>> the features for that region (the masked locations) as >>>>>> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >>>>>> >>>> I mean, to get the vector image with all the features but just >>>>>> >>>> calculate it for the regions belonging to the mask image. >>>>>> Positions not >>>>>> >>>> belonging to the mask region could have a pixel value of 0, for >>>>>> instance. >>>>>> >>>> >>>>>> >>>> I don?t know if it is very costly for you, but I would thank >>>>>> you so >>>>>> >>>> much. Otherwise, I could try it but I'd need your suggestions on >>>>>> how to do >>>>>> >>>> it. >>>>>> >>>> >>>>>> >>>> Thanks a lot. >>>>>> >>>> Best regards. >>>>>> >>>> >>>>>> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca <[hidden >>>>>> email] >>>>>> >>>> >: >>>>>> >>>> >>>>>> >>>>> Hello Bradley again, >>>>>> >>>>> I would like to ask you for a couple of favours. In the one >>>>>> hand, >>>>>> >>>>> could you please send me your 3D image so that I can test on >>>>>> it? And on the >>>>>> >>>>> other hand, could you test the example I have referenced in the >>>>>> previous >>>>>> >>>>> email with your image, not changing anything in the code, such >>>>>> as it is, >>>>>> >>>>> and tell me if the execution time is normal? >>>>>> >>>>> Thank you very much. >>>>>> >>>>> Regards, >>>>>> >>>>> /Francisco >>>>>> >>>>> >>>>>> >>>>> PS: All my application trace is printed via standard 'cout' >>>>>> command, >>>>>> >>>>> not due to a debugging compilation mode. >>>>>> >>>>> >>>>>> >>>>> >>>>>> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp >>>>>> <[hidden >>>>>> >>>>> email] > >>>>>> >>>>> escribi?: >>>>>> >>>>> >>>>>> >>>>>> Hello, >>>>>> >>>>>> >>>>>> >>>>>> Did you compile TextureFeatureImage in Release mode? >>>>>> >>>>>> >>>>>> >>>>>> 1) The filter does not scale well with a large radius. And >>>>>> given by >>>>>> >>>>>> your initial report of print a very large number of offset >>>>>> you, it sounds >>>>>> >>>>>> like you are using a large radius with many offsets. I created >>>>>> a >>>>>> >>>>>> 224x224x300 unsigned short image and ran with the default >>>>>> offset and a >>>>>> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this >>>>>> filter is was ~10x >>>>>> >>>>>> faster than this example... things change though... >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> 2) I sounds like the boundaries/limits of the histogram may be >>>>>> >>>>>> clipping you values. I would inspect the co-occurance matrix. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> HTH, >>>>>> >>>>>> Brad >>>>>> >>>>>> >>>>>> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca >>>>>> <[hidden >>>>>> >>>>>> email] >>>>> >> >>>>>> >>>>>> wrote: >>>>>> >>>>>> >>>>>> >>>>>> I've tested with itkTextureFeatureImageFilter, with >>>>>> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>>>> >>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures >>>>>> example, >>>>>> >>>>>> for a 3D image and here are my comments: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> 1. I had to interrupt the test after several hours and it kept >>>>>> on >>>>>> >>>>>> calculating. And this is for only a 3D image (224x224x300). I >>>>>> need to >>>>>> >>>>>> process around 35 images. >>>>>> >>>>>> 2. The result (texture features: entropy, energy, correlation, >>>>>> LH, >>>>>> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, >>>>>> 7.83083e+247]. >>>>>> >>>>>> These values were not what I expected based on my experience >>>>>> on another >>>>>> >>>>>> application I developed, but in that case, I calculated the >>>>>> texture >>>>>> >>>>>> features for an image as a whole, not voxel by voxel. >>>>>> >>>>>> >>>>>> >>>>>> Regards. >>>>>> >>>>>> >>>>>> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >>>>>> >>>>>> >: >>>>>> >>>>>> >>>>>> >>>>>>> i yes i have tried radius = 3; >>>>>> >>>>>>> still no luck >>>>>> >>>>>>> >>>>>> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via >>>>>> ITK >>>>>> >>>>>>> Insight >>>>>> >>>>>>> Users] <[hidden email] >>>>>> >>>>>>> > >>>>>> wrote: >>>>>> >>>>>>> >>>>>> >>>>>>> > Have you tried with a radius of 3 instead of 1? >>>>>> >>>>>>> > >>>>>> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>>>> >>>>>>> > >: >>>>>> >>>>>>> > >>>>>> >>>>>>> >> hey Matt, >>>>>> >>>>>>> >> thanks for ur advice.. it did build successfully... but im >>>>>> not >>>>>> >>>>>>> able to run >>>>>> >>>>>>> >> the code for 2D png image... i tried to change the >>>>>> dimension to 2 >>>>>> >>>>>>> and >>>>>> >>>>>>> >> build >>>>>> >>>>>>> >> it which it did.. but when i run the code using the command >>>>>> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png >>>>>> putput.png >>>>>> >>>>>>> 1... i see >>>>>> >>>>>>> >> this output >>>>>> >>>>>>> >> >>>>>> >>>>>>> >> offset: [-1, -1] [0, -1] >>>>>> >>>>>>> >> offset: [0, -1] [1, -1] >>>>>> >>>>>>> >> offset: [-1, 0] [0, 0] >>>>>> >>>>>>> >> offset: [0, 0] [1, 0] >>>>>> >>>>>>> >> offset: [-1, 1] [0, 1] >>>>>> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... >>>>>> if pls >>>>>> >>>>>>> tel me >>>>>> >>>>>>> >> how can i modify this code to work wid 2d image... forgive >>>>>> me if >>>>>> >>>>>>> my ques >>>>>> >>>>>>> >> are really silly im trying to learn something.. >>>>>> >>>>>>> >> regards >>>>>> >>>>>>> >> Vis >>>>>> >>>>>>> >> >>>>>> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK >>>>>> >>>>>>> Insight Users] >>>>>> >>>>>>> >> < >>>>>> >>>>>>> >> [hidden email] < >>>>>> >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>>>>> >>>>>>> >> wrote: >>>>>> >>>>>>> >> >>>>>> >>>>>>> >> > Hi, >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > The function: >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char >>>>>> *argv[]) >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > must be renamed to >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > main(int argc, char* argv[]) >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > HTH, >>>>>> >>>>>>> >> > Matt >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>>>> >>>>>>> >> > > >>>>>> wrote: >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > > hi all, >>>>>> >>>>>>> >> > > im trying to build the >>>>>> itkTextureFeatureImageFilterTest.cxx >>>>>> >>>>>>> code but >>>>>> >>>>>>> >> im >>>>>> >>>>>>> >> > not >>>>>> >>>>>>> >> > > able to it is showing the following error >>>>>> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>>>> >>>>>>> Configuration: >>>>>> >>>>>>> >> Debug >>>>>> >>>>>>> >> > x64 >>>>>> >>>>>>> >> > > ------ >>>>>> >>>>>>> >> > > 1> Checking Build System >>>>>> >>>>>>> >> > > 1> CMake does not need to re-run because >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>>>> >>>>>>> >> > is >>>>>> >>>>>>> >> > > up-to-date. >>>>>> >>>>>>> >> > > 2>------ Rebuild All started: Project: >>>>>> >>>>>>> >> itkTextureFeatureImageFilterTest, >>>>>> >>>>>>> >> > > Configuration: Debug x64 ------ >>>>>> >>>>>>> >> > > 2> Building Custom Rule >>>>>> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>> >>>>>>> >> > > 2> CMake does not need to re-run because >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>> >>>>>>> >> > is >>>>>> >>>>>>> >> > > up-to-date. >>>>>> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>>>> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>>>> >>>>>>> 'std::_Copy_impl': >>>>>> >>>>>>> >> > Function >>>>>> >>>>>>> >> > > call with parameters that may be unsafe - this call >>>>>> relies on >>>>>> >>>>>>> the >>>>>> >>>>>>> >> caller >>>>>> >>>>>>> >> > to >>>>>> >>>>>>> >> > > check that the passed values are correct. To disable >>>>>> this >>>>>> >>>>>>> warning, use >>>>>> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to >>>>>> use >>>>>> >>>>>>> Visual C++ >>>>>> >>>>>>> >> > > 'Checked Iterators' >>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>> Studio >>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>> >>>>>>> 'std::_Copy_impl' >>>>>> >>>>>>> >> > > 2> >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>>>> >>>>>>> >> > see >>>>>> >>>>>>> >> > > reference to function template instantiation '_OutIt >>>>>> >>>>>>> std::copy>>>>> >>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' >>>>>> being >>>>>> >>>>>>> compiled >>>>>> >>>>>>> >> > > 2> with >>>>>> >>>>>>> >> > > 2> [ >>>>>> >>>>>>> >> > > 2> _OutIt=unsigned char *, >>>>>> >>>>>>> >> > > 2> _InIt=const unsigned char * >>>>>> >>>>>>> >> > > 2> ] >>>>>> >>>>>>> >> > > 2> >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>>>> >>>>>>> >> > > while compiling class template member function 'void >>>>>> >>>>>>> >> > > itk::ImageFileReader::GenerateData(void)' >>>>>> >>>>>>> >> > > 2> with >>>>>> >>>>>>> >> > > 2> [ >>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>> >>>>>>> >> > > 2> ] >>>>>> >>>>>>> >> > > 2> >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > > : see reference to class template instantiation >>>>>> >>>>>>> >> > > 'itk::ImageFileReader' being compiled >>>>>> >>>>>>> >> > > 2> with >>>>>> >>>>>>> >> > > 2> [ >>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>> >>>>>>> >> > > 2> ] >>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>> Studio >>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>> >>>>>>> 'std::_Copy_impl' >>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>> Studio >>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>> >>>>>>> 'std::_Copy_impl' >>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>> Studio >>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>> >>>>>>> 'std::_Copy_impl' >>>>>> >>>>>>> >> > > 2> Creating library >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > > and object >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved >>>>>> >>>>>>> external symbol >>>>>> >>>>>>> >> > main >>>>>> >>>>>>> >> > > referenced in function __tmainCRTStartup >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>>>> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>>>> >>>>>>> Configuration: Debug >>>>>> >>>>>>> >> > x64 >>>>>> >>>>>>> >> > > ------ >>>>>> >>>>>>> >> > > 3> Building Custom Rule >>>>>> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>> >>>>>>> >> > > 3> CMake does not need to re-run because >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>> >>>>>>> >> > is >>>>>> >>>>>>> >> > > up-to-date. >>>>>> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 >>>>>> skipped >>>>>> >>>>>>> ========== >>>>>> >>>>>>> >> > > im using the follwing CMakeList.txt >>>>>> >>>>>>> >> > > # This is the root ITK CMakeLists file. >>>>>> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>>>> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >>>>>> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>>>> >>>>>>> >> > > endif() >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > # This project is designed to be built outside the >>>>>> Insight >>>>>> >>>>>>> source >>>>>> >>>>>>> >> tree. >>>>>> >>>>>>> >> > > project(HelloWorld) >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > # Find ITK. >>>>>> >>>>>>> >> > > find_package(ITK REQUIRED) >>>>>> >>>>>>> >> > > include(${ITK_USE_FILE}) >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>>>> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest >>>>>> >>>>>>> >> ${ITK_LIBRARIES}) >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > please tel me wat the error is?? >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > -- >>>>>> >>>>>>> >> > > View this message in context: >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>>>> >>>>>>> >> > > Sent from the ITK Insight Users mailing list archive at >>>>>> >>>>>>> Nabble.com . >>>>>> >>>>>>> >> > > _____________________________________ >>>>>> >>>>>>> >> > > Powered by www.kitware.com >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > Visit other Kitware open-source projects at >>>>>> >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > Kitware offers ITK Training Courses, for more >>>>>> information >>>>>> >>>>>>> visit: >>>>>> >>>>>>> >> > > http://www.kitware.com/products/protraining.php >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > Please keep messages on-topic and check the ITK FAQ at: >>>>>> >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > Follow this link to subscribe/unsubscribe: >>>>>> >>>>>>> >> > > >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >>>>>>> >> > _____________________________________ >>>>>> >>>>>>> >> > Powered by www.kitware.com >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > Visit other Kitware open-source projects at >>>>>> >>>>>>> >> > http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > Kitware offers ITK Training Courses, for more >>>>>> information visit: >>>>>> >>>>>>> >> > http://www.kitware.com/products/protraining.php >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > Please keep messages on-topic and check the ITK FAQ at: >>>>>> >>>>>>> >> > http://www.itk.org/Wiki/ITK_FAQ >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > Follow this link to subscribe/unsubscribe: >>>>>> >>>>>>> >> > http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > ------------------------------ >>>>>> >>>>>>> >> > If you reply to this email, your message will be added >>>>>> to the >>>>>> >>>>>>> discussion >>>>>> >>>>>>> >> > below: >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587952.html >>>>>> >>>>>>> >> > To unsubscribe from [ITK-users] Texture pixel by pixel, >>>>>> click >>>>>> >>>>>>> here >>>>>> >>>>>>> >> > < > . >>>>>> >>>>>>> >> > NAML >>>>>> >>>>>>> >> > < >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> >>>>>> >>>>>>> >> >>>>>> >>>>>>> >> >>>>>> >>>>>>> >> >>>>>> >>>>>>> >> -- >>>>>> >>>>>>> >> View this message in context: >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587960.html >>>>>> >>>>>>> >> Sent from the ITK Insight Users mailing list archive at >>>>>> >>>>>>> Nabble.com . >>>>>> >>>>>>> >> _____________________________________ >>>>>> >>>>>>> >> Powered by www.kitware.com >>>>>> >>>>>>> >> >>>>>> >>>>>>> >> Visit other Kitware open-source projects at >>>>>> >>>>>>> >> http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>>> >> >>>>>> >>>>>>> >> Kitware offers ITK Training Courses, for more information >>>>>> visit: >>>>>> >>>>>>> >> http://www.kitware.com/products/protraining.php >>>>>> >>>>>>> >> >>>>>> >>>>>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>> >>>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>> >>>>>>> >> >>>>>> >>>>>>> >> Follow this link to subscribe/unsubscribe: >>>>>> >>>>>>> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >>>>>>> >> >>>>>> >>>>>>> > >>>>>> >>>>>>> > >>>>>> >>>>>>> > _____________________________________ >>>>>> >>>>>>> > Powered by www.kitware.com >>>>>> >>>>>>> > >>>>>> >>>>>>> > Visit other Kitware open-source projects at >>>>>> >>>>>>> > http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>>> > >>>>>> >>>>>>> > Kitware offers ITK Training Courses, for more information >>>>>> visit: >>>>>> >>>>>>> > http://www.kitware.com/products/protraining.php >>>>>> >>>>>>> > >>>>>> >>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>>> >>>>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>>> >>>>>>> > >>>>>> >>>>>>> > Follow this link to subscribe/unsubscribe: >>>>>> >>>>>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >>>>>>> > >>>>>> >>>>>>> > >>>>>> >>>>>>> > ------------------------------ >>>>>> >>>>>>> > If you reply to this email, your message will be added to >>>>>> the >>>>>> >>>>>>> discussion >>>>>> >>>>>>> > below: >>>>>> >>>>>>> > >>>>>> >>>>>>> > >>>>>> >>>>>>> >>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587961.html >>>>>> >>>>>>> > To unsubscribe from [ITK-users] Texture pixel by pixel, >>>>>> click here >>>>>> >>>>>>> > < > . >>>>>> >>>>>>> > NAML >>>>>> >>>>>>> > < >>>>>> >>>>>>> >>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>> >>>>>>> > >>>>>> >>>>>>> > >>>>>> >>>>>>> >>>>>> >>>>>>> >>>>>> >>>>>>> >>>>>> >>>>>>> >>>>>> >>>>>>> -- >>>>>> >>>>>>> View this message in context: >>>>>> >>>>>>> >>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587963.html >>>>>> >>>>>>> Sent from the ITK Insight Users mailing list archive at >>>>>> Nabble.com . >>>>>> >>>>>>> _____________________________________ >>>>>> >>>>>>> Powered by www.kitware.com >>>>>> >>>>>>> >>>>>> >>>>>>> Visit other Kitware open-source projects at >>>>>> >>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>>> >>>>>> >>>>>>> Kitware offers ITK Training Courses, for more information >>>>>> visit: >>>>>> >>>>>>> http://www.kitware.com/products/protraining.php >>>>>> >>>>>>> >>>>>> >>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>> >>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>> >>>>>>> >>>>>> >>>>>>> Follow this link to subscribe/unsubscribe: >>>>>> >>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _____________________________________ >>>>>> >>>>>> Powered by www.kitware.com >>>>>> >>>>>> >>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>> >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>> >>>>>> >>>>>> Kitware offers ITK Training Courses, for more information >>>>>> visit: >>>>>> >>>>>> http://www.kitware.com/products/protraining.php >>>>>> >>>>>> >>>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>> >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>> >>>>>> >>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>> >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> >>>>>> >>> >>>>>> >> >>>>>> >> _____________________________________ >>>>>> >> Powered by www.kitware.com >>>>>> >> >>>>>> >> Visit other Kitware open-source projects at >>>>>> >> http://www.kitware.com/opensource/opensource.html >>>>>> >> >>>>>> >> Kitware offers ITK Training Courses, for more information visit: >>>>>> >> http://www.kitware.com/products/protraining.php >>>>>> >> >>>>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>> >> >>>>>> >> Follow this link to subscribe/unsubscribe: >>>>>> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >> >>>>>> >> >>>>>> > >>>>>> > _____________________________________ >>>>>> > Powered by www.kitware.com >>>>>> > >>>>>> > Visit other Kitware open-source projects at >>>>>> > http://www.kitware.com/opensource/opensource.html >>>>>> > >>>>>> > Kitware offers ITK Training Courses, for more information visit: >>>>>> > http://www.kitware.com/products/protraining.php >>>>>> > >>>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>>> > >>>>>> > Follow this link to subscribe/unsubscribe: >>>>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>>> > >>>>>> > >>>>>> > ------------------------------ >>>>>> > If you reply to this email, your message will be added to the >>>>>> discussion >>>>>> > below: >>>>>> > >>>>>> > >>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588477.html >>>>>> > To start a new topic under ITK Insight Users, email >>>>>> > [hidden email] >>>>>> >>>>>> > To unsubscribe from ITK Insight Users, click here >>>>>> > < > . >>>>>> > NAML >>>>>> > < >>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>> > >>>>>> > >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> View this message in context: >>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588483.html >>>>>> Sent from the ITK Insight Users mailing list archive at Nabble.com >>>>>> . >>>>>> _____________________________________ >>>>>> Powered by www.kitware.com >>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>> http://www.kitware.com/products/protraining.php >>>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >>>>> >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>>> >>>>> ------------------------------ >>>>> If you reply to this email, your message will be added to the >>>>> discussion below: >>>>> >>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588490.html >>>>> To start a new topic under ITK Insight Users, email [hidden email] >>>>> >>>>> To unsubscribe from ITK Insight Users, click here. >>>>> NAML >>>>> >>>>> >>>> >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>> ------------------------------ >>> If you reply to this email, your message will be added to the discussion >>> below: >>> >>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588495.html >>> To start a new topic under ITK Insight Users, email [hidden email] >>> >>> To unsubscribe from ITK Insight Users, click here. >>> NAML >>> >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588505.html > To start a new topic under ITK Insight Users, email > ml-node+s2283740n2283740h75 at n2.nabble.com > To unsubscribe from ITK Insight Users, click here > > . > NAML > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Thu Feb 18 06:37:23 2016 From: franciscolopezdelafranca at gmail.com (=?UTF-8?Q?Francisco_L=C3=B3pez-Franca?=) Date: Thu, 18 Feb 2016 04:37:23 -0700 (MST) Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: <3F877AC4-BCD1-43FF-B8B3-7B30F9B6D30B@mail.nih.gov> References: <3F877AC4-BCD1-43FF-B8B3-7B30F9B6D30B@mail.nih.gov> Message-ID: Hi again, I've got ITK version 4.5.1 (a little bit old, I know), and after making the changes suggested by Dzenanz and recompiling ITK, the problem continues, that is, my code crashes at the same point. Then, I've downloaded the latest stable ITK version, ITK 4.9.0 and compiled from scratch and I get the following error: [ 98%] Building CXX object Modules/IO/TransformBase/src/CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.obj C:/MINGW/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: too many sections (33106) C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Assembler messages: C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Fatal error: can't write CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: File too big After doing some "googling" and follow some of the instructions referred on the web, I've been unable to solve this. Has anyone met this problem and solved it? Thanks. KR. /Francisco 2016-02-16 22:13 GMT+01:00 Bradley Lowekamp [via ITK Insight Users] < ml-node+s2283740n7588505h90 at n2.nabble.com>: > Hello, > > Please take a look at these changes: > > https://github.com/blowekamp/itkTextureAnalysis/commit/9654d74ea1d09f0677f1d1b93242cc94340591bf > > Brad > > On Feb 16, 2016, at 10:35 AM, D?enan Zuki? <[hidden email] > > wrote: > > I have set up a project using one of the tests from Brad's repository > (attached), and it works in debug mode both with his original code and with > your modified class, and crashes in release mode both with his original > code and with your modified class. I will now compile ITK in RelWithDebInfo > in an attempt to figure out where is the crash occurring. > > Regards, > D?enan > > On Tue, Feb 16, 2016 at 1:52 AM, Francisco Lopez de la Franca <[hidden > email] > wrote: > >> Excuse me Dzenanz, but that's not completely true, because I've tested >> Brad's class and it works right. >> The problem seems to be that when you add a new neighbor iterator to >> include just the mask points in the "histogram" then it is when the >> application crashes, and I donot understand why. >> If you just comment the 'maskIter' references you'll see that the >> application works. >> I've created a single threaded class based on the Brad's code and it >> works but it is twice slower, that is why I'm interesting on Brad's class >> (multi-threaded) to make it work. >> >> >> 2016-02-15 17:15 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >> email] >: >> >>> Hi Francisco, >>> >>> both your code and Brad's code run in debug mode (I did not wait for the >>> end), and both crash in release mode immediately on startup. Here is a >>> sample output: >>> >>> Progress input: 0000000002868970 >>> input: 0000000002868970 >>> _maskImage: 0000000002868970 >>> _maskImage: 0000000002868970 >>> input: 0000000002868970 >>> _maskImage: 0000000002868970 >>> iter.first: iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>> [-5, -5, -5] iter.second: [-4, -5, -5] >>> niter index: [5, 5, 210] >>> niter index: [5, 5, 140] >>> maskIter index: [5, 5, 140] >>> maskIter index: [5, 5, 210] >>> Before p3 >>> input: 0000000002868970 >>> _maskImage: 0000000002868970 >>> After p3: | 0niter index: [5, 5, 70] >>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>> niter index: [5, 5, 5] >>> ? >>> maskIter index: [5, 5, 70] >>> After p4: ? >>> Before p3 >>> Before p3 >>> After p3: ?iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>> niter index: [5, 5, 140] >>> maskIter index: [5, 5, 140] >>> maskIter index: [5, 5, 5] >>> Before p3 >>> After p3: ? >>> After p3: ? >>> After p4: ? >>> After p4: ? >>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>> niter index: [5, 5, 5] >>> maskIter index: [5, 5, 5] >>> >>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>> Before p3 >>> Before p3 >>> After p4: ? >>> After p3: ? >>> After p4: ? >>> >>> Regards, >>> D?enan >>> >>> On Mon, Feb 15, 2016 at 1:36 AM, Francisco Lopez de la Franca <[hidden >>> email] > wrote: >>> >>>> Hi, >>>> Here they are. >>>> KR. >>>> >>>> 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>> email] >: >>>> >>>>> Hi Francisco, >>>>> >>>>> do you mind attaching the modified files or pointing to your fork of >>>>> it on GitHub? >>>>> >>>>> Regards >>>>> >>>>> On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden >>>>> email] > wrote: >>>>> >>>>>> Hi Dzenan, >>>>>> The original class is here: >>>>>> >>>>>> >>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >>>>>> >>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >>>>>> >>>>>> I've just added setInput and setMaskImage methods and modify some >>>>>> lines in >>>>>> the original class as I indicated in the yesterday mail within this >>>>>> thread. >>>>>> I'm running it on Windows, and there is no error at all, just a >>>>>> crash. I >>>>>> may have to include exceptions management. >>>>>> The crash occurs just when calling p3 = maskIter.GetPixel(iter->first) >>>>>> >>>>>> If you know why it could be or if you need more clarification, please >>>>>> let >>>>>> me know. >>>>>> Many thanks >>>>>> >>>>>> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >>>>>> [hidden email] >>>>>> >: >>>>>> >>>>>> > Hi Francisco, >>>>>> > >>>>>> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the error >>>>>> message >>>>>> > that goes along with the crash? In which file and line does it >>>>>> crash? >>>>>> > >>>>>> > Regards >>>>>> > >>>>>> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca >>>>>> <[hidden >>>>>> > email] > >>>>>> wrote: >>>>>> > >>>>>> >> Hi, >>>>>> >> Please, someone that could help me. I'm working in a pre-doctorate >>>>>> >> project and I need this class to work. >>>>>> >> I've read the chapter 13 in the ITK Software Guide on how to write >>>>>> a >>>>>> >> filter and now I see the fact of the threads due to inheritance of >>>>>> >> ImageToImageFilter. >>>>>> >> But, I keep on without understanding why the code crashes just when >>>>>> >> calling >>>>>> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >>>>>> >> It is just a call to read data, not to write. >>>>>> >> >>>>>> >> I guess somebody that had worked with creation of filters might see >>>>>> >> "easily" the problem, but not me. >>>>>> >> >>>>>> >> So, again, please, I need someone to help me with this because I'm >>>>>> stuck >>>>>> >> on this point. >>>>>> >> >>>>>> >> Thank you very much. >>>>>> >> KR. >>>>>> >> /Francisco >>>>>> >> >>>>>> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden >>>>>> email] >>>>>> >> >: >>>>>> >> >>>>>> >>> Hi Bradley again. >>>>>> >>> I'm modifying your class in order to be able to set a mask image >>>>>> (a >>>>>> >>> binary image) to be used as a limit in the histogram >>>>>> calculations, I mean, >>>>>> >>> I set an input, a mask and the class should take into account to >>>>>> calculate >>>>>> >>> the histograms only the voxels that belong to the input and to >>>>>> the mask >>>>>> >>> image and having the value 1 in the mask image. >>>>>> >>> The changes seem to be easy but I don?t know why my tests are not >>>>>> >>> working. It seems that 2 threads are working at the same time and >>>>>> when I >>>>>> >>> added my mask iterator, the code crashes. >>>>>> >>> >>>>>> >>> *** Consider that the input and mask images are the same origin, >>>>>> spacing >>>>>> >>> and size. >>>>>> >>> >>>>>> >>> I attach the main changes I've done, and I would thank you a lot >>>>>> if you >>>>>> >>> don't mind having a look and help me to find what I'm doing wrong: >>>>>> >>> >>>>>> >>> template< class TImageType, class TOutputImage > >>>>>> >>> void >>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>> >::*SetInput*(InputImageType >>>>>> >>> *image) >>>>>> >>> { >>>>>> >>> // Process object is not const-correct so the const_cast is >>>>>> required >>>>>> >>> here >>>>>> >>> this->ProcessObject::SetNthInput( 0, >>>>>> >>> const_cast< InputImageType * >>>>>> >( >>>>>> >>> image ) ); >>>>>> >>> } >>>>>> >>> >>>>>> >>> template< class TImageType, class TOutputImage > >>>>>> >>> void >>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>> >::*SetMaskImage*(InputImageType >>>>>> >>> *image) >>>>>> >>> { >>>>>> >>> // Process object is not const-correct so the const_cast is >>>>>> required >>>>>> >>> here >>>>>> >>> this->ProcessObject::SetNthInput( 1, const_cast< InputImageType >>>>>> * >( >>>>>> >>> image ) ); >>>>>> >>> >>>>>> >>> _maskImage = image; // _maskImage is a private member >>>>>> >>> } >>>>>> >>> >>>>>> >>> In the *ThreadedGenerateData*(const RegionType& >>>>>> outputRegionForThread, >>>>>> >>> ThreadIdType threadId ) method: >>>>>> >>> { >>>>>> >>> >>>>>> >>> ... >>>>>> >>> >>>>>> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >>>>>> >>> { >>>>>> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >>>>>> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, >>>>>> *fit);* >>>>>> >>> OutputIterator outIter(output, *fit); >>>>>> >>> >>>>>> >>> OutputPixelType out; >>>>>> >>> NumericTraits::SetLength( out, >>>>>> >>> this->GetNumberOfOutputComponents() ); >>>>>> >>> >>>>>> >>> while( !nIter.IsAtEnd() ) >>>>>> >>> { >>>>>> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >>>>>> >>> >>>>>> >>> ... >>>>>> >>> >>>>>> >>> ++nIter; >>>>>> >>> ++outIter; >>>>>> >>> * ++maskIter;* >>>>>> >>> ... >>>>>> >>> >>>>>> >>> In the *FillHistogram *method: >>>>>> >>> { >>>>>> >>> >>>>>> >>> ... >>>>>> >>> >>>>>> >>> while( iter != m_CooccurenceOffsetVector.end() ) >>>>>> >>> { >>>>>> >>> >>>>>> >>> const PixelType p1 = niter.GetPixel(iter->first); >>>>>> >>> const PixelType p2 = niter.GetPixel(iter->second); >>>>>> >>> std::cout << "Before p3" << std::endl; >>>>>> >>> >>>>>> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); >>>>>> *std::cout >>>>>> >>> << "After p3: " << p3 << std::endl; >>>>>> >>> >>>>>> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >>>>>> >>> std::cout << "After p4: " << p4 << std::endl; >>>>>> >>> >>>>>> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= >>>>>> m_Max >>>>>> >>> *&& p3 == _insidePixelValue && p4 == >>>>>> _insidePixelValue* ) >>>>>> >>> // The point >>>>>> >>> { >>>>>> >>> >>>>>> >>> ... >>>>>> >>> >>>>>> >>> >>>>>> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >>>>>> >>> >>>>>> >>> Thank you so much. >>>>>> >>> My kind regards. >>>>>> >>> /Paco >>>>>> >>> >>>>>> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca <[hidden >>>>>> email] >>>>>> >>> >: >>>>>> >>> >>>>>> >>>> Hello Bradley again. >>>>>> >>>> Sorry but I'd like to re-open this issue because I need your >>>>>> class but >>>>>> >>>> with some modification. >>>>>> >>>> I pass to tell you. >>>>>> >>>> >>>>>> >>>> As my tests with your external class were not good taking into >>>>>> account >>>>>> >>>> the performance, I wonder if you could create a variant of it, >>>>>> but in which >>>>>> >>>> I can set a mask image and your class just return the >>>>>> VectorImage with all >>>>>> >>>> the features for that region (the masked locations) as >>>>>> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >>>>>> >>>> I mean, to get the vector image with all the features but just >>>>>> >>>> calculate it for the regions belonging to the mask image. >>>>>> Positions not >>>>>> >>>> belonging to the mask region could have a pixel value of 0, for >>>>>> instance. >>>>>> >>>> >>>>>> >>>> I don?t know if it is very costly for you, but I would thank >>>>>> you so >>>>>> >>>> much. Otherwise, I could try it but I'd need your suggestions on >>>>>> how to do >>>>>> >>>> it. >>>>>> >>>> >>>>>> >>>> Thanks a lot. >>>>>> >>>> Best regards. >>>>>> >>>> >>>>>> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca <[hidden >>>>>> email] >>>>>> >>>> >: >>>>>> >>>> >>>>>> >>>>> Hello Bradley again, >>>>>> >>>>> I would like to ask you for a couple of favours. In the one >>>>>> hand, >>>>>> >>>>> could you please send me your 3D image so that I can test on >>>>>> it? And on the >>>>>> >>>>> other hand, could you test the example I have referenced in the >>>>>> previous >>>>>> >>>>> email with your image, not changing anything in the code, such >>>>>> as it is, >>>>>> >>>>> and tell me if the execution time is normal? >>>>>> >>>>> Thank you very much. >>>>>> >>>>> Regards, >>>>>> >>>>> /Francisco >>>>>> >>>>> >>>>>> >>>>> PS: All my application trace is printed via standard 'cout' >>>>>> command, >>>>>> >>>>> not due to a debugging compilation mode. >>>>>> >>>>> >>>>>> >>>>> >>>>>> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp >>>>>> <[hidden >>>>>> >>>>> email] > >>>>>> >>>>> escribi?: >>>>>> >>>>> >>>>>> >>>>>> Hello, >>>>>> >>>>>> >>>>>> >>>>>> Did you compile TextureFeatureImage in Release mode? >>>>>> >>>>>> >>>>>> >>>>>> 1) The filter does not scale well with a large radius. And >>>>>> given by >>>>>> >>>>>> your initial report of print a very large number of offset >>>>>> you, it sounds >>>>>> >>>>>> like you are using a large radius with many offsets. I created >>>>>> a >>>>>> >>>>>> 224x224x300 unsigned short image and ran with the default >>>>>> offset and a >>>>>> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this >>>>>> filter is was ~10x >>>>>> >>>>>> faster than this example... things change though... >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> 2) I sounds like the boundaries/limits of the histogram may be >>>>>> >>>>>> clipping you values. I would inspect the co-occurance matrix. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> HTH, >>>>>> >>>>>> Brad >>>>>> >>>>>> >>>>>> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca >>>>>> <[hidden >>>>>> >>>>>> email] >>>>> >> >>>>>> >>>>>> wrote: >>>>>> >>>>>> >>>>>> >>>>>> I've tested with itkTextureFeatureImageFilter, with >>>>>> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>>>> >>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures >>>>>> example, >>>>>> >>>>>> for a 3D image and here are my comments: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> 1. I had to interrupt the test after several hours and it kept >>>>>> on >>>>>> >>>>>> calculating. And this is for only a 3D image (224x224x300). I >>>>>> need to >>>>>> >>>>>> process around 35 images. >>>>>> >>>>>> 2. The result (texture features: entropy, energy, correlation, >>>>>> LH, >>>>>> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, >>>>>> 7.83083e+247]. >>>>>> >>>>>> These values were not what I expected based on my experience >>>>>> on another >>>>>> >>>>>> application I developed, but in that case, I calculated the >>>>>> texture >>>>>> >>>>>> features for an image as a whole, not voxel by voxel. >>>>>> >>>>>> >>>>>> >>>>>> Regards. >>>>>> >>>>>> >>>>>> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >>>>>> >>>>>> >: >>>>>> >>>>>> >>>>>> >>>>>>> i yes i have tried radius = 3; >>>>>> >>>>>>> still no luck >>>>>> >>>>>>> >>>>>> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via >>>>>> ITK >>>>>> >>>>>>> Insight >>>>>> >>>>>>> Users] <[hidden email] >>>>>> >>>>>>> > >>>>>> wrote: >>>>>> >>>>>>> >>>>>> >>>>>>> > Have you tried with a radius of 3 instead of 1? >>>>>> >>>>>>> > >>>>>> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>>>> >>>>>>> > >: >>>>>> >>>>>>> > >>>>>> >>>>>>> >> hey Matt, >>>>>> >>>>>>> >> thanks for ur advice.. it did build successfully... but im >>>>>> not >>>>>> >>>>>>> able to run >>>>>> >>>>>>> >> the code for 2D png image... i tried to change the >>>>>> dimension to 2 >>>>>> >>>>>>> and >>>>>> >>>>>>> >> build >>>>>> >>>>>>> >> it which it did.. but when i run the code using the command >>>>>> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png >>>>>> putput.png >>>>>> >>>>>>> 1... i see >>>>>> >>>>>>> >> this output >>>>>> >>>>>>> >> >>>>>> >>>>>>> >> offset: [-1, -1] [0, -1] >>>>>> >>>>>>> >> offset: [0, -1] [1, -1] >>>>>> >>>>>>> >> offset: [-1, 0] [0, 0] >>>>>> >>>>>>> >> offset: [0, 0] [1, 0] >>>>>> >>>>>>> >> offset: [-1, 1] [0, 1] >>>>>> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... >>>>>> if pls >>>>>> >>>>>>> tel me >>>>>> >>>>>>> >> how can i modify this code to work wid 2d image... forgive >>>>>> me if >>>>>> >>>>>>> my ques >>>>>> >>>>>>> >> are really silly im trying to learn something.. >>>>>> >>>>>>> >> regards >>>>>> >>>>>>> >> Vis >>>>>> >>>>>>> >> >>>>>> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK >>>>>> >>>>>>> Insight Users] >>>>>> >>>>>>> >> < >>>>>> >>>>>>> >> [hidden email] < >>>>>> >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>>>>> >>>>>>> >> wrote: >>>>>> >>>>>>> >> >>>>>> >>>>>>> >> > Hi, >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > The function: >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char >>>>>> *argv[]) >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > must be renamed to >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > main(int argc, char* argv[]) >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > HTH, >>>>>> >>>>>>> >> > Matt >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>>>> >>>>>>> >> > > >>>>>> wrote: >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > > hi all, >>>>>> >>>>>>> >> > > im trying to build the >>>>>> itkTextureFeatureImageFilterTest.cxx >>>>>> >>>>>>> code but >>>>>> >>>>>>> >> im >>>>>> >>>>>>> >> > not >>>>>> >>>>>>> >> > > able to it is showing the following error >>>>>> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>>>> >>>>>>> Configuration: >>>>>> >>>>>>> >> Debug >>>>>> >>>>>>> >> > x64 >>>>>> >>>>>>> >> > > ------ >>>>>> >>>>>>> >> > > 1> Checking Build System >>>>>> >>>>>>> >> > > 1> CMake does not need to re-run because >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>>>> >>>>>>> >> > is >>>>>> >>>>>>> >> > > up-to-date. >>>>>> >>>>>>> >> > > 2>------ Rebuild All started: Project: >>>>>> >>>>>>> >> itkTextureFeatureImageFilterTest, >>>>>> >>>>>>> >> > > Configuration: Debug x64 ------ >>>>>> >>>>>>> >> > > 2> Building Custom Rule >>>>>> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>> >>>>>>> >> > > 2> CMake does not need to re-run because >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>> >>>>>>> >> > is >>>>>> >>>>>>> >> > > up-to-date. >>>>>> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>>>> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>>>> >>>>>>> 'std::_Copy_impl': >>>>>> >>>>>>> >> > Function >>>>>> >>>>>>> >> > > call with parameters that may be unsafe - this call >>>>>> relies on >>>>>> >>>>>>> the >>>>>> >>>>>>> >> caller >>>>>> >>>>>>> >> > to >>>>>> >>>>>>> >> > > check that the passed values are correct. To disable >>>>>> this >>>>>> >>>>>>> warning, use >>>>>> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to >>>>>> use >>>>>> >>>>>>> Visual C++ >>>>>> >>>>>>> >> > > 'Checked Iterators' >>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>> Studio >>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>> >>>>>>> 'std::_Copy_impl' >>>>>> >>>>>>> >> > > 2> >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>>>> >>>>>>> >> > see >>>>>> >>>>>>> >> > > reference to function template instantiation '_OutIt >>>>>> >>>>>>> std::copy>>>>> >>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' >>>>>> being >>>>>> >>>>>>> compiled >>>>>> >>>>>>> >> > > 2> with >>>>>> >>>>>>> >> > > 2> [ >>>>>> >>>>>>> >> > > 2> _OutIt=unsigned char *, >>>>>> >>>>>>> >> > > 2> _InIt=const unsigned char * >>>>>> >>>>>>> >> > > 2> ] >>>>>> >>>>>>> >> > > 2> >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>>>> >>>>>>> >> > > while compiling class template member function 'void >>>>>> >>>>>>> >> > > itk::ImageFileReader::GenerateData(void)' >>>>>> >>>>>>> >> > > 2> with >>>>>> >>>>>>> >> > > 2> [ >>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>> >>>>>>> >> > > 2> ] >>>>>> >>>>>>> >> > > 2> >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > > : see reference to class template instantiation >>>>>> >>>>>>> >> > > 'itk::ImageFileReader' being compiled >>>>>> >>>>>>> >> > > 2> with >>>>>> >>>>>>> >> > > 2> [ >>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>> >>>>>>> >> > > 2> ] >>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>> Studio >>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>> >>>>>>> 'std::_Copy_impl' >>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>> Studio >>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>> >>>>>>> 'std::_Copy_impl' >>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>> Studio >>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>> >>>>>>> 'std::_Copy_impl' >>>>>> >>>>>>> >> > > 2> Creating library >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > > and object >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved >>>>>> >>>>>>> external symbol >>>>>> >>>>>>> >> > main >>>>>> >>>>>>> >> > > referenced in function __tmainCRTStartup >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>>>> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>>>> >>>>>>> Configuration: Debug >>>>>> >>>>>>> >> > x64 >>>>>> >>>>>>> >> > > ------ >>>>>> >>>>>>> >> > > 3> Building Custom Rule >>>>>> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>> >>>>>>> >> > > 3> CMake does not need to re-run because >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>> >>>>>>> >> > is >>>>>> >>>>>>> >> > > up-to-date. >>>>>> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 >>>>>> skipped >>>>>> >>>>>>> ========== >>>>>> >>>>>>> >> > > im using the follwing CMakeList.txt >>>>>> >>>>>>> >> > > # This is the root ITK CMakeLists file. >>>>>> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>>>> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >>>>>> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>>>> >>>>>>> >> > > endif() >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > # This project is designed to be built outside the >>>>>> Insight >>>>>> >>>>>>> source >>>>>> >>>>>>> >> tree. >>>>>> >>>>>>> >> > > project(HelloWorld) >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > # Find ITK. >>>>>> >>>>>>> >> > > find_package(ITK REQUIRED) >>>>>> >>>>>>> >> > > include(${ITK_USE_FILE}) >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>>>> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest >>>>>> >>>>>>> >> ${ITK_LIBRARIES}) >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > please tel me wat the error is?? >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > -- >>>>>> >>>>>>> >> > > View this message in context: >>>>>> >>>>>>> >> > >>>>>> >>>>>>> >> >>>>>> >>>>>>> >>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>>>> >>>>>>> >> > > Sent from the ITK Insight Users mailing list archive at >>>>>> >>>>>>> Nabble.com . >>>>>> >>>>>>> >> > > _____________________________________ >>>>>> >>>>>>> >> > > Powered by www.kitware.com >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > Visit other Kitware open-source projects at >>>>>> >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > Kitware offers ITK Training Courses, for more >>>>>> information >>>>>> >>>>>>> visit: >>>>>> >>>>>>> >> > > http://www.kitware.com/products/protraining.php >>>>>> >>>>>>> >> > > >>>>>> >>>>>>> >> > > Please keep messages on-topic and check the ITK FAQ at: >>>>>> >>>>>>> >> > > 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http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588495.html >>> To start a new topic under ITK Insight Users, email [hidden email] >>> >>> To unsubscribe from ITK Insight Users, click here. >>> NAML >>> >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588505.html > To start a new topic under ITK Insight Users, email > ml-node+s2283740n2283740h75 at n2.nabble.com > To unsubscribe from ITK Insight Users, click here > > . > NAML > > -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588512.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Thu Feb 18 09:25:09 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 18 Feb 2016 09:25:09 -0500 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <3F877AC4-BCD1-43FF-B8B3-7B30F9B6D30B@mail.nih.gov> Message-ID: Have you tried /bigobj ? Are you using MinGW? Visual Studio is now free . HTH On Thu, Feb 18, 2016 at 6:37 AM, Francisco Lopez de la Franca < franciscolopezdelafranca at gmail.com> wrote: > Hi again, > I've got ITK version 4.5.1 (a little bit old, I know), and after making > the changes suggested by Dzenanz and recompiling ITK, the problem > continues, that is, my code crashes at the same point. > > Then, I've downloaded the latest stable ITK version, ITK 4.9.0 and > compiled from scratch and I get the following error: > > [ 98%] Building CXX object > Modules/IO/TransformBase/src/CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.obj > C:/MINGW/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: > CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: too many > sections (33106) > C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Assembler messages: > C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Fatal error: can't write > CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: File too > big > > After doing some "googling" and follow some of the instructions referred > on the web, I've been unable to solve this. > Has anyone met this problem and solved it? > Thanks. > KR. > /Francisco > > 2016-02-16 22:13 GMT+01:00 Bradley Lowekamp [via ITK Insight Users] < > ml-node+s2283740n7588505h90 at n2.nabble.com>: > >> Hello, >> >> Please take a look at these changes: >> >> https://github.com/blowekamp/itkTextureAnalysis/commit/9654d74ea1d09f0677f1d1b93242cc94340591bf >> >> Brad >> >> On Feb 16, 2016, at 10:35 AM, D?enan Zuki? <[hidden email] >> > wrote: >> >> I have set up a project using one of the tests from Brad's repository >> (attached), and it works in debug mode both with his original code and with >> your modified class, and crashes in release mode both with his original >> code and with your modified class. I will now compile ITK in RelWithDebInfo >> in an attempt to figure out where is the crash occurring. >> >> Regards, >> D?enan >> >> On Tue, Feb 16, 2016 at 1:52 AM, Francisco Lopez de la Franca <[hidden >> email] > wrote: >> >>> Excuse me Dzenanz, but that's not completely true, because I've tested >>> Brad's class and it works right. >>> The problem seems to be that when you add a new neighbor iterator to >>> include just the mask points in the "histogram" then it is when the >>> application crashes, and I donot understand why. >>> If you just comment the 'maskIter' references you'll see that the >>> application works. >>> I've created a single threaded class based on the Brad's code and it >>> works but it is twice slower, that is why I'm interesting on Brad's class >>> (multi-threaded) to make it work. >>> >>> >>> 2016-02-15 17:15 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>> email] >: >>> >>>> Hi Francisco, >>>> >>>> both your code and Brad's code run in debug mode (I did not wait for >>>> the end), and both crash in release mode immediately on startup. Here is a >>>> sample output: >>>> >>>> Progress input: 0000000002868970 >>>> input: 0000000002868970 >>>> _maskImage: 0000000002868970 >>>> _maskImage: 0000000002868970 >>>> input: 0000000002868970 >>>> _maskImage: 0000000002868970 >>>> iter.first: iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>> [-5, -5, -5] iter.second: [-4, -5, -5] >>>> niter index: [5, 5, 210] >>>> niter index: [5, 5, 140] >>>> maskIter index: [5, 5, 140] >>>> maskIter index: [5, 5, 210] >>>> Before p3 >>>> input: 0000000002868970 >>>> _maskImage: 0000000002868970 >>>> After p3: | 0niter index: [5, 5, 70] >>>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>> niter index: [5, 5, 5] >>>> ? >>>> maskIter index: [5, 5, 70] >>>> After p4: ? >>>> Before p3 >>>> Before p3 >>>> After p3: ?iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>> niter index: [5, 5, 140] >>>> maskIter index: [5, 5, 140] >>>> maskIter index: [5, 5, 5] >>>> Before p3 >>>> After p3: ? >>>> After p3: ? >>>> After p4: ? >>>> After p4: ? >>>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>> niter index: [5, 5, 5] >>>> maskIter index: [5, 5, 5] >>>> >>>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>> Before p3 >>>> Before p3 >>>> After p4: ? >>>> After p3: ? >>>> After p4: ? >>>> >>>> Regards, >>>> D?enan >>>> >>>> On Mon, Feb 15, 2016 at 1:36 AM, Francisco Lopez de la Franca <[hidden >>>> email] > wrote: >>>> >>>>> Hi, >>>>> Here they are. >>>>> KR. >>>>> >>>>> 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>>> email] >: >>>>> >>>>>> Hi Francisco, >>>>>> >>>>>> do you mind attaching the modified files or pointing to your fork of >>>>>> it on GitHub? >>>>>> >>>>>> Regards >>>>>> >>>>>> On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden >>>>>> email] > wrote: >>>>>> >>>>>>> Hi Dzenan, >>>>>>> The original class is here: >>>>>>> >>>>>>> >>>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >>>>>>> >>>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >>>>>>> >>>>>>> I've just added setInput and setMaskImage methods and modify some >>>>>>> lines in >>>>>>> the original class as I indicated in the yesterday mail within this >>>>>>> thread. >>>>>>> I'm running it on Windows, and there is no error at all, just a >>>>>>> crash. I >>>>>>> may have to include exceptions management. >>>>>>> The crash occurs just when calling p3 = >>>>>>> maskIter.GetPixel(iter->first) >>>>>>> >>>>>>> If you know why it could be or if you need more clarification, >>>>>>> please let >>>>>>> me know. >>>>>>> Many thanks >>>>>>> >>>>>>> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >>>>>>> [hidden email] >>>>>>> >: >>>>>>> >>>>>>> > Hi Francisco, >>>>>>> > >>>>>>> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the error >>>>>>> message >>>>>>> > that goes along with the crash? In which file and line does it >>>>>>> crash? >>>>>>> > >>>>>>> > Regards >>>>>>> > >>>>>>> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca >>>>>>> <[hidden >>>>>>> > email] > >>>>>>> wrote: >>>>>>> > >>>>>>> >> Hi, >>>>>>> >> Please, someone that could help me. I'm working in a pre-doctorate >>>>>>> >> project and I need this class to work. >>>>>>> >> I've read the chapter 13 in the ITK Software Guide on how to >>>>>>> write a >>>>>>> >> filter and now I see the fact of the threads due to inheritance of >>>>>>> >> ImageToImageFilter. >>>>>>> >> But, I keep on without understanding why the code crashes just >>>>>>> when >>>>>>> >> calling >>>>>>> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >>>>>>> >> It is just a call to read data, not to write. >>>>>>> >> >>>>>>> >> I guess somebody that had worked with creation of filters might >>>>>>> see >>>>>>> >> "easily" the problem, but not me. >>>>>>> >> >>>>>>> >> So, again, please, I need someone to help me with this because >>>>>>> I'm stuck >>>>>>> >> on this point. >>>>>>> >> >>>>>>> >> Thank you very much. >>>>>>> >> KR. >>>>>>> >> /Francisco >>>>>>> >> >>>>>>> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden >>>>>>> email] >>>>>>> >> >: >>>>>>> >> >>>>>>> >>> Hi Bradley again. >>>>>>> >>> I'm modifying your class in order to be able to set a mask image >>>>>>> (a >>>>>>> >>> binary image) to be used as a limit in the histogram >>>>>>> calculations, I mean, >>>>>>> >>> I set an input, a mask and the class should take into account to >>>>>>> calculate >>>>>>> >>> the histograms only the voxels that belong to the input and to >>>>>>> the mask >>>>>>> >>> image and having the value 1 in the mask image. >>>>>>> >>> The changes seem to be easy but I don?t know why my tests are not >>>>>>> >>> working. It seems that 2 threads are working at the same time >>>>>>> and when I >>>>>>> >>> added my mask iterator, the code crashes. >>>>>>> >>> >>>>>>> >>> *** Consider that the input and mask images are the same origin, >>>>>>> spacing >>>>>>> >>> and size. >>>>>>> >>> >>>>>>> >>> I attach the main changes I've done, and I would thank you a lot >>>>>>> if you >>>>>>> >>> don't mind having a look and help me to find what I'm doing >>>>>>> wrong: >>>>>>> >>> >>>>>>> >>> template< class TImageType, class TOutputImage > >>>>>>> >>> void >>>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>>> >::*SetInput*(InputImageType >>>>>>> >>> *image) >>>>>>> >>> { >>>>>>> >>> // Process object is not const-correct so the const_cast is >>>>>>> required >>>>>>> >>> here >>>>>>> >>> this->ProcessObject::SetNthInput( 0, >>>>>>> >>> const_cast< InputImageType * >>>>>>> >( >>>>>>> >>> image ) ); >>>>>>> >>> } >>>>>>> >>> >>>>>>> >>> template< class TImageType, class TOutputImage > >>>>>>> >>> void >>>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>>> >::*SetMaskImage*(InputImageType >>>>>>> >>> *image) >>>>>>> >>> { >>>>>>> >>> // Process object is not const-correct so the const_cast is >>>>>>> required >>>>>>> >>> here >>>>>>> >>> this->ProcessObject::SetNthInput( 1, const_cast< >>>>>>> InputImageType * >( >>>>>>> >>> image ) ); >>>>>>> >>> >>>>>>> >>> _maskImage = image; // _maskImage is a private member >>>>>>> >>> } >>>>>>> >>> >>>>>>> >>> In the *ThreadedGenerateData*(const RegionType& >>>>>>> outputRegionForThread, >>>>>>> >>> ThreadIdType threadId ) method: >>>>>>> >>> { >>>>>>> >>> >>>>>>> >>> ... >>>>>>> >>> >>>>>>> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >>>>>>> >>> { >>>>>>> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >>>>>>> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, >>>>>>> *fit);* >>>>>>> >>> OutputIterator outIter(output, *fit); >>>>>>> >>> >>>>>>> >>> OutputPixelType out; >>>>>>> >>> NumericTraits::SetLength( out, >>>>>>> >>> this->GetNumberOfOutputComponents() ); >>>>>>> >>> >>>>>>> >>> while( !nIter.IsAtEnd() ) >>>>>>> >>> { >>>>>>> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >>>>>>> >>> >>>>>>> >>> ... >>>>>>> >>> >>>>>>> >>> ++nIter; >>>>>>> >>> ++outIter; >>>>>>> >>> * ++maskIter;* >>>>>>> >>> ... >>>>>>> >>> >>>>>>> >>> In the *FillHistogram *method: >>>>>>> >>> { >>>>>>> >>> >>>>>>> >>> ... >>>>>>> >>> >>>>>>> >>> while( iter != m_CooccurenceOffsetVector.end() ) >>>>>>> >>> { >>>>>>> >>> >>>>>>> >>> const PixelType p1 = niter.GetPixel(iter->first); >>>>>>> >>> const PixelType p2 = niter.GetPixel(iter->second); >>>>>>> >>> std::cout << "Before p3" << std::endl; >>>>>>> >>> >>>>>>> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); >>>>>>> *std::cout >>>>>>> >>> << "After p3: " << p3 << std::endl; >>>>>>> >>> >>>>>>> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >>>>>>> >>> std::cout << "After p4: " << p4 << std::endl; >>>>>>> >>> >>>>>>> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= >>>>>>> m_Max >>>>>>> >>> *&& p3 == _insidePixelValue && p4 == >>>>>>> _insidePixelValue* ) >>>>>>> >>> // The point >>>>>>> >>> { >>>>>>> >>> >>>>>>> >>> ... >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >>>>>>> >>> >>>>>>> >>> Thank you so much. >>>>>>> >>> My kind regards. >>>>>>> >>> /Paco >>>>>>> >>> >>>>>>> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca <[hidden >>>>>>> email] >>>>>>> >>> >: >>>>>>> >>> >>>>>>> >>>> Hello Bradley again. >>>>>>> >>>> Sorry but I'd like to re-open this issue because I need your >>>>>>> class but >>>>>>> >>>> with some modification. >>>>>>> >>>> I pass to tell you. >>>>>>> >>>> >>>>>>> >>>> As my tests with your external class were not good taking into >>>>>>> account >>>>>>> >>>> the performance, I wonder if you could create a variant of it, >>>>>>> but in which >>>>>>> >>>> I can set a mask image and your class just return the >>>>>>> VectorImage with all >>>>>>> >>>> the features for that region (the masked locations) as >>>>>>> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >>>>>>> >>>> I mean, to get the vector image with all the features but just >>>>>>> >>>> calculate it for the regions belonging to the mask image. >>>>>>> Positions not >>>>>>> >>>> belonging to the mask region could have a pixel value of 0, for >>>>>>> instance. >>>>>>> >>>> >>>>>>> >>>> I don?t know if it is very costly for you, but I would thank >>>>>>> you so >>>>>>> >>>> much. Otherwise, I could try it but I'd need your suggestions >>>>>>> on how to do >>>>>>> >>>> it. >>>>>>> >>>> >>>>>>> >>>> Thanks a lot. >>>>>>> >>>> Best regards. >>>>>>> >>>> >>>>>>> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca >>>>>>> <[hidden email] >>>>>>> >>>> >: >>>>>>> >>>> >>>>>>> >>>>> Hello Bradley again, >>>>>>> >>>>> I would like to ask you for a couple of favours. In the one >>>>>>> hand, >>>>>>> >>>>> could you please send me your 3D image so that I can test on >>>>>>> it? And on the >>>>>>> >>>>> other hand, could you test the example I have referenced in >>>>>>> the previous >>>>>>> >>>>> email with your image, not changing anything in the code, such >>>>>>> as it is, >>>>>>> >>>>> and tell me if the execution time is normal? >>>>>>> >>>>> Thank you very much. >>>>>>> >>>>> Regards, >>>>>>> >>>>> /Francisco >>>>>>> >>>>> >>>>>>> >>>>> PS: All my application trace is printed via standard 'cout' >>>>>>> command, >>>>>>> >>>>> not due to a debugging compilation mode. >>>>>>> >>>>> >>>>>>> >>>>> >>>>>>> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp >>>>>>> <[hidden >>>>>>> >>>>> email] >>>>>> >> >>>>>>> >>>>> escribi?: >>>>>>> >>>>> >>>>>>> >>>>>> Hello, >>>>>>> >>>>>> >>>>>>> >>>>>> Did you compile TextureFeatureImage in Release mode? >>>>>>> >>>>>> >>>>>>> >>>>>> 1) The filter does not scale well with a large radius. And >>>>>>> given by >>>>>>> >>>>>> your initial report of print a very large number of offset >>>>>>> you, it sounds >>>>>>> >>>>>> like you are using a large radius with many offsets. I >>>>>>> created a >>>>>>> >>>>>> 224x224x300 unsigned short image and ran with the default >>>>>>> offset and a >>>>>>> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this >>>>>>> filter is was ~10x >>>>>>> >>>>>> faster than this example... things change though... >>>>>>> >>>>>> >>>>>>> >>>>>> >>>>>>> >>>>>> 2) I sounds like the boundaries/limits of the histogram may be >>>>>>> >>>>>> clipping you values. I would inspect the co-occurance matrix. >>>>>>> >>>>>> >>>>>>> >>>>>> >>>>>>> >>>>>> HTH, >>>>>>> >>>>>> Brad >>>>>>> >>>>>> >>>>>>> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca >>>>>>> <[hidden >>>>>>> >>>>>> email] >>>>>> >> >>>>>>> >>>>>> wrote: >>>>>>> >>>>>> >>>>>>> >>>>>> I've tested with itkTextureFeatureImageFilter, with >>>>>>> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>>>>> >>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures >>>>>>> example, >>>>>>> >>>>>> for a 3D image and here are my comments: >>>>>>> >>>>>> >>>>>>> >>>>>> >>>>>>> >>>>>> 1. I had to interrupt the test after several hours and it >>>>>>> kept on >>>>>>> >>>>>> calculating. And this is for only a 3D image (224x224x300). I >>>>>>> need to >>>>>>> >>>>>> process around 35 images. >>>>>>> >>>>>> 2. The result (texture features: entropy, energy, >>>>>>> correlation, LH, >>>>>>> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, >>>>>>> 7.83083e+247]. >>>>>>> >>>>>> These values were not what I expected based on my experience >>>>>>> on another >>>>>>> >>>>>> application I developed, but in that case, I calculated the >>>>>>> texture >>>>>>> >>>>>> features for an image as a whole, not voxel by voxel. >>>>>>> >>>>>> >>>>>>> >>>>>> Regards. >>>>>>> >>>>>> >>>>>>> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >>>>>>> >>>>>> >: >>>>>>> >>>>>> >>>>>>> >>>>>>> i yes i have tried radius = 3; >>>>>>> >>>>>>> still no luck >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca >>>>>>> [via ITK >>>>>>> >>>>>>> Insight >>>>>>> >>>>>>> Users] <[hidden email] >>>>>>> >>>>>>> > >>>>>>> wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> > Have you tried with a radius of 3 instead of 1? >>>>>>> >>>>>>> > >>>>>>> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>>>>> >>>>>>> > >: >>>>>>> >>>>>>> > >>>>>>> >>>>>>> >> hey Matt, >>>>>>> >>>>>>> >> thanks for ur advice.. it did build successfully... but >>>>>>> im not >>>>>>> >>>>>>> able to run >>>>>>> >>>>>>> >> the code for 2D png image... i tried to change the >>>>>>> dimension to 2 >>>>>>> >>>>>>> and >>>>>>> >>>>>>> >> build >>>>>>> >>>>>>> >> it which it did.. but when i run the code using the >>>>>>> command >>>>>>> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png >>>>>>> putput.png >>>>>>> >>>>>>> 1... i see >>>>>>> >>>>>>> >> this output >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> offset: [-1, -1] [0, -1] >>>>>>> >>>>>>> >> offset: [0, -1] [1, -1] >>>>>>> >>>>>>> >> offset: [-1, 0] [0, 0] >>>>>>> >>>>>>> >> offset: [0, 0] [1, 0] >>>>>>> >>>>>>> >> offset: [-1, 1] [0, 1] >>>>>>> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the >>>>>>> program... if pls >>>>>>> >>>>>>> tel me >>>>>>> >>>>>>> >> how can i modify this code to work wid 2d image... >>>>>>> forgive me if >>>>>>> >>>>>>> my ques >>>>>>> >>>>>>> >> are really silly im trying to learn something.. >>>>>>> >>>>>>> >> regards >>>>>>> >>>>>>> >> Vis >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK >>>>>>> >>>>>>> Insight Users] >>>>>>> >>>>>>> >> < >>>>>>> >>>>>>> >> [hidden email] < >>>>>>> >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>>>>>> >>>>>>> >> wrote: >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> > Hi, >>>>>>> >>>>>>> >> > >>>>>>> >>>>>>> >> > The function: >>>>>>> >>>>>>> >> > >>>>>>> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char >>>>>>> *argv[]) >>>>>>> >>>>>>> >> > >>>>>>> >>>>>>> >> > must be renamed to >>>>>>> >>>>>>> >> > >>>>>>> >>>>>>> >> > main(int argc, char* argv[]) >>>>>>> >>>>>>> >> > >>>>>>> >>>>>>> >> > HTH, >>>>>>> >>>>>>> >> > Matt >>>>>>> >>>>>>> >> > >>>>>>> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>>>>> >>>>>>> >> > > >>>>>>> wrote: >>>>>>> >>>>>>> >> > >>>>>>> >>>>>>> >> > > hi all, >>>>>>> >>>>>>> >> > > im trying to build the >>>>>>> itkTextureFeatureImageFilterTest.cxx >>>>>>> >>>>>>> code but >>>>>>> >>>>>>> >> im >>>>>>> >>>>>>> >> > not >>>>>>> >>>>>>> >> > > able to it is showing the following error >>>>>>> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>>>>> >>>>>>> Configuration: >>>>>>> >>>>>>> >> Debug >>>>>>> >>>>>>> >> > x64 >>>>>>> >>>>>>> >> > > ------ >>>>>>> >>>>>>> >> > > 1> Checking Build System >>>>>>> >>>>>>> >> > > 1> CMake does not need to re-run because >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>>>>> >>>>>>> >> > is >>>>>>> >>>>>>> >> > > up-to-date. >>>>>>> >>>>>>> >> > > 2>------ Rebuild All started: Project: >>>>>>> >>>>>>> >> itkTextureFeatureImageFilterTest, >>>>>>> >>>>>>> >> > > Configuration: Debug x64 ------ >>>>>>> >>>>>>> >> > > 2> Building Custom Rule >>>>>>> >>>>>>> >> > > >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>> >>>>>>> >> > > 2> CMake does not need to re-run because >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>> >>>>>>> >> > is >>>>>>> >>>>>>> >> > > up-to-date. >>>>>>> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>>>>> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>>>>> >>>>>>> 'std::_Copy_impl': >>>>>>> >>>>>>> >> > Function >>>>>>> >>>>>>> >> > > call with parameters that may be unsafe - this call >>>>>>> relies on >>>>>>> >>>>>>> the >>>>>>> >>>>>>> >> caller >>>>>>> >>>>>>> >> > to >>>>>>> >>>>>>> >> > > check that the passed values are correct. To disable >>>>>>> this >>>>>>> >>>>>>> warning, use >>>>>>> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how >>>>>>> to use >>>>>>> >>>>>>> Visual C++ >>>>>>> >>>>>>> >> > > 'Checked Iterators' >>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>>> Studio >>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>> >>>>>>> >> > > 2> >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>>>>> >>>>>>> >> > see >>>>>>> >>>>>>> >> > > reference to function template instantiation '_OutIt >>>>>>> >>>>>>> std::copy>>>>>> >>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' >>>>>>> being >>>>>>> >>>>>>> compiled >>>>>>> >>>>>>> >> > > 2> with >>>>>>> >>>>>>> >> > > 2> [ >>>>>>> >>>>>>> >> > > 2> _OutIt=unsigned char *, >>>>>>> >>>>>>> >> > > 2> _InIt=const unsigned char * >>>>>>> >>>>>>> >> > > 2> ] >>>>>>> >>>>>>> >> > > 2> >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>>>>> >>>>>>> >> > > while compiling class template member function 'void >>>>>>> >>>>>>> >> > > >>>>>>> itk::ImageFileReader::GenerateData(void)' >>>>>>> >>>>>>> >> > > 2> with >>>>>>> >>>>>>> >> > > 2> [ >>>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>> >>>>>>> >> > > 2> ] >>>>>>> >>>>>>> >> > > 2> >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> > >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>>>>> >>>>>>> >> > >>>>>>> >>>>>>> >> > > : see reference to class template instantiation >>>>>>> >>>>>>> >> > > 'itk::ImageFileReader' being compiled >>>>>>> >>>>>>> >> > > 2> with >>>>>>> >>>>>>> >> > > 2> [ >>>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>> >>>>>>> >> > > 2> ] >>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>>> Studio >>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>>> Studio >>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>>> Studio >>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>> >>>>>>> >> > > 2> Creating library >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> > >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>>>>> >>>>>>> >> > >>>>>>> >>>>>>> >> > > and object >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> > >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>>>>> >>>>>>> >> > >>>>>>> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved >>>>>>> >>>>>>> external symbol >>>>>>> >>>>>>> >> > main >>>>>>> >>>>>>> >> > > referenced in function __tmainCRTStartup >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> > >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >>>>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>>>>> >>>>>>> >> > >>>>>>> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>>>>> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>>>>> >>>>>>> Configuration: Debug >>>>>>> >>>>>>> >> > x64 >>>>>>> >>>>>>> >> > > ------ >>>>>>> >>>>>>> >> > > 3> Building Custom Rule >>>>>>> >>>>>>> >> > > >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>> >>>>>>> >> > > 3> CMake does not need to re-run because >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>> >>>>>>> >> > is >>>>>>> >>>>>>> >> > > up-to-date. >>>>>>> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 >>>>>>> skipped >>>>>>> >>>>>>> ========== >>>>>>> >>>>>>> >> > > im using the follwing CMakeList.txt >>>>>>> >>>>>>> >> > > # This is the root ITK CMakeLists file. >>>>>>> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>>>>> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >>>>>>> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>>>>> >>>>>>> >> > > endif() >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> > > # This project is designed to be built outside the >>>>>>> Insight >>>>>>> >>>>>>> source >>>>>>> >>>>>>> >> tree. >>>>>>> >>>>>>> >> > > project(HelloWorld) >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> > > # Find ITK. >>>>>>> >>>>>>> >> > > find_package(ITK REQUIRED) >>>>>>> >>>>>>> >> > > include(${ITK_USE_FILE}) >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>>>>> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest >>>>>>> >>>>>>> >> ${ITK_LIBRARIES}) >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> > > please tel me wat the error is?? >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> > > -- >>>>>>> >>>>>>> >> > > View this message in context: >>>>>>> >>>>>>> >> > >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>>>>> >>>>>>> >> > > Sent from the ITK Insight Users mailing list archive >>>>>>> at >>>>>>> >>>>>>> Nabble.com . >>>>>>> >>>>>>> >> > > _____________________________________ >>>>>>> >>>>>>> >> > > Powered by www.kitware.com >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> > > Visit other Kitware open-source projects at >>>>>>> >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>>>>> >>>>>>> >> > > >>>>>>> >>>>>>> >> > > Kitware offers ITK Training Courses, for more >>>>>>> information >>>>>>> >>>>>>> visit: >>>>>>> >>>>>>> >> > > 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open-source projects at >>>>>>> >>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>> >>>>>>> >>>>>>> >>>>>>> Kitware offers ITK Training Courses, for more information >>>>>>> visit: >>>>>>> >>>>>>> http://www.kitware.com/products/protraining.php >>>>>>> >>>>>>> >>>>>>> >>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>> >>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>> >>>>>>> >>>>>>> >>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>> >>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>>> >>>>>> _____________________________________ >>>>>>> >>>>>> Powered by www.kitware.com >>>>>>> >>>>>> >>>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>>> >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>> >>>>>> >>>>>>> >>>>>> Kitware offers ITK Training Courses, for more information >>>>>>> visit: >>>>>>> >>>>>> http://www.kitware.com/products/protraining.php >>>>>>> >>>>>> >>>>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>> >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>> >>>>>> >>>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>>> >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>> >>>>>> >>>>>>> >>>>>> >>>>>>> >>>>>> >>>>>>> >>>> >>>>>>> >>> >>>>>>> >> >>>>>>> >> _____________________________________ >>>>>>> >> Powered by www.kitware.com >>>>>>> >> >>>>>>> >> Visit other Kitware open-source projects at >>>>>>> >> http://www.kitware.com/opensource/opensource.html >>>>>>> >> >>>>>>> >> Kitware offers ITK Training Courses, for more information visit: >>>>>>> >> http://www.kitware.com/products/protraining.php >>>>>>> >> >>>>>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>> >> >>>>>>> >> Follow this link to subscribe/unsubscribe: >>>>>>> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>> >> >>>>>>> >> >>>>>>> > >>>>>>> > 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projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> ------------------------------ >> If you reply to this email, your message will be added to the discussion >> below: >> >> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588505.html >> To start a new topic under ITK Insight Users, email >> ml-node+s2283740n2283740h75 at n2.nabble.com >> To unsubscribe from ITK Insight Users, click here >> >> . >> NAML >> >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Feb 18 09:38:22 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 18 Feb 2016 09:38:22 -0500 Subject: [ITK] [ITK-users] [New Example] Convert an itk::Image to vtkImageData Message-ID: Hi folks, We have a new example, Convert an itk::Image to vtkImageData: http://itk.org/ITKExamples/src/Bridge/VtkGlue/ConvertAnitkImageTovtkImageData/Documentation.html There is also the inverse, Convert vtkImageData to an itk::Image: http://itk.org/ITKExamples/src/Bridge/VtkGlue/ConvertvtkImageDataToAnitkImage/Documentation.html Matt _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Thu Feb 18 12:30:28 2016 From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca) Date: Thu, 18 Feb 2016 18:30:28 +0100 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <3F877AC4-BCD1-43FF-B8B3-7B30F9B6D30B@mail.nih.gov> Message-ID: Yes. I use mingw (x86_64-w64-mingw32-g++.exe) and I set in CMAKE GUI the entry CMAKE_CXX_FLAGS to -bigobj and the result is "unrecognized option". 2016-02-18 15:25 GMT+01:00 dzenanz [via ITK Insight Users] < ml-node+s2283740n7588513h38 at n2.nabble.com>: > Have you tried /bigobj > ? > Are you using MinGW? Visual Studio is now free > . > > HTH > > On Thu, Feb 18, 2016 at 6:37 AM, Francisco Lopez de la Franca <[hidden > email] > wrote: > >> Hi again, >> I've got ITK version 4.5.1 (a little bit old, I know), and after making >> the changes suggested by Dzenanz and recompiling ITK, the problem >> continues, that is, my code crashes at the same point. >> >> Then, I've downloaded the latest stable ITK version, ITK 4.9.0 and >> compiled from scratch and I get the following error: >> >> [ 98%] Building CXX object >> Modules/IO/TransformBase/src/CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.obj >> C:/MINGW/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: >> CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: too many >> sections (33106) >> C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Assembler messages: >> C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Fatal error: can't write >> CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: File too >> big >> >> After doing some "googling" and follow some of the instructions referred >> on the web, I've been unable to solve this. >> Has anyone met this problem and solved it? >> Thanks. >> KR. >> /Francisco >> >> 2016-02-16 22:13 GMT+01:00 Bradley Lowekamp [via ITK Insight Users] <[hidden >> email] >: >> >>> Hello, >>> >>> Please take a look at these changes: >>> >>> https://github.com/blowekamp/itkTextureAnalysis/commit/9654d74ea1d09f0677f1d1b93242cc94340591bf >>> >>> Brad >>> >>> On Feb 16, 2016, at 10:35 AM, D?enan Zuki? <[hidden email] >>> > wrote: >>> >>> I have set up a project using one of the tests from Brad's repository >>> (attached), and it works in debug mode both with his original code and with >>> your modified class, and crashes in release mode both with his original >>> code and with your modified class. I will now compile ITK in RelWithDebInfo >>> in an attempt to figure out where is the crash occurring. >>> >>> Regards, >>> D?enan >>> >>> On Tue, Feb 16, 2016 at 1:52 AM, Francisco Lopez de la Franca <[hidden >>> email] > wrote: >>> >>>> Excuse me Dzenanz, but that's not completely true, because I've tested >>>> Brad's class and it works right. >>>> The problem seems to be that when you add a new neighbor iterator to >>>> include just the mask points in the "histogram" then it is when the >>>> application crashes, and I donot understand why. >>>> If you just comment the 'maskIter' references you'll see that the >>>> application works. >>>> I've created a single threaded class based on the Brad's code and it >>>> works but it is twice slower, that is why I'm interesting on Brad's class >>>> (multi-threaded) to make it work. >>>> >>>> >>>> 2016-02-15 17:15 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>> email] >: >>>> >>>>> Hi Francisco, >>>>> >>>>> both your code and Brad's code run in debug mode (I did not wait for >>>>> the end), and both crash in release mode immediately on startup. Here is a >>>>> sample output: >>>>> >>>>> Progress input: 0000000002868970 >>>>> input: 0000000002868970 >>>>> _maskImage: 0000000002868970 >>>>> _maskImage: 0000000002868970 >>>>> input: 0000000002868970 >>>>> _maskImage: 0000000002868970 >>>>> iter.first: iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>> [-5, -5, -5] iter.second: [-4, -5, -5] >>>>> niter index: [5, 5, 210] >>>>> niter index: [5, 5, 140] >>>>> maskIter index: [5, 5, 140] >>>>> maskIter index: [5, 5, 210] >>>>> Before p3 >>>>> input: 0000000002868970 >>>>> _maskImage: 0000000002868970 >>>>> After p3: | 0niter index: [5, 5, 70] >>>>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>> niter index: [5, 5, 5] >>>>> ? >>>>> maskIter index: [5, 5, 70] >>>>> After p4: ? >>>>> Before p3 >>>>> Before p3 >>>>> After p3: ?iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>> niter index: [5, 5, 140] >>>>> maskIter index: [5, 5, 140] >>>>> maskIter index: [5, 5, 5] >>>>> Before p3 >>>>> After p3: ? >>>>> After p3: ? >>>>> After p4: ? >>>>> After p4: ? >>>>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>> niter index: [5, 5, 5] >>>>> maskIter index: [5, 5, 5] >>>>> >>>>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>> Before p3 >>>>> Before p3 >>>>> After p4: ? >>>>> After p3: ? >>>>> After p4: ? >>>>> >>>>> Regards, >>>>> D?enan >>>>> >>>>> On Mon, Feb 15, 2016 at 1:36 AM, Francisco Lopez de la Franca <[hidden >>>>> email] > wrote: >>>>> >>>>>> Hi, >>>>>> Here they are. >>>>>> KR. >>>>>> >>>>>> 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>>>> email] >: >>>>>> >>>>>>> Hi Francisco, >>>>>>> >>>>>>> do you mind attaching the modified files or pointing to your fork of >>>>>>> it on GitHub? >>>>>>> >>>>>>> Regards >>>>>>> >>>>>>> On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden >>>>>>> email] > >>>>>>> wrote: >>>>>>> >>>>>>>> Hi Dzenan, >>>>>>>> The original class is here: >>>>>>>> >>>>>>>> >>>>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >>>>>>>> >>>>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >>>>>>>> >>>>>>>> I've just added setInput and setMaskImage methods and modify some >>>>>>>> lines in >>>>>>>> the original class as I indicated in the yesterday mail within this >>>>>>>> thread. >>>>>>>> I'm running it on Windows, and there is no error at all, just a >>>>>>>> crash. I >>>>>>>> may have to include exceptions management. >>>>>>>> The crash occurs just when calling p3 = >>>>>>>> maskIter.GetPixel(iter->first) >>>>>>>> >>>>>>>> If you know why it could be or if you need more clarification, >>>>>>>> please let >>>>>>>> me know. >>>>>>>> Many thanks >>>>>>>> >>>>>>>> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >>>>>>>> [hidden email] >>>>>>>> >: >>>>>>>> >>>>>>>> > Hi Francisco, >>>>>>>> > >>>>>>>> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the >>>>>>>> error message >>>>>>>> > that goes along with the crash? In which file and line does it >>>>>>>> crash? >>>>>>>> > >>>>>>>> > Regards >>>>>>>> > >>>>>>>> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca >>>>>>>> <[hidden >>>>>>>> > email] > >>>>>>>> wrote: >>>>>>>> > >>>>>>>> >> Hi, >>>>>>>> >> Please, someone that could help me. I'm working in a >>>>>>>> pre-doctorate >>>>>>>> >> project and I need this class to work. >>>>>>>> >> I've read the chapter 13 in the ITK Software Guide on how to >>>>>>>> write a >>>>>>>> >> filter and now I see the fact of the threads due to inheritance >>>>>>>> of >>>>>>>> >> ImageToImageFilter. >>>>>>>> >> But, I keep on without understanding why the code crashes just >>>>>>>> when >>>>>>>> >> calling >>>>>>>> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >>>>>>>> >> It is just a call to read data, not to write. >>>>>>>> >> >>>>>>>> >> I guess somebody that had worked with creation of filters might >>>>>>>> see >>>>>>>> >> "easily" the problem, but not me. >>>>>>>> >> >>>>>>>> >> So, again, please, I need someone to help me with this because >>>>>>>> I'm stuck >>>>>>>> >> on this point. >>>>>>>> >> >>>>>>>> >> Thank you very much. >>>>>>>> >> KR. >>>>>>>> >> /Francisco >>>>>>>> >> >>>>>>>> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden >>>>>>>> email] >>>>>>>> >> >: >>>>>>>> >> >>>>>>>> >>> Hi Bradley again. >>>>>>>> >>> I'm modifying your class in order to be able to set a mask >>>>>>>> image (a >>>>>>>> >>> binary image) to be used as a limit in the histogram >>>>>>>> calculations, I mean, >>>>>>>> >>> I set an input, a mask and the class should take into account >>>>>>>> to calculate >>>>>>>> >>> the histograms only the voxels that belong to the input and to >>>>>>>> the mask >>>>>>>> >>> image and having the value 1 in the mask image. >>>>>>>> >>> The changes seem to be easy but I don?t know why my tests are >>>>>>>> not >>>>>>>> >>> working. It seems that 2 threads are working at the same time >>>>>>>> and when I >>>>>>>> >>> added my mask iterator, the code crashes. >>>>>>>> >>> >>>>>>>> >>> *** Consider that the input and mask images are the same >>>>>>>> origin, spacing >>>>>>>> >>> and size. >>>>>>>> >>> >>>>>>>> >>> I attach the main changes I've done, and I would thank you a >>>>>>>> lot if you >>>>>>>> >>> don't mind having a look and help me to find what I'm doing >>>>>>>> wrong: >>>>>>>> >>> >>>>>>>> >>> template< class TImageType, class TOutputImage > >>>>>>>> >>> void >>>>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>>>> >::*SetInput*(InputImageType >>>>>>>> >>> *image) >>>>>>>> >>> { >>>>>>>> >>> // Process object is not const-correct so the const_cast is >>>>>>>> required >>>>>>>> >>> here >>>>>>>> >>> this->ProcessObject::SetNthInput( 0, >>>>>>>> >>> const_cast< InputImageType >>>>>>>> * >( >>>>>>>> >>> image ) ); >>>>>>>> >>> } >>>>>>>> >>> >>>>>>>> >>> template< class TImageType, class TOutputImage > >>>>>>>> >>> void >>>>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>>>> >::*SetMaskImage*(InputImageType >>>>>>>> >>> *image) >>>>>>>> >>> { >>>>>>>> >>> // Process object is not const-correct so the const_cast is >>>>>>>> required >>>>>>>> >>> here >>>>>>>> >>> this->ProcessObject::SetNthInput( 1, const_cast< >>>>>>>> InputImageType * >( >>>>>>>> >>> image ) ); >>>>>>>> >>> >>>>>>>> >>> _maskImage = image; // _maskImage is a private member >>>>>>>> >>> } >>>>>>>> >>> >>>>>>>> >>> In the *ThreadedGenerateData*(const RegionType& >>>>>>>> outputRegionForThread, >>>>>>>> >>> ThreadIdType threadId ) method: >>>>>>>> >>> { >>>>>>>> >>> >>>>>>>> >>> ... >>>>>>>> >>> >>>>>>>> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >>>>>>>> >>> { >>>>>>>> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >>>>>>>> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, >>>>>>>> *fit);* >>>>>>>> >>> OutputIterator outIter(output, *fit); >>>>>>>> >>> >>>>>>>> >>> OutputPixelType out; >>>>>>>> >>> NumericTraits::SetLength( out, >>>>>>>> >>> this->GetNumberOfOutputComponents() ); >>>>>>>> >>> >>>>>>>> >>> while( !nIter.IsAtEnd() ) >>>>>>>> >>> { >>>>>>>> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >>>>>>>> >>> >>>>>>>> >>> ... >>>>>>>> >>> >>>>>>>> >>> ++nIter; >>>>>>>> >>> ++outIter; >>>>>>>> >>> * ++maskIter;* >>>>>>>> >>> ... >>>>>>>> >>> >>>>>>>> >>> In the *FillHistogram *method: >>>>>>>> >>> { >>>>>>>> >>> >>>>>>>> >>> ... >>>>>>>> >>> >>>>>>>> >>> while( iter != m_CooccurenceOffsetVector.end() ) >>>>>>>> >>> { >>>>>>>> >>> >>>>>>>> >>> const PixelType p1 = niter.GetPixel(iter->first); >>>>>>>> >>> const PixelType p2 = niter.GetPixel(iter->second); >>>>>>>> >>> std::cout << "Before p3" << std::endl; >>>>>>>> >>> >>>>>>>> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); >>>>>>>> *std::cout >>>>>>>> >>> << "After p3: " << p3 << std::endl; >>>>>>>> >>> >>>>>>>> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >>>>>>>> >>> std::cout << "After p4: " << p4 << std::endl; >>>>>>>> >>> >>>>>>>> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= >>>>>>>> m_Max >>>>>>>> >>> *&& p3 == _insidePixelValue && p4 == >>>>>>>> _insidePixelValue* ) >>>>>>>> >>> // The point >>>>>>>> >>> { >>>>>>>> >>> >>>>>>>> >>> ... >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >>>>>>>> >>> >>>>>>>> >>> Thank you so much. >>>>>>>> >>> My kind regards. >>>>>>>> >>> /Paco >>>>>>>> >>> >>>>>>>> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca >>>>>>>> <[hidden email] >>>>>>>> >>> >: >>>>>>>> >>> >>>>>>>> >>>> Hello Bradley again. >>>>>>>> >>>> Sorry but I'd like to re-open this issue because I need your >>>>>>>> class but >>>>>>>> >>>> with some modification. >>>>>>>> >>>> I pass to tell you. >>>>>>>> >>>> >>>>>>>> >>>> As my tests with your external class were not good taking into >>>>>>>> account >>>>>>>> >>>> the performance, I wonder if you could create a variant of it, >>>>>>>> but in which >>>>>>>> >>>> I can set a mask image and your class just return the >>>>>>>> VectorImage with all >>>>>>>> >>>> the features for that region (the masked locations) as >>>>>>>> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >>>>>>>> >>>> I mean, to get the vector image with all the features but just >>>>>>>> >>>> calculate it for the regions belonging to the mask image. >>>>>>>> Positions not >>>>>>>> >>>> belonging to the mask region could have a pixel value of 0, >>>>>>>> for instance. >>>>>>>> >>>> >>>>>>>> >>>> I don?t know if it is very costly for you, but I would thank >>>>>>>> you so >>>>>>>> >>>> much. Otherwise, I could try it but I'd need your suggestions >>>>>>>> on how to do >>>>>>>> >>>> it. >>>>>>>> >>>> >>>>>>>> >>>> Thanks a lot. >>>>>>>> >>>> Best regards. >>>>>>>> >>>> >>>>>>>> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca >>>>>>>> <[hidden email] >>>>>>>> >>>> >: >>>>>>>> >>>> >>>>>>>> >>>>> Hello Bradley again, >>>>>>>> >>>>> I would like to ask you for a couple of favours. In the one >>>>>>>> hand, >>>>>>>> >>>>> could you please send me your 3D image so that I can test on >>>>>>>> it? And on the >>>>>>>> >>>>> other hand, could you test the example I have referenced in >>>>>>>> the previous >>>>>>>> >>>>> email with your image, not changing anything in the code, >>>>>>>> such as it is, >>>>>>>> >>>>> and tell me if the execution time is normal? >>>>>>>> >>>>> Thank you very much. >>>>>>>> >>>>> Regards, >>>>>>>> >>>>> /Francisco >>>>>>>> >>>>> >>>>>>>> >>>>> PS: All my application trace is printed via standard 'cout' >>>>>>>> command, >>>>>>>> >>>>> not due to a debugging compilation mode. >>>>>>>> >>>>> >>>>>>>> >>>>> >>>>>>>> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp >>>>>>>> <[hidden >>>>>>>> >>>>> email] >>>>>>> >> >>>>>>>> >>>>> escribi?: >>>>>>>> >>>>> >>>>>>>> >>>>>> Hello, >>>>>>>> >>>>>> >>>>>>>> >>>>>> Did you compile TextureFeatureImage in Release mode? >>>>>>>> >>>>>> >>>>>>>> >>>>>> 1) The filter does not scale well with a large radius. And >>>>>>>> given by >>>>>>>> >>>>>> your initial report of print a very large number of offset >>>>>>>> you, it sounds >>>>>>>> >>>>>> like you are using a large radius with many offsets. I >>>>>>>> created a >>>>>>>> >>>>>> 224x224x300 unsigned short image and ran with the default >>>>>>>> offset and a >>>>>>>> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this >>>>>>>> filter is was ~10x >>>>>>>> >>>>>> faster than this example... things change though... >>>>>>>> >>>>>> >>>>>>>> >>>>>> >>>>>>>> >>>>>> 2) I sounds like the boundaries/limits of the histogram may >>>>>>>> be >>>>>>>> >>>>>> clipping you values. I would inspect the co-occurance matrix. >>>>>>>> >>>>>> >>>>>>>> >>>>>> >>>>>>>> >>>>>> HTH, >>>>>>>> >>>>>> Brad >>>>>>>> >>>>>> >>>>>>>> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca >>>>>>>> <[hidden >>>>>>>> >>>>>> email] < >>>>>>>> http:///user/SendEmail.jtp?type=node&node=7588477&i=5>> >>>>>>>> >>>>>> wrote: >>>>>>>> >>>>>> >>>>>>>> >>>>>> I've tested with itkTextureFeatureImageFilter, with >>>>>>>> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>>>>>> >>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures >>>>>>>> example, >>>>>>>> >>>>>> for a 3D image and here are my comments: >>>>>>>> >>>>>> >>>>>>>> >>>>>> >>>>>>>> >>>>>> 1. I had to interrupt the test after several hours and it >>>>>>>> kept on >>>>>>>> >>>>>> calculating. And this is for only a 3D image (224x224x300). >>>>>>>> I need to >>>>>>>> >>>>>> process around 35 images. >>>>>>>> >>>>>> 2. The result (texture features: entropy, energy, >>>>>>>> correlation, LH, >>>>>>>> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, >>>>>>>> 7.83083e+247]. >>>>>>>> >>>>>> These values were not what I expected based on my experience >>>>>>>> on another >>>>>>>> >>>>>> application I developed, but in that case, I calculated the >>>>>>>> texture >>>>>>>> >>>>>> features for an image as a whole, not voxel by voxel. >>>>>>>> >>>>>> >>>>>>>> >>>>>> Regards. >>>>>>>> >>>>>> >>>>>>>> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >>>>>>>> >>>>>> >: >>>>>>>> >>>>>> >>>>>>>> >>>>>>> i yes i have tried radius = 3; >>>>>>>> >>>>>>> still no luck >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca >>>>>>>> [via ITK >>>>>>>> >>>>>>> Insight >>>>>>>> >>>>>>> Users] <[hidden email] >>>>>>>> >>>>>>> > >>>>>>>> wrote: >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> > Have you tried with a radius of 3 instead of 1? >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>>>>>> >>>>>>> > >: >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> >> hey Matt, >>>>>>>> >>>>>>> >> thanks for ur advice.. it did build successfully... but >>>>>>>> im not >>>>>>>> >>>>>>> able to run >>>>>>>> >>>>>>> >> the code for 2D png image... i tried to change the >>>>>>>> dimension to 2 >>>>>>>> >>>>>>> and >>>>>>>> >>>>>>> >> build >>>>>>>> >>>>>>> >> it which it did.. but when i run the code using the >>>>>>>> command >>>>>>>> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png >>>>>>>> putput.png >>>>>>>> >>>>>>> 1... i see >>>>>>>> >>>>>>> >> this output >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> offset: [-1, -1] [0, -1] >>>>>>>> >>>>>>> >> offset: [0, -1] [1, -1] >>>>>>>> >>>>>>> >> offset: [-1, 0] [0, 0] >>>>>>>> >>>>>>> >> offset: [0, 0] [1, 0] >>>>>>>> >>>>>>> >> offset: [-1, 1] [0, 1] >>>>>>>> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the >>>>>>>> program... if pls >>>>>>>> >>>>>>> tel me >>>>>>>> >>>>>>> >> how can i modify this code to work wid 2d image... >>>>>>>> forgive me if >>>>>>>> >>>>>>> my ques >>>>>>>> >>>>>>> >> are really silly im trying to learn something.. >>>>>>>> >>>>>>> >> regards >>>>>>>> >>>>>>> >> Vis >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via >>>>>>>> ITK >>>>>>>> >>>>>>> Insight Users] >>>>>>>> >>>>>>> >> < >>>>>>>> >>>>>>> >> [hidden email] < >>>>>>>> >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>>>>>>> >>>>>>> >> wrote: >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> > Hi, >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > The function: >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char >>>>>>>> *argv[]) >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > must be renamed to >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > main(int argc, char* argv[]) >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > HTH, >>>>>>>> >>>>>>> >> > Matt >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>>>>>> >>>>>>> >> > > >>>>>>>> wrote: >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > > hi all, >>>>>>>> >>>>>>> >> > > im trying to build the >>>>>>>> itkTextureFeatureImageFilterTest.cxx >>>>>>>> >>>>>>> code but >>>>>>>> >>>>>>> >> im >>>>>>>> >>>>>>> >> > not >>>>>>>> >>>>>>> >> > > able to it is showing the following error >>>>>>>> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>>>>>> >>>>>>> Configuration: >>>>>>>> >>>>>>> >> Debug >>>>>>>> >>>>>>> >> > x64 >>>>>>>> >>>>>>> >> > > ------ >>>>>>>> >>>>>>> >> > > 1> Checking Build System >>>>>>>> >>>>>>> >> > > 1> CMake does not need to re-run because >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>>>>>> >>>>>>> >> > is >>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>> >>>>>>> >> > > 2>------ Rebuild All started: Project: >>>>>>>> >>>>>>> >> itkTextureFeatureImageFilterTest, >>>>>>>> >>>>>>> >> > > Configuration: Debug x64 ------ >>>>>>>> >>>>>>> >> > > 2> Building Custom Rule >>>>>>>> >>>>>>> >> > > >>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>>> >>>>>>> >> > > 2> CMake does not need to re-run because >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>>> >>>>>>> >> > is >>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>>>>>> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>>>>>> >>>>>>> 'std::_Copy_impl': >>>>>>>> >>>>>>> >> > Function >>>>>>>> >>>>>>> >> > > call with parameters that may be unsafe - this call >>>>>>>> relies on >>>>>>>> >>>>>>> the >>>>>>>> >>>>>>> >> caller >>>>>>>> >>>>>>> >> > to >>>>>>>> >>>>>>> >> > > check that the passed values are correct. To disable >>>>>>>> this >>>>>>>> >>>>>>> warning, use >>>>>>>> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how >>>>>>>> to use >>>>>>>> >>>>>>> Visual C++ >>>>>>>> >>>>>>> >> > > 'Checked Iterators' >>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>>>> Studio >>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>> >>>>>>> >> > > 2> >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>>>>>> >>>>>>> >> > see >>>>>>>> >>>>>>> >> > > reference to function template instantiation '_OutIt >>>>>>>> >>>>>>> std::copy>>>>>>> >>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' >>>>>>>> being >>>>>>>> >>>>>>> compiled >>>>>>>> >>>>>>> >> > > 2> with >>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>> >>>>>>> >> > > 2> _OutIt=unsigned char *, >>>>>>>> >>>>>>> >> > > 2> _InIt=const unsigned char * >>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>> >>>>>>> >> > > 2> >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>>>>>> >>>>>>> >> > > while compiling class template member function 'void >>>>>>>> >>>>>>> >> > > >>>>>>>> itk::ImageFileReader::GenerateData(void)' >>>>>>>> >>>>>>> >> > > 2> with >>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>> >>>>>>> >> > > 2> >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > > : see reference to class template instantiation >>>>>>>> >>>>>>> >> > > 'itk::ImageFileReader' being compiled >>>>>>>> >>>>>>> >> > > 2> with >>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>>>> Studio >>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>>>> Studio >>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>>>> Studio >>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>> >>>>>>> >> > > 2> Creating library >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > > and object >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved >>>>>>>> >>>>>>> external symbol >>>>>>>> >>>>>>> >> > main >>>>>>>> >>>>>>> >> > > referenced in function __tmainCRTStartup >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>>>>>> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>>>>>> >>>>>>> Configuration: Debug >>>>>>>> >>>>>>> >> > x64 >>>>>>>> >>>>>>> >> > > ------ >>>>>>>> >>>>>>> >> > > 3> Building Custom Rule >>>>>>>> >>>>>>> >> > > >>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>>> >>>>>>> >> > > 3> CMake does not need to re-run because >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>>> >>>>>>> >> > is >>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 >>>>>>>> skipped >>>>>>>> >>>>>>> ========== >>>>>>>> >>>>>>> >> > > im using the follwing CMakeList.txt >>>>>>>> >>>>>>> >> > > # This is the root ITK CMakeLists file. >>>>>>>> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>>>>>> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >>>>>>>> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>>>>>> >>>>>>> >> > > endif() >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > # This project is designed to be built outside the >>>>>>>> Insight >>>>>>>> >>>>>>> source >>>>>>>> >>>>>>> >> tree. >>>>>>>> >>>>>>> >> > > project(HelloWorld) >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > # Find ITK. >>>>>>>> >>>>>>> >> > > find_package(ITK REQUIRED) >>>>>>>> >>>>>>> >> > > include(${ITK_USE_FILE}) >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>>>>>> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > >>>>>>>> target_link_libraries(itkTextureFeatureImageFilterTest >>>>>>>> >>>>>>> >> ${ITK_LIBRARIES}) >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > please tel me wat the error is?? >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > -- >>>>>>>> >>>>>>> >> > > View this message in context: >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>>>>>> >>>>>>> >> > > Sent from the ITK Insight Users mailing list archive >>>>>>>> at >>>>>>>> >>>>>>> Nabble.com . >>>>>>>> >>>>>>> >> > > _____________________________________ >>>>>>>> >>>>>>> >> > > Powered by www.kitware.com >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > Visit other Kitware open-source projects at >>>>>>>> >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > Kitware offers ITK Training Courses, for more >>>>>>>> information >>>>>>>> >>>>>>> visit: >>>>>>>> >>>>>>> >> > > http://www.kitware.com/products/protraining.php >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > Please keep messages on-topic and check the ITK FAQ >>>>>>>> at: >>>>>>>> >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > Follow this link to subscribe/unsubscribe: >>>>>>>> >>>>>>> >> > > >>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >>>>>>> >> > _____________________________________ >>>>>>>> >>>>>>> >> > Powered by www.kitware.com >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > Visit other Kitware open-source projects at >>>>>>>> >>>>>>> >> > http://www.kitware.com/opensource/opensource.html >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > Kitware offers ITK Training Courses, for more >>>>>>>> information visit: >>>>>>>> >>>>>>> >> > http://www.kitware.com/products/protraining.php >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> >>>>>>> >> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > Follow this link to subscribe/unsubscribe: >>>>>>>> >>>>>>> >> > >>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > ------------------------------ >>>>>>>> >>>>>>> >> > If you reply to this email, your message will be added >>>>>>>> to the >>>>>>>> >>>>>>> discussion >>>>>>>> >>>>>>> >> > below: >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587952.html >>>>>>>> >>>>>>> >> > To unsubscribe from [ITK-users] Texture pixel by >>>>>>>> pixel, click >>>>>>>> >>>>>>> here >>>>>>>> >>>>>>> >> > < > . >>>>>>>> >>>>>>> >> > NAML >>>>>>>> >>>>>>> >> > < >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> -- >>>>>>>> >>>>>>> >> View this message in context: >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587960.html >>>>>>>> >>>>>>> >> Sent from the ITK Insight Users mailing list archive at >>>>>>>> >>>>>>> Nabble.com . >>>>>>>> >>>>>>> >> _____________________________________ >>>>>>>> >>>>>>> >> Powered by www.kitware.com >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> Visit other Kitware open-source projects at >>>>>>>> >>>>>>> >> http://www.kitware.com/opensource/opensource.html >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> Kitware offers ITK Training Courses, for more >>>>>>>> information visit: >>>>>>>> >>>>>>> >> http://www.kitware.com/products/protraining.php >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> >>>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> Follow this link to subscribe/unsubscribe: >>>>>>>> >>>>>>> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > _____________________________________ >>>>>>>> >>>>>>> > Powered by www.kitware.com >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > Visit other Kitware open-source projects at >>>>>>>> >>>>>>> > http://www.kitware.com/opensource/opensource.html >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > Kitware offers ITK Training Courses, for more information >>>>>>>> visit: >>>>>>>> >>>>>>> > http://www.kitware.com/products/protraining.php >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> >>>>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > Follow this link to subscribe/unsubscribe: >>>>>>>> >>>>>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > ------------------------------ >>>>>>>> >>>>>>> > If you reply to this email, your message will be added to >>>>>>>> the >>>>>>>> >>>>>>> discussion >>>>>>>> >>>>>>> > below: >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587961.html >>>>>>>> >>>>>>> > To unsubscribe from [ITK-users] Texture pixel by pixel, >>>>>>>> click here >>>>>>>> >>>>>>> > < > . >>>>>>>> >>>>>>> > NAML >>>>>>>> >>>>>>> > < >>>>>>>> >>>>>>> >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> -- >>>>>>>> >>>>>>> View this message in context: >>>>>>>> >>>>>>> >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587963.html >>>>>>>> >>>>>>> Sent from the ITK Insight Users mailing list archive at >>>>>>>> Nabble.com . >>>>>>>> >>>>>>> _____________________________________ >>>>>>>> >>>>>>> Powered by www.kitware.com >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> Visit other Kitware open-source projects at >>>>>>>> >>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> Kitware offers ITK Training Courses, for more information >>>>>>>> visit: >>>>>>>> >>>>>>> http://www.kitware.com/products/protraining.php >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> >>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>> >>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >>>>>>> >>>>>>>> >>>>>> >>>>>>>> >>>>>> _____________________________________ >>>>>>>> >>>>>> Powered by www.kitware.com >>>>>>>> >>>>>> >>>>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>>>> >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>> >>>>>> >>>>>>>> >>>>>> Kitware offers ITK Training Courses, for more information >>>>>>>> visit: >>>>>>>> >>>>>> http://www.kitware.com/products/protraining.php >>>>>>>> >>>>>> >>>>>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >>>>>> >>>>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>> >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >>>>>> >>>>>>>> >>>>>> >>>>>>>> >>>>>> >>>>>>>> >>>> >>>>>>>> >>> >>>>>>>> >> >>>>>>>> >> _____________________________________ >>>>>>>> >> Powered by www.kitware.com >>>>>>>> >> >>>>>>>> >> Visit other Kitware open-source projects at >>>>>>>> >> http://www.kitware.com/opensource/opensource.html >>>>>>>> >> >>>>>>>> >> Kitware offers ITK Training Courses, for more information visit: >>>>>>>> >> http://www.kitware.com/products/protraining.php >>>>>>>> >> >>>>>>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >> >>>>>>>> >> Follow this link to subscribe/unsubscribe: >>>>>>>> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >> >>>>>>>> >> >>>>>>>> > >>>>>>>> > _____________________________________ >>>>>>>> > Powered by www.kitware.com >>>>>>>> > >>>>>>>> > Visit other Kitware open-source projects at >>>>>>>> > http://www.kitware.com/opensource/opensource.html >>>>>>>> > >>>>>>>> > Kitware offers ITK Training Courses, for more information visit: >>>>>>>> > http://www.kitware.com/products/protraining.php >>>>>>>> > >>>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> > >>>>>>>> > Follow this link to subscribe/unsubscribe: >>>>>>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> > >>>>>>>> > >>>>>>>> > ------------------------------ >>>>>>>> > If you reply to this email, your message will be added to the >>>>>>>> discussion >>>>>>>> > below: >>>>>>>> > >>>>>>>> > >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588477.html >>>>>>>> > To start a new topic under ITK Insight Users, email >>>>>>>> > [hidden email] >>>>>>>> >>>>>>>> > To unsubscribe from ITK Insight Users, click here >>>>>>>> > < > . >>>>>>>> > NAML >>>>>>>> > < >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>>>> > >>>>>>>> > >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> View this message in context: >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588483.html >>>>>>>> Sent from the ITK Insight Users mailing list archive at Nabble.com >>>>>>>> . >>>>>>>> _____________________________________ >>>>>>>> Powered by www.kitware.com >>>>>>>> >>>>>>>> Visit other Kitware open-source projects at >>>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>> >>>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>>> http://www.kitware.com/products/protraining.php >>>>>>>> >>>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >>>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >>>>>>> >>>>>>> >>>>>>> _____________________________________ >>>>>>> Powered by www.kitware.com >>>>>>> >>>>>>> Visit other Kitware open-source projects at >>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>> >>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>> http://www.kitware.com/products/protraining.php >>>>>>> >>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>> >>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> If you reply to this email, your message will be added to the >>>>>>> discussion below: >>>>>>> >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588490.html >>>>>>> To start a new topic under ITK Insight Users, email [hidden email] >>>>>>> >>>>>>> To unsubscribe from ITK Insight Users, click here. >>>>>>> NAML >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> _____________________________________ >>>>>> Powered by www.kitware.com >>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>> http://www.kitware.com/products/protraining.php >>>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >>>>>> >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>>> >>>>> ------------------------------ >>>>> If you reply to this email, your message will be added to the >>>>> discussion below: >>>>> >>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588495.html >>>>> To start a new topic under ITK Insight Users, email [hidden email] >>>>> >>>>> To unsubscribe from ITK Insight Users, click here. >>>>> NAML >>>>> >>>>> >>>> >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>> ------------------------------ >>> If you reply to this email, your message will be added to the discussion >>> below: >>> >>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588505.html >>> To start a new topic under ITK Insight Users, email [hidden email] >>> >>> To unsubscribe from ITK Insight Users, click here. >>> NAML >>> >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588513.html > To start a new topic under ITK Insight Users, email > ml-node+s2283740n2283740h75 at n2.nabble.com > To unsubscribe from ITK Insight Users, click here > > . > NAML > > -------------- next part -------------- An HTML 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URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Thu Feb 18 12:30:40 2016 From: franciscolopezdelafranca at gmail.com (=?UTF-8?Q?Francisco_L=C3=B3pez-Franca?=) Date: Thu, 18 Feb 2016 10:30:40 -0700 (MST) Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <3F877AC4-BCD1-43FF-B8B3-7B30F9B6D30B@mail.nih.gov> Message-ID: Yes. I use mingw (x86_64-w64-mingw32-g++.exe) and I set in CMAKE GUI the entry CMAKE_CXX_FLAGS to -bigobj and the result is "unrecognized option". 2016-02-18 15:25 GMT+01:00 dzenanz [via ITK Insight Users] < ml-node+s2283740n7588513h38 at n2.nabble.com>: > Have you tried /bigobj > ? > Are you using MinGW? Visual Studio is now free > . > > HTH > > On Thu, Feb 18, 2016 at 6:37 AM, Francisco Lopez de la Franca <[hidden > email] > wrote: > >> Hi again, >> I've got ITK version 4.5.1 (a little bit old, I know), and after making >> the changes suggested by Dzenanz and recompiling ITK, the problem >> continues, that is, my code crashes at the same point. >> >> Then, I've downloaded the latest stable ITK version, ITK 4.9.0 and >> compiled from scratch and I get the following error: >> >> [ 98%] Building CXX object >> Modules/IO/TransformBase/src/CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.obj >> C:/MINGW/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: >> CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: too many >> sections (33106) >> C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Assembler messages: >> C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Fatal error: can't write >> CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: File too >> big >> >> After doing some "googling" and follow some of the instructions referred >> on the web, I've been unable to solve this. >> Has anyone met this problem and solved it? >> Thanks. >> KR. >> /Francisco >> >> 2016-02-16 22:13 GMT+01:00 Bradley Lowekamp [via ITK Insight Users] <[hidden >> email] >: >> >>> Hello, >>> >>> Please take a look at these changes: >>> >>> https://github.com/blowekamp/itkTextureAnalysis/commit/9654d74ea1d09f0677f1d1b93242cc94340591bf >>> >>> Brad >>> >>> On Feb 16, 2016, at 10:35 AM, D?enan Zuki? <[hidden email] >>> > wrote: >>> >>> I have set up a project using one of the tests from Brad's repository >>> (attached), and it works in debug mode both with his original code and with >>> your modified class, and crashes in release mode both with his original >>> code and with your modified class. I will now compile ITK in RelWithDebInfo >>> in an attempt to figure out where is the crash occurring. >>> >>> Regards, >>> D?enan >>> >>> On Tue, Feb 16, 2016 at 1:52 AM, Francisco Lopez de la Franca <[hidden >>> email] > wrote: >>> >>>> Excuse me Dzenanz, but that's not completely true, because I've tested >>>> Brad's class and it works right. >>>> The problem seems to be that when you add a new neighbor iterator to >>>> include just the mask points in the "histogram" then it is when the >>>> application crashes, and I donot understand why. >>>> If you just comment the 'maskIter' references you'll see that the >>>> application works. >>>> I've created a single threaded class based on the Brad's code and it >>>> works but it is twice slower, that is why I'm interesting on Brad's class >>>> (multi-threaded) to make it work. >>>> >>>> >>>> 2016-02-15 17:15 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>> email] >: >>>> >>>>> Hi Francisco, >>>>> >>>>> both your code and Brad's code run in debug mode (I did not wait for >>>>> the end), and both crash in release mode immediately on startup. Here is a >>>>> sample output: >>>>> >>>>> Progress input: 0000000002868970 >>>>> input: 0000000002868970 >>>>> _maskImage: 0000000002868970 >>>>> _maskImage: 0000000002868970 >>>>> input: 0000000002868970 >>>>> _maskImage: 0000000002868970 >>>>> iter.first: iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>> [-5, -5, -5] iter.second: [-4, -5, -5] >>>>> niter index: [5, 5, 210] >>>>> niter index: [5, 5, 140] >>>>> maskIter index: [5, 5, 140] >>>>> maskIter index: [5, 5, 210] >>>>> Before p3 >>>>> input: 0000000002868970 >>>>> _maskImage: 0000000002868970 >>>>> After p3: | 0niter index: [5, 5, 70] >>>>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>> niter index: [5, 5, 5] >>>>> ? >>>>> maskIter index: [5, 5, 70] >>>>> After p4: ? >>>>> Before p3 >>>>> Before p3 >>>>> After p3: ?iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>> niter index: [5, 5, 140] >>>>> maskIter index: [5, 5, 140] >>>>> maskIter index: [5, 5, 5] >>>>> Before p3 >>>>> After p3: ? >>>>> After p3: ? >>>>> After p4: ? >>>>> After p4: ? >>>>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>> niter index: [5, 5, 5] >>>>> maskIter index: [5, 5, 5] >>>>> >>>>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>> Before p3 >>>>> Before p3 >>>>> After p4: ? >>>>> After p3: ? >>>>> After p4: ? >>>>> >>>>> Regards, >>>>> D?enan >>>>> >>>>> On Mon, Feb 15, 2016 at 1:36 AM, Francisco Lopez de la Franca <[hidden >>>>> email] > wrote: >>>>> >>>>>> Hi, >>>>>> Here they are. >>>>>> KR. >>>>>> >>>>>> 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>>>> email] >: >>>>>> >>>>>>> Hi Francisco, >>>>>>> >>>>>>> do you mind attaching the modified files or pointing to your fork of >>>>>>> it on GitHub? >>>>>>> >>>>>>> Regards >>>>>>> >>>>>>> On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden >>>>>>> email] > >>>>>>> wrote: >>>>>>> >>>>>>>> Hi Dzenan, >>>>>>>> The original class is here: >>>>>>>> >>>>>>>> >>>>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >>>>>>>> >>>>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >>>>>>>> >>>>>>>> I've just added setInput and setMaskImage methods and modify some >>>>>>>> lines in >>>>>>>> the original class as I indicated in the yesterday mail within this >>>>>>>> thread. >>>>>>>> I'm running it on Windows, and there is no error at all, just a >>>>>>>> crash. I >>>>>>>> may have to include exceptions management. >>>>>>>> The crash occurs just when calling p3 = >>>>>>>> maskIter.GetPixel(iter->first) >>>>>>>> >>>>>>>> If you know why it could be or if you need more clarification, >>>>>>>> please let >>>>>>>> me know. >>>>>>>> Many thanks >>>>>>>> >>>>>>>> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >>>>>>>> [hidden email] >>>>>>>> >: >>>>>>>> >>>>>>>> > Hi Francisco, >>>>>>>> > >>>>>>>> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the >>>>>>>> error message >>>>>>>> > that goes along with the crash? In which file and line does it >>>>>>>> crash? >>>>>>>> > >>>>>>>> > Regards >>>>>>>> > >>>>>>>> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca >>>>>>>> <[hidden >>>>>>>> > email] > >>>>>>>> wrote: >>>>>>>> > >>>>>>>> >> Hi, >>>>>>>> >> Please, someone that could help me. I'm working in a >>>>>>>> pre-doctorate >>>>>>>> >> project and I need this class to work. >>>>>>>> >> I've read the chapter 13 in the ITK Software Guide on how to >>>>>>>> write a >>>>>>>> >> filter and now I see the fact of the threads due to inheritance >>>>>>>> of >>>>>>>> >> ImageToImageFilter. >>>>>>>> >> But, I keep on without understanding why the code crashes just >>>>>>>> when >>>>>>>> >> calling >>>>>>>> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >>>>>>>> >> It is just a call to read data, not to write. >>>>>>>> >> >>>>>>>> >> I guess somebody that had worked with creation of filters might >>>>>>>> see >>>>>>>> >> "easily" the problem, but not me. >>>>>>>> >> >>>>>>>> >> So, again, please, I need someone to help me with this because >>>>>>>> I'm stuck >>>>>>>> >> on this point. >>>>>>>> >> >>>>>>>> >> Thank you very much. >>>>>>>> >> KR. >>>>>>>> >> /Francisco >>>>>>>> >> >>>>>>>> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden >>>>>>>> email] >>>>>>>> >> >: >>>>>>>> >> >>>>>>>> >>> Hi Bradley again. >>>>>>>> >>> I'm modifying your class in order to be able to set a mask >>>>>>>> image (a >>>>>>>> >>> binary image) to be used as a limit in the histogram >>>>>>>> calculations, I mean, >>>>>>>> >>> I set an input, a mask and the class should take into account >>>>>>>> to calculate >>>>>>>> >>> the histograms only the voxels that belong to the input and to >>>>>>>> the mask >>>>>>>> >>> image and having the value 1 in the mask image. >>>>>>>> >>> The changes seem to be easy but I don?t know why my tests are >>>>>>>> not >>>>>>>> >>> working. It seems that 2 threads are working at the same time >>>>>>>> and when I >>>>>>>> >>> added my mask iterator, the code crashes. >>>>>>>> >>> >>>>>>>> >>> *** Consider that the input and mask images are the same >>>>>>>> origin, spacing >>>>>>>> >>> and size. >>>>>>>> >>> >>>>>>>> >>> I attach the main changes I've done, and I would thank you a >>>>>>>> lot if you >>>>>>>> >>> don't mind having a look and help me to find what I'm doing >>>>>>>> wrong: >>>>>>>> >>> >>>>>>>> >>> template< class TImageType, class TOutputImage > >>>>>>>> >>> void >>>>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>>>> >::*SetInput*(InputImageType >>>>>>>> >>> *image) >>>>>>>> >>> { >>>>>>>> >>> // Process object is not const-correct so the const_cast is >>>>>>>> required >>>>>>>> >>> here >>>>>>>> >>> this->ProcessObject::SetNthInput( 0, >>>>>>>> >>> const_cast< InputImageType >>>>>>>> * >( >>>>>>>> >>> image ) ); >>>>>>>> >>> } >>>>>>>> >>> >>>>>>>> >>> template< class TImageType, class TOutputImage > >>>>>>>> >>> void >>>>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>>>> >::*SetMaskImage*(InputImageType >>>>>>>> >>> *image) >>>>>>>> >>> { >>>>>>>> >>> // Process object is not const-correct so the const_cast is >>>>>>>> required >>>>>>>> >>> here >>>>>>>> >>> this->ProcessObject::SetNthInput( 1, const_cast< >>>>>>>> InputImageType * >( >>>>>>>> >>> image ) ); >>>>>>>> >>> >>>>>>>> >>> _maskImage = image; // _maskImage is a private member >>>>>>>> >>> } >>>>>>>> >>> >>>>>>>> >>> In the *ThreadedGenerateData*(const RegionType& >>>>>>>> outputRegionForThread, >>>>>>>> >>> ThreadIdType threadId ) method: >>>>>>>> >>> { >>>>>>>> >>> >>>>>>>> >>> ... >>>>>>>> >>> >>>>>>>> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >>>>>>>> >>> { >>>>>>>> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >>>>>>>> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, >>>>>>>> *fit);* >>>>>>>> >>> OutputIterator outIter(output, *fit); >>>>>>>> >>> >>>>>>>> >>> OutputPixelType out; >>>>>>>> >>> NumericTraits::SetLength( out, >>>>>>>> >>> this->GetNumberOfOutputComponents() ); >>>>>>>> >>> >>>>>>>> >>> while( !nIter.IsAtEnd() ) >>>>>>>> >>> { >>>>>>>> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >>>>>>>> >>> >>>>>>>> >>> ... >>>>>>>> >>> >>>>>>>> >>> ++nIter; >>>>>>>> >>> ++outIter; >>>>>>>> >>> * ++maskIter;* >>>>>>>> >>> ... >>>>>>>> >>> >>>>>>>> >>> In the *FillHistogram *method: >>>>>>>> >>> { >>>>>>>> >>> >>>>>>>> >>> ... >>>>>>>> >>> >>>>>>>> >>> while( iter != m_CooccurenceOffsetVector.end() ) >>>>>>>> >>> { >>>>>>>> >>> >>>>>>>> >>> const PixelType p1 = niter.GetPixel(iter->first); >>>>>>>> >>> const PixelType p2 = niter.GetPixel(iter->second); >>>>>>>> >>> std::cout << "Before p3" << std::endl; >>>>>>>> >>> >>>>>>>> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); >>>>>>>> *std::cout >>>>>>>> >>> << "After p3: " << p3 << std::endl; >>>>>>>> >>> >>>>>>>> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >>>>>>>> >>> std::cout << "After p4: " << p4 << std::endl; >>>>>>>> >>> >>>>>>>> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= >>>>>>>> m_Max >>>>>>>> >>> *&& p3 == _insidePixelValue && p4 == >>>>>>>> _insidePixelValue* ) >>>>>>>> >>> // The point >>>>>>>> >>> { >>>>>>>> >>> >>>>>>>> >>> ... >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >>>>>>>> >>> >>>>>>>> >>> Thank you so much. >>>>>>>> >>> My kind regards. >>>>>>>> >>> /Paco >>>>>>>> >>> >>>>>>>> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca >>>>>>>> <[hidden email] >>>>>>>> >>> >: >>>>>>>> >>> >>>>>>>> >>>> Hello Bradley again. >>>>>>>> >>>> Sorry but I'd like to re-open this issue because I need your >>>>>>>> class but >>>>>>>> >>>> with some modification. >>>>>>>> >>>> I pass to tell you. >>>>>>>> >>>> >>>>>>>> >>>> As my tests with your external class were not good taking into >>>>>>>> account >>>>>>>> >>>> the performance, I wonder if you could create a variant of it, >>>>>>>> but in which >>>>>>>> >>>> I can set a mask image and your class just return the >>>>>>>> VectorImage with all >>>>>>>> >>>> the features for that region (the masked locations) as >>>>>>>> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >>>>>>>> >>>> I mean, to get the vector image with all the features but just >>>>>>>> >>>> calculate it for the regions belonging to the mask image. >>>>>>>> Positions not >>>>>>>> >>>> belonging to the mask region could have a pixel value of 0, >>>>>>>> for instance. >>>>>>>> >>>> >>>>>>>> >>>> I don?t know if it is very costly for you, but I would thank >>>>>>>> you so >>>>>>>> >>>> much. Otherwise, I could try it but I'd need your suggestions >>>>>>>> on how to do >>>>>>>> >>>> it. >>>>>>>> >>>> >>>>>>>> >>>> Thanks a lot. >>>>>>>> >>>> Best regards. >>>>>>>> >>>> >>>>>>>> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca >>>>>>>> <[hidden email] >>>>>>>> >>>> >: >>>>>>>> >>>> >>>>>>>> >>>>> Hello Bradley again, >>>>>>>> >>>>> I would like to ask you for a couple of favours. In the one >>>>>>>> hand, >>>>>>>> >>>>> could you please send me your 3D image so that I can test on >>>>>>>> it? And on the >>>>>>>> >>>>> other hand, could you test the example I have referenced in >>>>>>>> the previous >>>>>>>> >>>>> email with your image, not changing anything in the code, >>>>>>>> such as it is, >>>>>>>> >>>>> and tell me if the execution time is normal? >>>>>>>> >>>>> Thank you very much. >>>>>>>> >>>>> Regards, >>>>>>>> >>>>> /Francisco >>>>>>>> >>>>> >>>>>>>> >>>>> PS: All my application trace is printed via standard 'cout' >>>>>>>> command, >>>>>>>> >>>>> not due to a debugging compilation mode. >>>>>>>> >>>>> >>>>>>>> >>>>> >>>>>>>> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp >>>>>>>> <[hidden >>>>>>>> >>>>> email] >>>>>>> >> >>>>>>>> >>>>> escribi?: >>>>>>>> >>>>> >>>>>>>> >>>>>> Hello, >>>>>>>> >>>>>> >>>>>>>> >>>>>> Did you compile TextureFeatureImage in Release mode? >>>>>>>> >>>>>> >>>>>>>> >>>>>> 1) The filter does not scale well with a large radius. And >>>>>>>> given by >>>>>>>> >>>>>> your initial report of print a very large number of offset >>>>>>>> you, it sounds >>>>>>>> >>>>>> like you are using a large radius with many offsets. I >>>>>>>> created a >>>>>>>> >>>>>> 224x224x300 unsigned short image and ran with the default >>>>>>>> offset and a >>>>>>>> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this >>>>>>>> filter is was ~10x >>>>>>>> >>>>>> faster than this example... things change though... >>>>>>>> >>>>>> >>>>>>>> >>>>>> >>>>>>>> >>>>>> 2) I sounds like the boundaries/limits of the histogram may >>>>>>>> be >>>>>>>> >>>>>> clipping you values. I would inspect the co-occurance matrix. >>>>>>>> >>>>>> >>>>>>>> >>>>>> >>>>>>>> >>>>>> HTH, >>>>>>>> >>>>>> Brad >>>>>>>> >>>>>> >>>>>>>> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca >>>>>>>> <[hidden >>>>>>>> >>>>>> email] < >>>>>>>> http:///user/SendEmail.jtp?type=node&node=7588477&i=5>> >>>>>>>> >>>>>> wrote: >>>>>>>> >>>>>> >>>>>>>> >>>>>> I've tested with itkTextureFeatureImageFilter, with >>>>>>>> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>>>>>> >>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures >>>>>>>> example, >>>>>>>> >>>>>> for a 3D image and here are my comments: >>>>>>>> >>>>>> >>>>>>>> >>>>>> >>>>>>>> >>>>>> 1. I had to interrupt the test after several hours and it >>>>>>>> kept on >>>>>>>> >>>>>> calculating. And this is for only a 3D image (224x224x300). >>>>>>>> I need to >>>>>>>> >>>>>> process around 35 images. >>>>>>>> >>>>>> 2. The result (texture features: entropy, energy, >>>>>>>> correlation, LH, >>>>>>>> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, >>>>>>>> 7.83083e+247]. >>>>>>>> >>>>>> These values were not what I expected based on my experience >>>>>>>> on another >>>>>>>> >>>>>> application I developed, but in that case, I calculated the >>>>>>>> texture >>>>>>>> >>>>>> features for an image as a whole, not voxel by voxel. >>>>>>>> >>>>>> >>>>>>>> >>>>>> Regards. >>>>>>>> >>>>>> >>>>>>>> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >>>>>>>> >>>>>> >: >>>>>>>> >>>>>> >>>>>>>> >>>>>>> i yes i have tried radius = 3; >>>>>>>> >>>>>>> still no luck >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca >>>>>>>> [via ITK >>>>>>>> >>>>>>> Insight >>>>>>>> >>>>>>> Users] <[hidden email] >>>>>>>> >>>>>>> > >>>>>>>> wrote: >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> > Have you tried with a radius of 3 instead of 1? >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>>>>>> >>>>>>> > >: >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> >> hey Matt, >>>>>>>> >>>>>>> >> thanks for ur advice.. it did build successfully... but >>>>>>>> im not >>>>>>>> >>>>>>> able to run >>>>>>>> >>>>>>> >> the code for 2D png image... i tried to change the >>>>>>>> dimension to 2 >>>>>>>> >>>>>>> and >>>>>>>> >>>>>>> >> build >>>>>>>> >>>>>>> >> it which it did.. but when i run the code using the >>>>>>>> command >>>>>>>> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png >>>>>>>> putput.png >>>>>>>> >>>>>>> 1... i see >>>>>>>> >>>>>>> >> this output >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> offset: [-1, -1] [0, -1] >>>>>>>> >>>>>>> >> offset: [0, -1] [1, -1] >>>>>>>> >>>>>>> >> offset: [-1, 0] [0, 0] >>>>>>>> >>>>>>> >> offset: [0, 0] [1, 0] >>>>>>>> >>>>>>> >> offset: [-1, 1] [0, 1] >>>>>>>> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the >>>>>>>> program... if pls >>>>>>>> >>>>>>> tel me >>>>>>>> >>>>>>> >> how can i modify this code to work wid 2d image... >>>>>>>> forgive me if >>>>>>>> >>>>>>> my ques >>>>>>>> >>>>>>> >> are really silly im trying to learn something.. >>>>>>>> >>>>>>> >> regards >>>>>>>> >>>>>>> >> Vis >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via >>>>>>>> ITK >>>>>>>> >>>>>>> Insight Users] >>>>>>>> >>>>>>> >> < >>>>>>>> >>>>>>> >> [hidden email] < >>>>>>>> >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>>>>>>> >>>>>>> >> wrote: >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> > Hi, >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > The function: >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char >>>>>>>> *argv[]) >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > must be renamed to >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > main(int argc, char* argv[]) >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > HTH, >>>>>>>> >>>>>>> >> > Matt >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>>>>>> >>>>>>> >> > > >>>>>>>> wrote: >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > > hi all, >>>>>>>> >>>>>>> >> > > im trying to build the >>>>>>>> itkTextureFeatureImageFilterTest.cxx >>>>>>>> >>>>>>> code but >>>>>>>> >>>>>>> >> im >>>>>>>> >>>>>>> >> > not >>>>>>>> >>>>>>> >> > > able to it is showing the following error >>>>>>>> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>>>>>> >>>>>>> Configuration: >>>>>>>> >>>>>>> >> Debug >>>>>>>> >>>>>>> >> > x64 >>>>>>>> >>>>>>> >> > > ------ >>>>>>>> >>>>>>> >> > > 1> Checking Build System >>>>>>>> >>>>>>> >> > > 1> CMake does not need to re-run because >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>>>>>> >>>>>>> >> > is >>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>> >>>>>>> >> > > 2>------ Rebuild All started: Project: >>>>>>>> >>>>>>> >> itkTextureFeatureImageFilterTest, >>>>>>>> >>>>>>> >> > > Configuration: Debug x64 ------ >>>>>>>> >>>>>>> >> > > 2> Building Custom Rule >>>>>>>> >>>>>>> >> > > >>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>>> >>>>>>> >> > > 2> CMake does not need to re-run because >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>>> >>>>>>> >> > is >>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>>>>>> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>>>>>> >>>>>>> 'std::_Copy_impl': >>>>>>>> >>>>>>> >> > Function >>>>>>>> >>>>>>> >> > > call with parameters that may be unsafe - this call >>>>>>>> relies on >>>>>>>> >>>>>>> the >>>>>>>> >>>>>>> >> caller >>>>>>>> >>>>>>> >> > to >>>>>>>> >>>>>>> >> > > check that the passed values are correct. To disable >>>>>>>> this >>>>>>>> >>>>>>> warning, use >>>>>>>> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how >>>>>>>> to use >>>>>>>> >>>>>>> Visual C++ >>>>>>>> >>>>>>> >> > > 'Checked Iterators' >>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>>>> Studio >>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>> >>>>>>> >> > > 2> >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>>>>>> >>>>>>> >> > see >>>>>>>> >>>>>>> >> > > reference to function template instantiation '_OutIt >>>>>>>> >>>>>>> std::copy>>>>>>> >>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' >>>>>>>> being >>>>>>>> >>>>>>> compiled >>>>>>>> >>>>>>> >> > > 2> with >>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>> >>>>>>> >> > > 2> _OutIt=unsigned char *, >>>>>>>> >>>>>>> >> > > 2> _InIt=const unsigned char * >>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>> >>>>>>> >> > > 2> >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>>>>>> >>>>>>> >> > > while compiling class template member function 'void >>>>>>>> >>>>>>> >> > > >>>>>>>> itk::ImageFileReader::GenerateData(void)' >>>>>>>> >>>>>>> >> > > 2> with >>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>> >>>>>>> >> > > 2> >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > > : see reference to class template instantiation >>>>>>>> >>>>>>> >> > > 'itk::ImageFileReader' being compiled >>>>>>>> >>>>>>> >> > > 2> with >>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>>>> Studio >>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>>>> Studio >>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>>>> Studio >>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>> >>>>>>> >> > > 2> Creating library >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > > and object >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved >>>>>>>> >>>>>>> external symbol >>>>>>>> >>>>>>> >> > main >>>>>>>> >>>>>>> >> > > referenced in function __tmainCRTStartup >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>>>>>> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>>>>>> >>>>>>> Configuration: Debug >>>>>>>> >>>>>>> >> > x64 >>>>>>>> >>>>>>> >> > > ------ >>>>>>>> >>>>>>> >> > > 3> Building Custom Rule >>>>>>>> >>>>>>> >> > > >>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>>> >>>>>>> >> > > 3> CMake does not need to re-run because >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>>> >>>>>>> >> > is >>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 >>>>>>>> skipped >>>>>>>> >>>>>>> ========== >>>>>>>> >>>>>>> >> > > im using the follwing CMakeList.txt >>>>>>>> >>>>>>> >> > > # This is the root ITK CMakeLists file. >>>>>>>> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>>>>>> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >>>>>>>> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>>>>>> >>>>>>> >> > > endif() >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > # This project is designed to be built outside the >>>>>>>> Insight >>>>>>>> >>>>>>> source >>>>>>>> >>>>>>> >> tree. >>>>>>>> >>>>>>> >> > > project(HelloWorld) >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > # Find ITK. >>>>>>>> >>>>>>> >> > > find_package(ITK REQUIRED) >>>>>>>> >>>>>>> >> > > include(${ITK_USE_FILE}) >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>>>>>> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > >>>>>>>> target_link_libraries(itkTextureFeatureImageFilterTest >>>>>>>> >>>>>>> >> ${ITK_LIBRARIES}) >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > please tel me wat the error is?? >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > -- >>>>>>>> >>>>>>> >> > > View this message in context: >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>>>>>> >>>>>>> >> > > Sent from the ITK Insight Users mailing list archive >>>>>>>> at >>>>>>>> >>>>>>> Nabble.com . >>>>>>>> >>>>>>> >> > > _____________________________________ >>>>>>>> >>>>>>> >> > > Powered by www.kitware.com >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > Visit other Kitware open-source projects at >>>>>>>> >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > Kitware offers ITK Training Courses, for more >>>>>>>> information >>>>>>>> >>>>>>> visit: >>>>>>>> >>>>>>> >> > > http://www.kitware.com/products/protraining.php >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > Please keep messages on-topic and check the ITK FAQ >>>>>>>> at: >>>>>>>> >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >>>>>>> >> > > >>>>>>>> >>>>>>> >> > > Follow this link to subscribe/unsubscribe: >>>>>>>> >>>>>>> >> > > >>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >>>>>>> >> > _____________________________________ >>>>>>>> >>>>>>> >> > Powered by www.kitware.com >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > Visit other Kitware open-source projects at >>>>>>>> >>>>>>> >> > http://www.kitware.com/opensource/opensource.html >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > Kitware offers ITK Training Courses, for more >>>>>>>> information visit: >>>>>>>> >>>>>>> >> > http://www.kitware.com/products/protraining.php >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> >>>>>>> >> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > Follow this link to subscribe/unsubscribe: >>>>>>>> >>>>>>> >> > >>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > ------------------------------ >>>>>>>> >>>>>>> >> > If you reply to this email, your message will be added >>>>>>>> to the >>>>>>>> >>>>>>> discussion >>>>>>>> >>>>>>> >> > below: >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587952.html >>>>>>>> >>>>>>> >> > To unsubscribe from [ITK-users] Texture pixel by >>>>>>>> pixel, click >>>>>>>> >>>>>>> here >>>>>>>> >>>>>>> >> > < > . >>>>>>>> >>>>>>> >> > NAML >>>>>>>> >>>>>>> >> > < >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> > >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> -- >>>>>>>> >>>>>>> >> View this message in context: >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587960.html >>>>>>>> >>>>>>> >> Sent from the ITK Insight Users mailing list archive at >>>>>>>> >>>>>>> Nabble.com . >>>>>>>> >>>>>>> >> _____________________________________ >>>>>>>> >>>>>>> >> Powered by www.kitware.com >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> Visit other Kitware open-source projects at >>>>>>>> >>>>>>> >> http://www.kitware.com/opensource/opensource.html >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> Kitware offers ITK Training Courses, for more >>>>>>>> information visit: >>>>>>>> >>>>>>> >> http://www.kitware.com/products/protraining.php >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> >>>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> >> Follow this link to subscribe/unsubscribe: >>>>>>>> >>>>>>> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >>>>>>> >> >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > _____________________________________ >>>>>>>> >>>>>>> > Powered by www.kitware.com >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > Visit other Kitware open-source projects at >>>>>>>> >>>>>>> > http://www.kitware.com/opensource/opensource.html >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > Kitware offers ITK Training Courses, for more information >>>>>>>> visit: >>>>>>>> >>>>>>> > http://www.kitware.com/products/protraining.php >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> >>>>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > Follow this link to subscribe/unsubscribe: >>>>>>>> >>>>>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > ------------------------------ >>>>>>>> >>>>>>> > If you reply to this email, your message will be added to >>>>>>>> the >>>>>>>> >>>>>>> discussion >>>>>>>> >>>>>>> > below: >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587961.html >>>>>>>> >>>>>>> > To unsubscribe from [ITK-users] Texture pixel by pixel, >>>>>>>> click here >>>>>>>> >>>>>>> > < > . >>>>>>>> >>>>>>> > NAML >>>>>>>> >>>>>>> > < >>>>>>>> >>>>>>> >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> > >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> -- >>>>>>>> >>>>>>> View this message in context: >>>>>>>> >>>>>>> >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587963.html >>>>>>>> >>>>>>> Sent from the ITK Insight Users mailing list archive at >>>>>>>> Nabble.com . >>>>>>>> >>>>>>> _____________________________________ >>>>>>>> >>>>>>> Powered by www.kitware.com >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> Visit other Kitware open-source projects at >>>>>>>> >>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> Kitware offers ITK Training Courses, for more information >>>>>>>> visit: >>>>>>>> >>>>>>> http://www.kitware.com/products/protraining.php >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> >>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >>>>>>> >>>>>>>> >>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>> >>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >>>>>>> >>>>>>>> >>>>>> >>>>>>>> >>>>>> _____________________________________ >>>>>>>> >>>>>> Powered by www.kitware.com >>>>>>>> >>>>>> >>>>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>>>> >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>> >>>>>> >>>>>>>> >>>>>> Kitware offers ITK Training Courses, for more information >>>>>>>> visit: >>>>>>>> >>>>>> http://www.kitware.com/products/protraining.php >>>>>>>> >>>>>> >>>>>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >>>>>> >>>>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>> >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >>>>>> >>>>>>>> >>>>>> >>>>>>>> >>>>>> >>>>>>>> >>>> >>>>>>>> >>> >>>>>>>> >> >>>>>>>> >> _____________________________________ >>>>>>>> >> Powered by www.kitware.com >>>>>>>> >> >>>>>>>> >> Visit other Kitware open-source projects at >>>>>>>> >> http://www.kitware.com/opensource/opensource.html >>>>>>>> >> >>>>>>>> >> Kitware offers ITK Training Courses, for more information visit: >>>>>>>> >> http://www.kitware.com/products/protraining.php >>>>>>>> >> >>>>>>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >> >>>>>>>> >> Follow this link to subscribe/unsubscribe: >>>>>>>> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >> >>>>>>>> >> >>>>>>>> > >>>>>>>> > _____________________________________ >>>>>>>> > Powered by www.kitware.com >>>>>>>> > >>>>>>>> > Visit other Kitware open-source projects at >>>>>>>> > http://www.kitware.com/opensource/opensource.html >>>>>>>> > >>>>>>>> > Kitware offers ITK Training Courses, for more information visit: >>>>>>>> > http://www.kitware.com/products/protraining.php >>>>>>>> > >>>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> > >>>>>>>> > Follow this link to subscribe/unsubscribe: >>>>>>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> > >>>>>>>> > >>>>>>>> > ------------------------------ >>>>>>>> > If you reply to this email, your message will be added to the >>>>>>>> discussion >>>>>>>> > below: >>>>>>>> > >>>>>>>> > >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588477.html >>>>>>>> > To start a new topic under ITK Insight Users, email >>>>>>>> > [hidden email] >>>>>>>> >>>>>>>> > To unsubscribe from ITK Insight Users, click here >>>>>>>> > < > . >>>>>>>> > NAML >>>>>>>> > < >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>>>> > >>>>>>>> > >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> View this message in context: >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588483.html >>>>>>>> Sent from the ITK Insight Users mailing list archive at Nabble.com >>>>>>>> . >>>>>>>> _____________________________________ >>>>>>>> Powered by www.kitware.com >>>>>>>> >>>>>>>> Visit other Kitware open-source projects at >>>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>> >>>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>>> http://www.kitware.com/products/protraining.php >>>>>>>> >>>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >>>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >>>>>>> >>>>>>> >>>>>>> _____________________________________ >>>>>>> Powered by www.kitware.com >>>>>>> >>>>>>> Visit other Kitware open-source projects at >>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>> >>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>> http://www.kitware.com/products/protraining.php >>>>>>> >>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>> >>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>> >>>>>>> >>>>>>> ------------------------------ >>>>>>> If you reply to this email, your message will be added to the >>>>>>> discussion below: >>>>>>> >>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588490.html >>>>>>> To start a new topic under ITK Insight Users, email [hidden email] >>>>>>> >>>>>>> To unsubscribe from ITK Insight Users, click here. >>>>>>> NAML >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> _____________________________________ >>>>>> Powered by www.kitware.com >>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>> http://www.kitware.com/products/protraining.php >>>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >>>>>> >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> 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http://public.kitware.com/mailman/listinfo/insight-users >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588513.html > To start a new topic under ITK Insight Users, email > ml-node+s2283740n2283740h75 at n2.nabble.com > To unsubscribe from ITK Insight Users, click here > > . > NAML > > -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588515.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Thu Feb 18 13:00:13 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 18 Feb 2016 13:00:13 -0500 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <3F877AC4-BCD1-43FF-B8B3-7B30F9B6D30B@mail.nih.gov> Message-ID: /bigobj is an option for msvc, not mingw. But that is a different problem from crashing code. If you start a new thread, somebody with MinGW experience might help you. On Thu, Feb 18, 2016 at 12:30 PM, Francisco Lopez de la Franca < franciscolopezdelafranca at gmail.com> wrote: > Yes. I use mingw (x86_64-w64-mingw32-g++.exe) and I set in CMAKE GUI the > entry CMAKE_CXX_FLAGS to -bigobj and the result is "unrecognized option". > > > 2016-02-18 15:25 GMT+01:00 dzenanz [via ITK Insight Users] < > ml-node+s2283740n7588513h38 at n2.nabble.com>: > >> Have you tried /bigobj >> ? >> Are you using MinGW? Visual Studio is now free >> . >> >> HTH >> >> On Thu, Feb 18, 2016 at 6:37 AM, Francisco Lopez de la Franca <[hidden >> email] > wrote: >> >>> Hi again, >>> I've got ITK version 4.5.1 (a little bit old, I know), and after making >>> the changes suggested by Dzenanz and recompiling ITK, the problem >>> continues, that is, my code crashes at the same point. >>> >>> Then, I've downloaded the latest stable ITK version, ITK 4.9.0 and >>> compiled from scratch and I get the following error: >>> >>> [ 98%] Building CXX object >>> Modules/IO/TransformBase/src/CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.obj >>> C:/MINGW/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: >>> CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: too many >>> sections (33106) >>> C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Assembler messages: >>> C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Fatal error: can't write >>> CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: File too >>> big >>> >>> After doing some "googling" and follow some of the instructions referred >>> on the web, I've been unable to solve this. >>> Has anyone met this problem and solved it? >>> Thanks. >>> KR. >>> /Francisco >>> >>> 2016-02-16 22:13 GMT+01:00 Bradley Lowekamp [via ITK Insight Users] <[hidden >>> email] >: >>> >>>> Hello, >>>> >>>> Please take a look at these changes: >>>> >>>> https://github.com/blowekamp/itkTextureAnalysis/commit/9654d74ea1d09f0677f1d1b93242cc94340591bf >>>> >>>> Brad >>>> >>>> On Feb 16, 2016, at 10:35 AM, D?enan Zuki? <[hidden email] >>>> > wrote: >>>> >>>> I have set up a project using one of the tests from Brad's repository >>>> (attached), and it works in debug mode both with his original code and with >>>> your modified class, and crashes in release mode both with his original >>>> code and with your modified class. I will now compile ITK in RelWithDebInfo >>>> in an attempt to figure out where is the crash occurring. >>>> >>>> Regards, >>>> D?enan >>>> >>>> On Tue, Feb 16, 2016 at 1:52 AM, Francisco Lopez de la Franca <[hidden >>>> email] > wrote: >>>> >>>>> Excuse me Dzenanz, but that's not completely true, because I've tested >>>>> Brad's class and it works right. >>>>> The problem seems to be that when you add a new neighbor iterator to >>>>> include just the mask points in the "histogram" then it is when the >>>>> application crashes, and I donot understand why. >>>>> If you just comment the 'maskIter' references you'll see that the >>>>> application works. >>>>> I've created a single threaded class based on the Brad's code and it >>>>> works but it is twice slower, that is why I'm interesting on Brad's class >>>>> (multi-threaded) to make it work. >>>>> >>>>> >>>>> 2016-02-15 17:15 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>>> email] >: >>>>> >>>>>> Hi Francisco, >>>>>> >>>>>> both your code and Brad's code run in debug mode (I did not wait for >>>>>> the end), and both crash in release mode immediately on startup. Here is a >>>>>> sample output: >>>>>> >>>>>> Progress input: 0000000002868970 >>>>>> input: 0000000002868970 >>>>>> _maskImage: 0000000002868970 >>>>>> _maskImage: 0000000002868970 >>>>>> input: 0000000002868970 >>>>>> _maskImage: 0000000002868970 >>>>>> iter.first: iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>> [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>> niter index: [5, 5, 210] >>>>>> niter index: [5, 5, 140] >>>>>> maskIter index: [5, 5, 140] >>>>>> maskIter index: [5, 5, 210] >>>>>> Before p3 >>>>>> input: 0000000002868970 >>>>>> _maskImage: 0000000002868970 >>>>>> After p3: | 0niter index: [5, 5, 70] >>>>>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>> niter index: [5, 5, 5] >>>>>> ? >>>>>> maskIter index: [5, 5, 70] >>>>>> After p4: ? >>>>>> Before p3 >>>>>> Before p3 >>>>>> After p3: ?iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>>> niter index: [5, 5, 140] >>>>>> maskIter index: [5, 5, 140] >>>>>> maskIter index: [5, 5, 5] >>>>>> Before p3 >>>>>> After p3: ? >>>>>> After p3: ? >>>>>> After p4: ? >>>>>> After p4: ? >>>>>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>>> niter index: [5, 5, 5] >>>>>> maskIter index: [5, 5, 5] >>>>>> >>>>>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>>> Before p3 >>>>>> Before p3 >>>>>> After p4: ? >>>>>> After p3: ? >>>>>> After p4: ? >>>>>> >>>>>> Regards, >>>>>> D?enan >>>>>> >>>>>> On Mon, Feb 15, 2016 at 1:36 AM, Francisco Lopez de la Franca <[hidden >>>>>> email] > wrote: >>>>>> >>>>>>> Hi, >>>>>>> Here they are. >>>>>>> KR. >>>>>>> >>>>>>> 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>>>>> email] >: >>>>>>> >>>>>>>> Hi Francisco, >>>>>>>> >>>>>>>> do you mind attaching the modified files or pointing to your fork >>>>>>>> of it on GitHub? >>>>>>>> >>>>>>>> Regards >>>>>>>> >>>>>>>> On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden >>>>>>>> email] > >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi Dzenan, >>>>>>>>> The original class is here: >>>>>>>>> >>>>>>>>> >>>>>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >>>>>>>>> >>>>>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >>>>>>>>> >>>>>>>>> I've just added setInput and setMaskImage methods and modify some >>>>>>>>> lines in >>>>>>>>> the original class as I indicated in the yesterday mail within >>>>>>>>> this thread. >>>>>>>>> I'm running it on Windows, and there is no error at all, just a >>>>>>>>> crash. I >>>>>>>>> may have to include exceptions management. >>>>>>>>> The crash occurs just when calling p3 = >>>>>>>>> maskIter.GetPixel(iter->first) >>>>>>>>> >>>>>>>>> If you know why it could be or if you need more clarification, >>>>>>>>> please let >>>>>>>>> me know. >>>>>>>>> Many thanks >>>>>>>>> >>>>>>>>> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >>>>>>>>> [hidden email] >>>>>>>>> >: >>>>>>>>> >>>>>>>>> > Hi Francisco, >>>>>>>>> > >>>>>>>>> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the >>>>>>>>> error message >>>>>>>>> > that goes along with the crash? In which file and line does it >>>>>>>>> crash? >>>>>>>>> > >>>>>>>>> > Regards >>>>>>>>> > >>>>>>>>> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca >>>>>>>>> <[hidden >>>>>>>>> > email] > >>>>>>>>> wrote: >>>>>>>>> > >>>>>>>>> >> Hi, >>>>>>>>> >> Please, someone that could help me. I'm working in a >>>>>>>>> pre-doctorate >>>>>>>>> >> project and I need this class to work. >>>>>>>>> >> I've read the chapter 13 in the ITK Software Guide on how to >>>>>>>>> write a >>>>>>>>> >> filter and now I see the fact of the threads due to inheritance >>>>>>>>> of >>>>>>>>> >> ImageToImageFilter. >>>>>>>>> >> But, I keep on without understanding why the code crashes just >>>>>>>>> when >>>>>>>>> >> calling >>>>>>>>> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >>>>>>>>> >> It is just a call to read data, not to write. >>>>>>>>> >> >>>>>>>>> >> I guess somebody that had worked with creation of filters might >>>>>>>>> see >>>>>>>>> >> "easily" the problem, but not me. >>>>>>>>> >> >>>>>>>>> >> So, again, please, I need someone to help me with this because >>>>>>>>> I'm stuck >>>>>>>>> >> on this point. >>>>>>>>> >> >>>>>>>>> >> Thank you very much. >>>>>>>>> >> KR. >>>>>>>>> >> /Francisco >>>>>>>>> >> >>>>>>>>> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca >>>>>>>>> <[hidden email] >>>>>>>>> >> >: >>>>>>>>> >> >>>>>>>>> >>> Hi Bradley again. >>>>>>>>> >>> I'm modifying your class in order to be able to set a mask >>>>>>>>> image (a >>>>>>>>> >>> binary image) to be used as a limit in the histogram >>>>>>>>> calculations, I mean, >>>>>>>>> >>> I set an input, a mask and the class should take into account >>>>>>>>> to calculate >>>>>>>>> >>> the histograms only the voxels that belong to the input and to >>>>>>>>> the mask >>>>>>>>> >>> image and having the value 1 in the mask image. >>>>>>>>> >>> The changes seem to be easy but I don?t know why my tests are >>>>>>>>> not >>>>>>>>> >>> working. It seems that 2 threads are working at the same time >>>>>>>>> and when I >>>>>>>>> >>> added my mask iterator, the code crashes. >>>>>>>>> >>> >>>>>>>>> >>> *** Consider that the input and mask images are the same >>>>>>>>> origin, spacing >>>>>>>>> >>> and size. >>>>>>>>> >>> >>>>>>>>> >>> I attach the main changes I've done, and I would thank you a >>>>>>>>> lot if you >>>>>>>>> >>> don't mind having a look and help me to find what I'm doing >>>>>>>>> wrong: >>>>>>>>> >>> >>>>>>>>> >>> template< class TImageType, class TOutputImage > >>>>>>>>> >>> void >>>>>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>>>>> >::*SetInput*(InputImageType >>>>>>>>> >>> *image) >>>>>>>>> >>> { >>>>>>>>> >>> // Process object is not const-correct so the const_cast is >>>>>>>>> required >>>>>>>>> >>> here >>>>>>>>> >>> this->ProcessObject::SetNthInput( 0, >>>>>>>>> >>> const_cast< InputImageType >>>>>>>>> * >( >>>>>>>>> >>> image ) ); >>>>>>>>> >>> } >>>>>>>>> >>> >>>>>>>>> >>> template< class TImageType, class TOutputImage > >>>>>>>>> >>> void >>>>>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>>>>> >::*SetMaskImage*(InputImageType >>>>>>>>> >>> *image) >>>>>>>>> >>> { >>>>>>>>> >>> // Process object is not const-correct so the const_cast is >>>>>>>>> required >>>>>>>>> >>> here >>>>>>>>> >>> this->ProcessObject::SetNthInput( 1, const_cast< >>>>>>>>> InputImageType * >( >>>>>>>>> >>> image ) ); >>>>>>>>> >>> >>>>>>>>> >>> _maskImage = image; // _maskImage is a private member >>>>>>>>> >>> } >>>>>>>>> >>> >>>>>>>>> >>> In the *ThreadedGenerateData*(const RegionType& >>>>>>>>> outputRegionForThread, >>>>>>>>> >>> ThreadIdType threadId ) method: >>>>>>>>> >>> { >>>>>>>>> >>> >>>>>>>>> >>> ... >>>>>>>>> >>> >>>>>>>>> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >>>>>>>>> >>> { >>>>>>>>> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >>>>>>>>> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, >>>>>>>>> *fit);* >>>>>>>>> >>> OutputIterator outIter(output, *fit); >>>>>>>>> >>> >>>>>>>>> >>> OutputPixelType out; >>>>>>>>> >>> NumericTraits::SetLength( out, >>>>>>>>> >>> this->GetNumberOfOutputComponents() ); >>>>>>>>> >>> >>>>>>>>> >>> while( !nIter.IsAtEnd() ) >>>>>>>>> >>> { >>>>>>>>> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >>>>>>>>> >>> >>>>>>>>> >>> ... >>>>>>>>> >>> >>>>>>>>> >>> ++nIter; >>>>>>>>> >>> ++outIter; >>>>>>>>> >>> * ++maskIter;* >>>>>>>>> >>> ... >>>>>>>>> >>> >>>>>>>>> >>> In the *FillHistogram *method: >>>>>>>>> >>> { >>>>>>>>> >>> >>>>>>>>> >>> ... >>>>>>>>> >>> >>>>>>>>> >>> while( iter != m_CooccurenceOffsetVector.end() ) >>>>>>>>> >>> { >>>>>>>>> >>> >>>>>>>>> >>> const PixelType p1 = niter.GetPixel(iter->first); >>>>>>>>> >>> const PixelType p2 = niter.GetPixel(iter->second); >>>>>>>>> >>> std::cout << "Before p3" << std::endl; >>>>>>>>> >>> >>>>>>>>> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); >>>>>>>>> *std::cout >>>>>>>>> >>> << "After p3: " << p3 << std::endl; >>>>>>>>> >>> >>>>>>>>> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >>>>>>>>> >>> std::cout << "After p4: " << p4 << std::endl; >>>>>>>>> >>> >>>>>>>>> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= >>>>>>>>> m_Max >>>>>>>>> >>> *&& p3 == _insidePixelValue && p4 == >>>>>>>>> _insidePixelValue* ) >>>>>>>>> >>> // The point >>>>>>>>> >>> { >>>>>>>>> >>> >>>>>>>>> >>> ... >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >>>>>>>>> >>> >>>>>>>>> >>> Thank you so much. >>>>>>>>> >>> My kind regards. >>>>>>>>> >>> /Paco >>>>>>>>> >>> >>>>>>>>> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca >>>>>>>>> <[hidden email] >>>>>>>>> >>> >: >>>>>>>>> >>> >>>>>>>>> >>>> Hello Bradley again. >>>>>>>>> >>>> Sorry but I'd like to re-open this issue because I need your >>>>>>>>> class but >>>>>>>>> >>>> with some modification. >>>>>>>>> >>>> I pass to tell you. >>>>>>>>> >>>> >>>>>>>>> >>>> As my tests with your external class were not good taking >>>>>>>>> into account >>>>>>>>> >>>> the performance, I wonder if you could create a variant of >>>>>>>>> it, but in which >>>>>>>>> >>>> I can set a mask image and your class just return the >>>>>>>>> VectorImage with all >>>>>>>>> >>>> the features for that region (the masked locations) as >>>>>>>>> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >>>>>>>>> >>>> I mean, to get the vector image with all the features but just >>>>>>>>> >>>> calculate it for the regions belonging to the mask image. >>>>>>>>> Positions not >>>>>>>>> >>>> belonging to the mask region could have a pixel value of 0, >>>>>>>>> for instance. >>>>>>>>> >>>> >>>>>>>>> >>>> I don?t know if it is very costly for you, but I would thank >>>>>>>>> you so >>>>>>>>> >>>> much. Otherwise, I could try it but I'd need your suggestions >>>>>>>>> on how to do >>>>>>>>> >>>> it. >>>>>>>>> >>>> >>>>>>>>> >>>> Thanks a lot. >>>>>>>>> >>>> Best regards. >>>>>>>>> >>>> >>>>>>>>> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca >>>>>>>>> <[hidden email] >>>>>>>>> >>>> >: >>>>>>>>> >>>> >>>>>>>>> >>>>> Hello Bradley again, >>>>>>>>> >>>>> I would like to ask you for a couple of favours. In the one >>>>>>>>> hand, >>>>>>>>> >>>>> could you please send me your 3D image so that I can test on >>>>>>>>> it? And on the >>>>>>>>> >>>>> other hand, could you test the example I have referenced in >>>>>>>>> the previous >>>>>>>>> >>>>> email with your image, not changing anything in the code, >>>>>>>>> such as it is, >>>>>>>>> >>>>> and tell me if the execution time is normal? >>>>>>>>> >>>>> Thank you very much. >>>>>>>>> >>>>> Regards, >>>>>>>>> >>>>> /Francisco >>>>>>>>> >>>>> >>>>>>>>> >>>>> PS: All my application trace is printed via standard 'cout' >>>>>>>>> command, >>>>>>>>> >>>>> not due to a debugging compilation mode. >>>>>>>>> >>>>> >>>>>>>>> >>>>> >>>>>>>>> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp >>>>>>>>> <[hidden >>>>>>>>> >>>>> email] < >>>>>>>>> http:///user/SendEmail.jtp?type=node&node=7588477&i=4>> >>>>>>>>> >>>>> escribi?: >>>>>>>>> >>>>> >>>>>>>>> >>>>>> Hello, >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Did you compile TextureFeatureImage in Release mode? >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> 1) The filter does not scale well with a large radius. And >>>>>>>>> given by >>>>>>>>> >>>>>> your initial report of print a very large number of offset >>>>>>>>> you, it sounds >>>>>>>>> >>>>>> like you are using a large radius with many offsets. I >>>>>>>>> created a >>>>>>>>> >>>>>> 224x224x300 unsigned short image and ran with the default >>>>>>>>> offset and a >>>>>>>>> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this >>>>>>>>> filter is was ~10x >>>>>>>>> >>>>>> faster than this example... things change though... >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> 2) I sounds like the boundaries/limits of the histogram may >>>>>>>>> be >>>>>>>>> >>>>>> clipping you values. I would inspect the co-occurance >>>>>>>>> matrix. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> HTH, >>>>>>>>> >>>>>> Brad >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca >>>>>>>>> <[hidden >>>>>>>>> >>>>>> email] < >>>>>>>>> http:///user/SendEmail.jtp?type=node&node=7588477&i=5>> >>>>>>>>> >>>>>> wrote: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> I've tested with itkTextureFeatureImageFilter, with >>>>>>>>> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>>>>>>> >>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures >>>>>>>>> example, >>>>>>>>> >>>>>> for a 3D image and here are my comments: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> 1. I had to interrupt the test after several hours and it >>>>>>>>> kept on >>>>>>>>> >>>>>> calculating. And this is for only a 3D image (224x224x300). >>>>>>>>> I need to >>>>>>>>> >>>>>> process around 35 images. >>>>>>>>> >>>>>> 2. The result (texture features: entropy, energy, >>>>>>>>> correlation, LH, >>>>>>>>> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, >>>>>>>>> 7.83083e+247]. >>>>>>>>> >>>>>> These values were not what I expected based on my >>>>>>>>> experience on another >>>>>>>>> >>>>>> application I developed, but in that case, I calculated the >>>>>>>>> texture >>>>>>>>> >>>>>> features for an image as a whole, not voxel by voxel. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Regards. >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >>>>>>>>> >>>>>> >: >>>>>>>>> >>>>>> >>>>>>>>> >>>>>>> i yes i have tried radius = 3; >>>>>>>>> >>>>>>> still no luck >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca >>>>>>>>> [via ITK >>>>>>>>> >>>>>>> Insight >>>>>>>>> >>>>>>> Users] <[hidden email] >>>>>>>>> >>>>>>> > >>>>>>>>> wrote: >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> > Have you tried with a radius of 3 instead of 1? >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>>>>>>> >>>>>>> > >>>>>>>> >>: >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> >> hey Matt, >>>>>>>>> >>>>>>> >> thanks for ur advice.. it did build successfully... but >>>>>>>>> im not >>>>>>>>> >>>>>>> able to run >>>>>>>>> >>>>>>> >> the code for 2D png image... i tried to change the >>>>>>>>> dimension to 2 >>>>>>>>> >>>>>>> and >>>>>>>>> >>>>>>> >> build >>>>>>>>> >>>>>>> >> it which it did.. but when i run the code using the >>>>>>>>> command >>>>>>>>> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png >>>>>>>>> putput.png >>>>>>>>> >>>>>>> 1... i see >>>>>>>>> >>>>>>> >> this output >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> offset: [-1, -1] [0, -1] >>>>>>>>> >>>>>>> >> offset: [0, -1] [1, -1] >>>>>>>>> >>>>>>> >> offset: [-1, 0] [0, 0] >>>>>>>>> >>>>>>> >> offset: [0, 0] [1, 0] >>>>>>>>> >>>>>>> >> offset: [-1, 1] [0, 1] >>>>>>>>> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the >>>>>>>>> program... if pls >>>>>>>>> >>>>>>> tel me >>>>>>>>> >>>>>>> >> how can i modify this code to work wid 2d image... >>>>>>>>> forgive me if >>>>>>>>> >>>>>>> my ques >>>>>>>>> >>>>>>> >> are really silly im trying to learn something.. >>>>>>>>> >>>>>>> >> regards >>>>>>>>> >>>>>>> >> Vis >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via >>>>>>>>> ITK >>>>>>>>> >>>>>>> Insight Users] >>>>>>>>> >>>>>>> >> < >>>>>>>>> >>>>>>> >> [hidden email] < >>>>>>>>> >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>>>>>>>> >>>>>>> >> wrote: >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> > Hi, >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > The function: >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char >>>>>>>>> *argv[]) >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > must be renamed to >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > main(int argc, char* argv[]) >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > HTH, >>>>>>>>> >>>>>>> >> > Matt >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>>>>>>> >>>>>>> >> > < >>>>>>>>> http:///user/SendEmail.jtp?type=node&node=7587952&i=0>> wrote: >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > > hi all, >>>>>>>>> >>>>>>> >> > > im trying to build the >>>>>>>>> itkTextureFeatureImageFilterTest.cxx >>>>>>>>> >>>>>>> code but >>>>>>>>> >>>>>>> >> im >>>>>>>>> >>>>>>> >> > not >>>>>>>>> >>>>>>> >> > > able to it is showing the following error >>>>>>>>> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>>>>>>> >>>>>>> Configuration: >>>>>>>>> >>>>>>> >> Debug >>>>>>>>> >>>>>>> >> > x64 >>>>>>>>> >>>>>>> >> > > ------ >>>>>>>>> >>>>>>> >> > > 1> Checking Build System >>>>>>>>> >>>>>>> >> > > 1> CMake does not need to re-run because >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>>>>>>> >>>>>>> >> > is >>>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>>> >>>>>>> >> > > 2>------ Rebuild All started: Project: >>>>>>>>> >>>>>>> >> itkTextureFeatureImageFilterTest, >>>>>>>>> >>>>>>> >> > > Configuration: Debug x64 ------ >>>>>>>>> >>>>>>> >> > > 2> Building Custom Rule >>>>>>>>> >>>>>>> >> > > >>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>>>> >>>>>>> >> > > 2> CMake does not need to re-run because >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >>>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>>>> >>>>>>> >> > is >>>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>>> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>>>>>>> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>>>>>>> >>>>>>> 'std::_Copy_impl': >>>>>>>>> >>>>>>> >> > Function >>>>>>>>> >>>>>>> >> > > call with parameters that may be unsafe - this call >>>>>>>>> relies on >>>>>>>>> >>>>>>> the >>>>>>>>> >>>>>>> >> caller >>>>>>>>> >>>>>>> >> > to >>>>>>>>> >>>>>>> >> > > check that the passed values are correct. To >>>>>>>>> disable this >>>>>>>>> >>>>>>> warning, use >>>>>>>>> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how >>>>>>>>> to use >>>>>>>>> >>>>>>> Visual C++ >>>>>>>>> >>>>>>> >> > > 'Checked Iterators' >>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>>>>> Studio >>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>> >>>>>>> >> > > 2> >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >>>>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>>>>>>> >>>>>>> >> > see >>>>>>>>> >>>>>>> >> > > reference to function template instantiation '_OutIt >>>>>>>>> >>>>>>> std::copy>>>>>>>> >>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' >>>>>>>>> being >>>>>>>>> >>>>>>> compiled >>>>>>>>> >>>>>>> >> > > 2> with >>>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>>> >>>>>>> >> > > 2> _OutIt=unsigned char *, >>>>>>>>> >>>>>>> >> > > 2> _InIt=const unsigned char * >>>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>>> >>>>>>> >> > > 2> >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >>>>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>>>>>>> >>>>>>> >> > > while compiling class template member function 'void >>>>>>>>> >>>>>>> >> > > >>>>>>>>> itk::ImageFileReader::GenerateData(void)' >>>>>>>>> >>>>>>> >> > > 2> with >>>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>>> >>>>>>> >> > > 2> >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >>>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > > : see reference to class template instantiation >>>>>>>>> >>>>>>> >> > > 'itk::ImageFileReader' being compiled >>>>>>>>> >>>>>>> >> > > 2> with >>>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>>>>> Studio >>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>>>>> Studio >>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual >>>>>>>>> Studio >>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>> >>>>>>> >> > > 2> Creating library >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > > and object >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: >>>>>>>>> unresolved >>>>>>>>> >>>>>>> external symbol >>>>>>>>> >>>>>>> >> > main >>>>>>>>> >>>>>>> >> > > referenced in function __tmainCRTStartup >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >>>>>>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>>>>>>> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>>>>>>> >>>>>>> Configuration: Debug >>>>>>>>> >>>>>>> >> > x64 >>>>>>>>> >>>>>>> >> > > ------ >>>>>>>>> >>>>>>> >> > > 3> Building Custom Rule >>>>>>>>> >>>>>>> >> > > >>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>>>> >>>>>>> >> > > 3> CMake does not need to re-run because >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >>>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>>>> >>>>>>> >> > is >>>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>>> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 >>>>>>>>> skipped >>>>>>>>> >>>>>>> ========== >>>>>>>>> >>>>>>> >> > > im using the follwing CMakeList.txt >>>>>>>>> >>>>>>> >> > > # This is the root ITK CMakeLists file. >>>>>>>>> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>>>>>>> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >>>>>>>>> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>>>>>>> >>>>>>> >> > > endif() >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > > # This project is designed to be built outside the >>>>>>>>> Insight >>>>>>>>> >>>>>>> source >>>>>>>>> >>>>>>> >> tree. >>>>>>>>> >>>>>>> >> > > project(HelloWorld) >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > > # Find ITK. >>>>>>>>> >>>>>>> >> > > find_package(ITK REQUIRED) >>>>>>>>> >>>>>>> >> > > include(${ITK_USE_FILE}) >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>>>>>>> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > > >>>>>>>>> target_link_libraries(itkTextureFeatureImageFilterTest >>>>>>>>> >>>>>>> >> ${ITK_LIBRARIES}) >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > > please tel me wat the error is?? >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > > -- >>>>>>>>> >>>>>>> >> > > View this message in context: >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>>>>>>> >>>>>>> >> > > Sent from the ITK Insight Users mailing list >>>>>>>>> archive at >>>>>>>>> >>>>>>> Nabble.com . >>>>>>>>> >>>>>>> >> > > _____________________________________ >>>>>>>>> >>>>>>> >> > > Powered by www.kitware.com >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > > Visit other Kitware open-source projects at >>>>>>>>> >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > > Kitware offers ITK Training Courses, for more >>>>>>>>> information >>>>>>>>> >>>>>>> visit: >>>>>>>>> >>>>>>> >> > > http://www.kitware.com/products/protraining.php >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > > Please keep messages on-topic and check the ITK FAQ >>>>>>>>> at: >>>>>>>>> >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>> >>>>>>> >> > > >>>>>>>>> >>>>>>> >> > > Follow this link to subscribe/unsubscribe: >>>>>>>>> >>>>>>> >> > > >>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>> >>>>>>> >> > _____________________________________ >>>>>>>>> >>>>>>> >> > Powered by www.kitware.com >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > Visit other Kitware open-source projects at >>>>>>>>> >>>>>>> >> > http://www.kitware.com/opensource/opensource.html >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > Kitware offers ITK Training Courses, for more >>>>>>>>> information visit: >>>>>>>>> >>>>>>> >> > http://www.kitware.com/products/protraining.php >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > Please keep messages on-topic and check the ITK FAQ >>>>>>>>> at: >>>>>>>>> >>>>>>> >> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > Follow this link to subscribe/unsubscribe: >>>>>>>>> >>>>>>> >> > >>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > ------------------------------ >>>>>>>>> >>>>>>> >> > If you reply to this email, your message will be >>>>>>>>> added to the >>>>>>>>> >>>>>>> discussion >>>>>>>>> >>>>>>> >> > below: >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> > >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >>>>>>>>> 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message in context: >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587960.html >>>>>>>>> >>>>>>> >> Sent from the ITK Insight Users mailing list archive at >>>>>>>>> >>>>>>> Nabble.com . >>>>>>>>> >>>>>>> >> _____________________________________ >>>>>>>>> >>>>>>> >> Powered by www.kitware.com >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> Visit other Kitware open-source projects at >>>>>>>>> >>>>>>> >> http://www.kitware.com/opensource/opensource.html >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> Kitware offers ITK Training Courses, for more >>>>>>>>> information visit: >>>>>>>>> >>>>>>> >> http://www.kitware.com/products/protraining.php >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>> >>>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> >> Follow this link to subscribe/unsubscribe: >>>>>>>>> >>>>>>> >> >>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>> >>>>>>> >> >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > _____________________________________ >>>>>>>>> >>>>>>> > Powered by www.kitware.com >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > Visit other Kitware open-source projects at >>>>>>>>> >>>>>>> > http://www.kitware.com/opensource/opensource.html >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > Kitware offers ITK Training Courses, for more >>>>>>>>> information visit: >>>>>>>>> >>>>>>> > http://www.kitware.com/products/protraining.php >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>> >>>>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > Follow this link to subscribe/unsubscribe: >>>>>>>>> >>>>>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > ------------------------------ >>>>>>>>> >>>>>>> > If you reply to this email, your message will be added >>>>>>>>> to the >>>>>>>>> >>>>>>> discussion >>>>>>>>> >>>>>>> > below: >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> >>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587961.html >>>>>>>>> >>>>>>> > To unsubscribe from [ITK-users] Texture pixel by pixel, >>>>>>>>> click here >>>>>>>>> >>>>>>> > < > . >>>>>>>>> >>>>>>> > NAML >>>>>>>>> >>>>>>> > < >>>>>>>>> >>>>>>> >>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> > >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> -- >>>>>>>>> >>>>>>> View this message in context: >>>>>>>>> >>>>>>> >>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587963.html >>>>>>>>> >>>>>>> Sent from the ITK Insight Users mailing list archive at >>>>>>>>> Nabble.com . >>>>>>>>> >>>>>>> _____________________________________ >>>>>>>>> >>>>>>> Powered by www.kitware.com >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> Visit other Kitware open-source projects at >>>>>>>>> >>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> Kitware offers ITK Training Courses, for more information >>>>>>>>> visit: >>>>>>>>> >>>>>>> http://www.kitware.com/products/protraining.php >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>> >>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>>> >>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> _____________________________________ >>>>>>>>> >>>>>> Powered by www.kitware.com >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>>>>> >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Kitware offers ITK Training Courses, for more information >>>>>>>>> visit: >>>>>>>>> >>>>>> http://www.kitware.com/products/protraining.php >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>> >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>>> >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>>>> >>>>>>>>> >>>> >>>>>>>>> >>> >>>>>>>>> >> >>>>>>>>> >> _____________________________________ >>>>>>>>> >> Powered by www.kitware.com >>>>>>>>> >> >>>>>>>>> >> Visit other Kitware open-source projects at >>>>>>>>> >> http://www.kitware.com/opensource/opensource.html >>>>>>>>> >> >>>>>>>>> >> Kitware offers ITK Training Courses, for more information visit: >>>>>>>>> >> http://www.kitware.com/products/protraining.php >>>>>>>>> >> >>>>>>>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>> >> >>>>>>>>> >> Follow this link to subscribe/unsubscribe: >>>>>>>>> >> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>> >> >>>>>>>>> >> >>>>>>>>> > >>>>>>>>> > _____________________________________ >>>>>>>>> > Powered by www.kitware.com >>>>>>>>> > >>>>>>>>> > Visit other Kitware open-source projects at >>>>>>>>> > http://www.kitware.com/opensource/opensource.html >>>>>>>>> > >>>>>>>>> > Kitware offers ITK Training Courses, for more information visit: >>>>>>>>> > http://www.kitware.com/products/protraining.php >>>>>>>>> > >>>>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>> > >>>>>>>>> > Follow this link to subscribe/unsubscribe: >>>>>>>>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > ------------------------------ >>>>>>>>> > If you reply to this email, your message will be added to the >>>>>>>>> discussion >>>>>>>>> > below: >>>>>>>>> > >>>>>>>>> > >>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588477.html >>>>>>>>> > To start a new topic under ITK Insight Users, email >>>>>>>>> > [hidden email] >>>>>>>>> >>>>>>>>> > To unsubscribe from ITK Insight Users, click here >>>>>>>>> > < > . >>>>>>>>> > NAML >>>>>>>>> > < >>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>>>>> > >>>>>>>>> > >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> View this message in context: >>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588483.html >>>>>>>>> Sent from the ITK Insight Users mailing list archive at Nabble.com >>>>>>>>> . >>>>>>>>> _____________________________________ >>>>>>>>> Powered by www.kitware.com >>>>>>>>> >>>>>>>>> Visit other Kitware open-source projects at >>>>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>>> >>>>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>>>> http://www.kitware.com/products/protraining.php >>>>>>>>> >>>>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>> >>>>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _____________________________________ >>>>>>>> Powered by www.kitware.com >>>>>>>> >>>>>>>> Visit other Kitware open-source projects at >>>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>> >>>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>>> http://www.kitware.com/products/protraining.php >>>>>>>> >>>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >>>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>> >>>>>>>> >>>>>>>> ------------------------------ >>>>>>>> If you reply to this email, your message will be added to the >>>>>>>> discussion below: >>>>>>>> >>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588490.html >>>>>>>> To start a new topic under ITK Insight Users, email [hidden email] >>>>>>>> >>>>>>>> To unsubscribe from ITK Insight Users, click here. >>>>>>>> NAML >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> _____________________________________ >>>>>>> Powered by www.kitware.com >>>>>>> >>>>>>> Visit other Kitware open-source projects at >>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>> >>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>> http://www.kitware.com/products/protraining.php >>>>>>> >>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>> >>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>> >>>>>>> >>>>>> >>>>>> _____________________________________ >>>>>> Powered by www.kitware.com >>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>> http://www.kitware.com/products/protraining.php >>>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>> >>>>>> >>>>>> ------------------------------ >>>>>> If you reply to this email, your message will be added to the >>>>>> discussion below: >>>>>> >>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588495.html >>>>>> To start a new topic under ITK Insight Users, email [hidden email] >>>>>> >>>>>> To unsubscribe from ITK Insight Users, click here. >>>>>> NAML >>>>>> >>>>>> >>>>> >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> >>>> ------------------------------ >>>> If you reply to this email, your message will be added to the >>>> discussion below: >>>> >>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588505.html >>>> To start a new topic under ITK Insight Users, email [hidden email] >>>> >>>> To unsubscribe from ITK Insight Users, click here. >>>> NAML >>>> >>>> >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> ------------------------------ >> If you reply to this email, your message will be added to the discussion >> below: >> >> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588513.html >> To start a new topic under ITK Insight Users, email >> ml-node+s2283740n2283740h75 at n2.nabble.com >> To unsubscribe from ITK Insight Users, click here >> >> . >> NAML >> >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From tj.jackson1226 at gmail.com Thu Feb 18 13:06:55 2016 From: tj.jackson1226 at gmail.com (Tim Jackson) Date: Thu, 18 Feb 2016 13:06:55 -0500 Subject: [ITK] [ITK-dev] method of concatenating 2D images into a 5D image Message-ID: Hi everyone, I've recently started working with a very large .nd2 format time lapse image, that was taken on a Nikon confocal microscope. These image sequences are 5D (x,y,z,time,channel). Because these images are so large, trying to work on the entire image at once will cause a memory allocation error. Therefore I set the reader up in ITK, use a series of ExtractImageFilters to break down the giant file into 2D images (I iterate over the time sequence in a for loop, obtaining a 2D x, y image for each time frame for each channel). This all works fine, and I'm able to complete the necessary image filtering/corrections on these 2D images within the for loop. My problem arises when I'm trying to write the output file. Ideally, I would like to be able to compose all of these images back into one large 5D .nd2 file, but if I do this outright, I'm guessing the writer will have a memory allocation error. Is there a way to write the file one frame at a time, adding the next frame onto the file as the filtering occurs? Or is there some other way to handle the writing of very large image files to skirt around memory allocation problems? I know I could write each frame as an individual file in an image sequence, but then I would have to use a third-party program like ImageJ to make them into a stack, merge channels, etc, which is not a simple task with the volume of image files I will be analyzing. Thanks for your help! Tim -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Thu Feb 18 13:45:37 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 18 Feb 2016 13:45:37 -0500 Subject: [ITK] [ITK-dev] method of concatenating 2D images into a 5D image In-Reply-To: References: Message-ID: Hi Tim, It is possible to stream-write an image if the output format supports streamed writing. MetaImage (.mha) has good support for this. See this example on how to stream the writer: http://www.itk.org/Doxygen/html/Examples_2IO_2VisibleHumanStreamReadWrite_8cxx-example.html#_a7 To generate the image, use an itk::PasteImageFilter. To keep track of the higher order indices, itk::RegionOfInterestImageFilter is suggested instead of itk::ExtractImageFilter. HTH, Matt On Thu, Feb 18, 2016 at 1:06 PM, Tim Jackson wrote: > Hi everyone, > > I've recently started working with a very large .nd2 format time lapse > image, that was taken on a Nikon confocal microscope. These image sequences > are 5D (x,y,z,time,channel). Because these images are so large, trying to > work on the entire image at once will cause a memory allocation error. > Therefore I set the reader up in ITK, use a series of ExtractImageFilters to > break down the giant file into 2D images (I iterate over the time sequence > in a for loop, obtaining a 2D x, y image for each time frame for each > channel). > > This all works fine, and I'm able to complete the necessary image > filtering/corrections on these 2D images within the for loop. My problem > arises when I'm trying to write the output file. Ideally, I would like to > be able to compose all of these images back into one large 5D .nd2 file, but > if I do this outright, I'm guessing the writer will have a memory allocation > error. Is there a way to write the file one frame at a time, adding the > next frame onto the file as the filtering occurs? Or is there some other > way to handle the writing of very large image files to skirt around memory > allocation problems? I know I could write each frame as an individual file > in an image sequence, but then I would have to use a third-party program > like ImageJ to make them into a stack, merge channels, etc, which is not a > simple task with the volume of image files I will be analyzing. > > Thanks for your help! > Tim > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From franciscolopezdelafranca at gmail.com Thu Feb 18 18:22:13 2016 From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca) Date: Fri, 19 Feb 2016 00:22:13 +0100 Subject: [ITK] [ITK-users] Compilation error when building ITK 4.9.0 with MinGW Message-ID: Hi, I've downloaded the last stable ITK version, 4.9.0, for Windows and compile it by using MinGW-64. When the compilation reaches almost the 100%, it gives the error: [ 98%] Building CXX object Modules/IO/TransformBase/src/CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.obj C:/MINGW/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: too many sections (33106) C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Assembler messages: C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Fatal error: can't write CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: File too big I've been searching for a solution on the web for several hours and all the attempts to solve it have not fix it. Has anyone ever faced this problem and fix it? Thanks a lot. Best regards. /Francisco -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From c.spanakis83 at gmail.com Fri Feb 19 05:30:54 2016 From: c.spanakis83 at gmail.com (Constantinus Spanakis) Date: Fri, 19 Feb 2016 12:30:54 +0200 Subject: [ITK] Number of spline parameters Message-ID: Hello. What does the number of spline parameters in image registration depend on? -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Feb 19 08:35:17 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 19 Feb 2016 08:35:17 -0500 Subject: [ITK] [ITK-users] [New example] Stream a Pipeline Message-ID: Hi Folks, We have a new example: Stream a pipeline http://itk.org/ITKExamples/src/Core/Common/StreamAPipeline/Documentation.html Matt _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Fri Feb 19 09:45:28 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 19 Feb 2016 09:45:28 -0500 Subject: [ITK] Number of spline parameters In-Reply-To: References: Message-ID: It depends on spline order and number of image dimensions. Regards On Fri, Feb 19, 2016 at 5:30 AM, Constantinus Spanakis < c.spanakis83 at gmail.com> wrote: > Hello. What does the number of spline parameters in image registration > depend on? > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From kolin9105 at gmail.com Fri Feb 19 10:05:13 2016 From: kolin9105 at gmail.com (meikolin saimara) Date: Fri, 19 Feb 2016 22:05:13 +0700 Subject: [ITK] [ITK-users] (no subject) Message-ID: hello every one I am beginner in itk.. I have a problem with my program. I am using E:\ITK\Source\Examples\Segmentation\ConfidenceConnected and then when I Input file with extension *dcm. I found message itk::ImageFileWriterException (0016F120) Location: "void __thiscall itk::ImageFileWriter >::Write(void)" File: e:\itk\source\modules\io\imagebase\include\itkImageFileWriter.hxx Line: 151 Description: Could not create IO object for writing file d.ccm Tried to create one of the following: NiftiImageIO NrrdImageIO GiplImageIO HDF5ImageIO JPEGImageIO GDCMImageIO BMPImageIO LSMImageIO PNGImageIO TIFFImageIO VTKImageIO StimulateImageIO BioRadImageIO MetaImageIO MRCImageIO GE4ImageIO GE5ImageIO You probably failed to set a file suffix, or set the suffix to an unsupported type. what I have to do guys?? help me guys.. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From chinander at gmail.com Fri Feb 19 10:28:18 2016 From: chinander at gmail.com (Mike Chinander) Date: Fri, 19 Feb 2016 09:28:18 -0600 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: Looks like you have a typo in your file name; see this line in your output: "Description: Could not create IO object for writing file d.ccm" On Fri, Feb 19, 2016 at 9:05 AM, meikolin saimara wrote: > hello every one I am beginner in itk.. > I have a problem with my program. > I am using E:\ITK\Source\Examples\Segmentation\ConfidenceConnected and > then when I Input file with extension *dcm. > I found message > > > > itk::ImageFileWriterException (0016F120) > Location: "void __thiscall itk::ImageFileWriter char,2 > > >::Write(void)" > File: e:\itk\source\modules\io\imagebase\include\itkImageFileWriter.hxx > Line: 151 > Description: Could not create IO object for writing file d.ccm > Tried to create one of the following: > NiftiImageIO > NrrdImageIO > GiplImageIO > HDF5ImageIO > JPEGImageIO > GDCMImageIO > BMPImageIO > LSMImageIO > PNGImageIO > TIFFImageIO > VTKImageIO > StimulateImageIO > BioRadImageIO > MetaImageIO > MRCImageIO > GE4ImageIO > GE5ImageIO > You probably failed to set a file suffix, or > set the suffix to an unsupported type. > what I have to do guys?? > help me guys.. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Fri Feb 19 12:00:42 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 19 Feb 2016 12:00:42 -0500 Subject: [ITK] [ITK-users] Compilation error when building ITK 4.9.0 with MinGW In-Reply-To: References: Message-ID: Hi Franscisco, According to this thread: https://cmake.org/pipermail/insight-users/2015-September/052511.html adding the flags -Wa,-mbig-obj helps at least with the build error. Does it help in your case? Thanks, Matt On Thu, Feb 18, 2016 at 6:22 PM, Francisco Lopez de la Franca wrote: > Hi, > I've downloaded the last stable ITK version, 4.9.0, for Windows and compile > it by using MinGW-64. > When the compilation reaches almost the 100%, it gives the error: > > [ 98%] Building CXX object > Modules/IO/TransformBase/src/CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.obj > C:/MINGW/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: > CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: too many > sections (33106) > C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Assembler messages: > C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Fatal error: can't write > CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: File too > big > > I've been searching for a solution on the web for several hours and all the > attempts to solve it have not fix it. > > Has anyone ever faced this problem and fix it? > > Thanks a lot. > Best regards. > /Francisco > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From simon.warfield at childrens.harvard.edu Fri Feb 19 12:14:30 2016 From: simon.warfield at childrens.harvard.edu (Simon Warfield) Date: Fri, 19 Feb 2016 12:14:30 -0500 Subject: [ITK] [ITK-dev] include file header double underscore In-Reply-To: References: Message-ID: <56C74D76.2090505@childrens.harvard.edu> Did itk include file ifndef lines lose their double underscore at some point? Was there a reason for that ? It has an impact on backwards compatibility. http://www.itk.org/Doxygen47/html/itkAbsImageFilter_8h_source.html line 18 : #ifndef __itkAbsImageFilter_h http://www.itk.org/Doxygen48/html/itkAbsImageFilter_8h_source.html line 18 : #ifndef itkAbsImageFilter_h --Simon _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From bill.lorensen at gmail.com Fri Feb 19 13:07:18 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Fri, 19 Feb 2016 13:07:18 -0500 Subject: [ITK] [ITK-dev] include file header double underscore In-Reply-To: <56C74D76.2090505@childrens.harvard.edu> References: <56C74D76.2090505@childrens.harvard.edu> Message-ID: Simon, Apparently the use of _ and __ is reserved and newer c++'s warn about it. These changes were made back in December 2014... http://itk.org/gitweb?p=ITK.git;a=commit;h=4d8c82c5bfdf340a4201e91d7d35694852328199 http://stackoverflow.com/questions/228783/what-are-the-rules-about-using-an-underscore-in-a-c-identifier What backward compatibility issues do you see? Bill On Fri, Feb 19, 2016 at 12:14 PM, Simon Warfield wrote: > > Did itk include file ifndef lines lose their double underscore at some > point? > Was there a reason for that ? It has an impact on backwards compatibility. > > http://www.itk.org/Doxygen47/html/itkAbsImageFilter_8h_source.html > line 18 : > #ifndef __itkAbsImageFilter_h > > http://www.itk.org/Doxygen48/html/itkAbsImageFilter_8h_source.html > line 18 : > #ifndef itkAbsImageFilter_h > > > --Simon > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers -- Unpaid intern in BillsBasement at noware dot com _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From kayarre at gmail.com Fri Feb 19 14:06:00 2016 From: kayarre at gmail.com (Kurt Sansom) Date: Fri, 19 Feb 2016 11:06:00 -0800 Subject: [ITK] BinaryMorphologicalOpening Filter compile error Message-ID: This is one of my first attempts at using the ITK library, using some code from someone elses masters thesis. I am getting the following type errors and and the subsequent code that I am compiling on a mac: Thanks so much. */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Core/Common/include/itkImageToImageFilter.h:126:20: **error: **type 'InputImageType' (aka 'unsigned char') cannot be* * used prior to '::' because it has no members* typedef typename InputImageType::Pointer InputImagePointer; * ^* */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/ImageFilterBase/include/itkBoxImageFilter.h:41:10: note: *in instantiation of template class 'itk::ImageToImageFilter >' requested here public ImageToImageFilter< TInputImage, TOutputImage > * ^* */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/ImageFilterBase/include/itkKernelImageFilter.h:41:10: note: *in instantiation of template class 'itk::BoxImageFilter >' requested here public BoxImageFilter< TInputImage, TOutputImage > * ^* */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryMorphologicalOpeningImageFilter.h:56:10: note: *in instantiation of template class 'itk::KernelImageFilter, itk::BinaryBallStructuringElement > >' requested here public KernelImageFilter< TInputImage, TOutputImage, TKernel > * ^* */Users/sansomk/code/cpp/us_seg/morph.cxx:63:3: note: *in instantiation of template class 'itk::BinaryMorphologicalOpeningImageFilter, itk::BinaryBallStructuringElement > >' requested here FilterType::Pointer filter = FilterType::New(); * ^* In file included from /Users/sansomk/code/cpp/us_seg/morph.cxx:12: In file included from /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/ImageIntensity/include/itkRescaleIntensityImageFilter.h:21: In file included from /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Core/Common/include/itkUnaryFunctorImageFilter.h:22: In file included from /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Core/Common/include/itkInPlaceImageFilter.h:31: */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Core/Common/include/itkImageToImageFilter.h:127:20: **error: **type 'InputImageType' (aka 'unsigned char') cannot be* * used prior to '::' because it has no members* typedef typename InputImageType::ConstPointer InputImageConstPointer; * ^* */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Core/Common/include/itkImageToImageFilter.h:128:20: **error: **type 'InputImageType' (aka 'unsigned char') cannot be* * used prior to '::' because it has no members* typedef typename InputImageType::RegionType InputImageRegionType; * ^* */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Core/Common/include/itkImageToImageFilter.h:129:20: **error: **type 'InputImageType' (aka 'unsigned char') cannot be* * used prior to '::' because it has no members* typedef typename InputImageType::PixelType InputImagePixelType; * ^* */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Core/Common/include/itkImageToImageFilter.h:133:23: **error: **type 'unsigned char' cannot be used prior to '::'* * because it has no members* TInputImage::ImageDimension); * ^* */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Core/Common/include/itkMacro.h:763:73: note: *expanded from macro 'itkStaticConstMacro' # define itkStaticConstMacro(name,type,value) static const type name = value * ^* In file included from /Users/sansomk/code/cpp/us_seg/morph.cxx:13: In file included from /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/MathematicalMorphology/include/itkBinaryBallStructuringElement.h:124: In file included from /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/MathematicalMorphology/include/itkBinaryBallStructuringElement.hxx:22: In file included from /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/MathematicalMorphology/include/itkFlatStructuringElement.h:246: In file included from /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/MathematicalMorphology/include/itkFlatStructuringElement.hxx:40: In file included from /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/MathematicalMorphology/include/itkVanHerkGilWermanDilateImageFilter.h:21: In file included from /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/MathematicalMorphology/include/itkVanHerkGilWermanErodeDilateImageFilter.h:21: In file included from /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/ImageFilterBase/include/itkKernelImageFilter.h:21: */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/ImageFilterBase/include/itkBoxImageFilter.h:59:20: **error: **type 'unsigned char' cannot be used prior to* * '::' because it has no members* typedef typename TInputImage::RegionType RegionType; * ^* */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/ImageFilterBase/include/itkKernelImageFilter.h:41:10: note: *in instantiation of template class 'itk::BoxImageFilter >' requested here public BoxImageFilter< TInputImage, TOutputImage > * ^* */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryMorphologicalOpeningImageFilter.h:56:10: note: *in instantiation of template class 'itk::KernelImageFilter, itk::BinaryBallStructuringElement > >' requested here public KernelImageFilter< TInputImage, TOutputImage, TKernel > * ^* */Users/sansomk/code/cpp/us_seg/morph.cxx:63:3: note: *in instantiation of template class 'itk::BinaryMorphologicalOpeningImageFilter, itk::BinaryBallStructuringElement > >' requested here FilterType::Pointer filter = FilterType::New(); * ^* In file included from /Users/sansomk/code/cpp/us_seg/morph.cxx:13: here is the code: #if defined(MSCVER) #pragma warning ( disable : 4786 ) #endif #ifdef _BORLANDC_ #define ITK_LEAN_AND_MEAN #endif #include "itkImage.h" #include "itkImageFileReader.h" #include "itkImageFileWriter.h" #include "itkRescaleIntensityImageFilter.h" #include "itkBinaryBallStructuringElement.h" #include "itkBinaryMorphologicalClosingImageFilter.h" #include "itkBinaryMorphologicalOpeningImageFilter.h" int main(int argc, char * argv[] ) { if( argc < 5 ) { std::cerr << "Usage: " << std::endl; std::cerr << argv [0] << " inputImageFile outputImageFile radiusX(int)" << " radiusY(int) radiusZ(int) " << std::endl; return EXIT_FAILURE; } const unsigned int Dimension = 3; typedef unsigned char InputPixelType; typedef unsigned char OutputPixelType; typedef itk::Image< InputPixelType, Dimension > InputImageType; typedef itk::Image< OutputPixelType, Dimension > OutputImageType; typedef itk::ImageFileReader< InputImageType> ReaderType; typedef itk::ImageFileWriter< OutputImageType> WriterType; typedef itk::BinaryBallStructuringElement< InputPixelType, Dimension > KernelType; typedef itk::BinaryMorphologicalOpeningImageFilter< InputPixelType, OutputImageType, KernelType > FilterType; typedef itk::RescaleIntensityImageFilter RescaleFilterType; // Read Image ReaderType::Pointer reader = ReaderType::New(); reader->SetFileName( argv[1] ); reader->Update(); //Create Kernel (structuring element) KernelType::RadiusType radius; radius[0] = atoi( argv[3] ); radius[1] = atoi( argv[4] ); radius[2] = atoi( argv[5] ); KernelType kernel; kernel.SetRadius( Dimension ); kernel.CreateStructuringElement(); // Create morphological filter FilterType::Pointer filter = FilterType::New(); filter->SetInput( reader ); filter->SetKernel( kernel ); filter->Update(); // Rescale for output RescaleFilterType::Pointer rescaler = RescaleFilterType::New(); rescaler->SetOutputMinimum( 0 ); rescaler->SetOutputMaximum( 255 ); rescaler->SetInput( filter->GetOutput() ); //rescaler->Update(); // Write output WriterType::Pointer writer = WriterType::New(); writer->SetFileName( argv[2] ); writer->SetInput( rescaler->GetOutput() ); writer->Update(); return EXIT_SUCCESS; } -- Kurt Sansom -------------- next part -------------- An HTML attachment was scrubbed... URL: From emily-hammond at uiowa.edu Fri Feb 19 16:43:31 2016 From: emily-hammond at uiowa.edu (Hammond, Emily M) Date: Fri, 19 Feb 2016 21:43:31 +0000 Subject: [ITK] [ITK-users] Apply rigid transform by changing image information Message-ID: Hello, Context: I am applying a rigid registration process to align two images. The transform allows for anisotropic scaling, a translation, and a versor rotation. I have perform the registration and checked my results by loading the resulting transform into 3D Slicer and applying it to the moving image. Problem: I am trying to apply the transform to the moving image without resampling, so just changing the image information. Essentially, I want to perform the equivalent of "Harden Transform" in Slicer. I have been following this example (http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv3_2ChangeInformationImageFilter_8cxx-example.html#_a3) to change my image information. To apply the scaling, I simply multiplied the spacing by the corresponding scale factor. For translation, I added the translation to the origin. For applying the rotation, the example shows to multiply the image direction matrix by the versor rotation matrix. The new spacing, origin, and direction matrix are then input into the new change information image filter. I have done this, however, when using Slicer to load in the final image, the transform does not show to have been applied correctly. I have been saving my images as MetaImage files (.mhd) so the image information is saved in the header file. Can anyone please give me some advice on how to perform this task appropriately? Here is my code: // get image properties ImageType::PointType origin = image->GetOrigin(); ImageType::SpacingType spacing = image->GetSpacing(); ImageType::DirectionType direction = image->GetDirection(); // get transform parameters TransformType::TranslationType translation = transform->GetTranslation(); TransformType::ScaleVectorType scale = transform->GetScale(); TransformType::VersorType versor = transform->GetVersor(); // apply scaling and translation parameters to image for( int i = 0; i < 3; i++ ) { spacing[i] *= scale[i]; origin[i] += translation[i]; } // apply rotation to image ImageType::DirectionType newDirection = direction*versor.GetMatrix(); // allocate hardening filter typedef itk::ChangeInformationImageFilter< ImageType > HardenTransformFilter; HardenTransformFilter::Pointer harden = HardenTransformFilter::New(); harden->SetInput( image ); // set new parameters harden->SetOutputSpacing( spacing ); harden->SetOutputOrigin( origin ); harden->SetOutputDirection( newDirection ); // turn change flags on harden->ChangeSpacingOn(); harden->ChangeOriginOn(); harden->ChangeDirectionOn(); harden->Update(); Thanks in advance! Emily Hammond -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Fri Feb 19 17:56:39 2016 From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca) Date: Fri, 19 Feb 2016 23:56:39 +0100 Subject: [ITK] [ITK-users] Compilation error when building ITK 4.9.0 with MinGW In-Reply-To: References: Message-ID: Hello Matt, I had already tested the -Wa,-mbig-obj options in CMAKE_CXX_FLAGS and in CMAKE_C_FLAGS and the answer was: C:/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: unrecognized option `-mbig-obj' So, I'm stuck at this point, and I'm thinking to change from Mingw to Visual Studio or another one. But it is very strange that ITK wasn't be prepared to be compiled via MinGW. Thanks for answering and if you have any suggestion, it wiil be very well received. /Francisco 2016-02-19 18:00 GMT+01:00 Matt McCormick : > Hi Franscisco, > > According to this thread: > > https://cmake.org/pipermail/insight-users/2015-September/052511.html > > adding the flags > > -Wa,-mbig-obj > > helps at least with the build error. Does it help in your case? > > Thanks, > Matt > > On Thu, Feb 18, 2016 at 6:22 PM, Francisco Lopez de la Franca > wrote: > > Hi, > > I've downloaded the last stable ITK version, 4.9.0, for Windows and > compile > > it by using MinGW-64. > > When the compilation reaches almost the 100%, it gives the error: > > > > [ 98%] Building CXX object > > > Modules/IO/TransformBase/src/CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.obj > > > C:/MINGW/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: > > CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: too > many > > sections (33106) > > C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Assembler messages: > > C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Fatal error: can't write > > CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: File > too > > big > > > > I've been searching for a solution on the web for several hours and all > the > > attempts to solve it have not fix it. > > > > Has anyone ever faced this problem and fix it? > > > > Thanks a lot. > > Best regards. > > /Francisco > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From hans-johnson at uiowa.edu Fri Feb 19 17:26:07 2016 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Fri, 19 Feb 2016 22:26:07 +0000 Subject: [ITK] [ITK-users] Apply rigid transform by changing image information Message-ID: Emily, Please review the following. https://github.com/BRAINSia/BRAINSTools/blob/master/BRAINSCommonLib/itkResampleInPlaceImageFilter.h This can do the translation and versor rotation parts of what you want, but currently requires isotropic 1mm scaling. Hopefully you could modify (and contribute back) an improvement that also incorporates the anisotropic scaleing component. Let me know if you want to work more closely on this. Hans -- From: Insight-users > on behalf of "Hammond, Emily M" > Date: Friday, February 19, 2016 at 3:43 PM To: Insight Users > Subject: [ITK-users] Apply rigid transform by changing image information Hello, Context: I am applying a rigid registration process to align two images. The transform allows for anisotropic scaling, a translation, and a versor rotation. I have perform the registration and checked my results by loading the resulting transform into 3D Slicer and applying it to the moving image. Problem: I am trying to apply the transform to the moving image without resampling, so just changing the image information. Essentially, I want to perform the equivalent of ?Harden Transform? in Slicer. I have been following this example (http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv3_2ChangeInformationImageFilter_8cxx-example.html#_a3) to change my image information. To apply the scaling, I simply multiplied the spacing by the corresponding scale factor. For translation, I added the translation to the origin. For applying the rotation, the example shows to multiply the image direction matrix by the versor rotation matrix. The new spacing, origin, and direction matrix are then input into the new change information image filter. I have done this, however, when using Slicer to load in the final image, the transform does not show to have been applied correctly. I have been saving my images as MetaImage files (.mhd) so the image information is saved in the header file. Can anyone please give me some advice on how to perform this task appropriately? Here is my code: // get image properties ImageType::PointType origin = image->GetOrigin(); ImageType::SpacingType spacing = image->GetSpacing(); ImageType::DirectionType direction = image->GetDirection(); // get transform parameters TransformType::TranslationType translation = transform->GetTranslation(); TransformType::ScaleVectorType scale = transform->GetScale(); TransformType::VersorType versor = transform->GetVersor(); // apply scaling and translation parameters to image for( int i = 0; i < 3; i++ ) { spacing[i] *= scale[i]; origin[i] += translation[i]; } // apply rotation to image ImageType::DirectionType newDirection = direction*versor.GetMatrix(); // allocate hardening filter typedef itk::ChangeInformationImageFilter< ImageType > HardenTransformFilter; HardenTransformFilter::Pointer harden = HardenTransformFilter::New(); harden->SetInput( image ); // set new parameters harden->SetOutputSpacing( spacing ); harden->SetOutputOrigin( origin ); harden->SetOutputDirection( newDirection ); // turn change flags on harden->ChangeSpacingOn(); harden->ChangeOriginOn(); harden->ChangeDirectionOn(); harden->Update(); Thanks in advance! Emily Hammond -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From lasso at queensu.ca Sat Feb 20 10:52:38 2016 From: lasso at queensu.ca (Andras Lasso) Date: Sat, 20 Feb 2016 15:52:38 +0000 Subject: [ITK] [ITK-users] Apply rigid transform by changing image information In-Reply-To: References: Message-ID: Probably the simplest method is the following: * create a homogeneous transformation matrix that transforms between image coordinate indices and physical coordinates (computed from origin, spacing, and axis directions) * multiply it with the matrix of the transformation applied to the image * compute spacing, origin, and directions from the resulting matrix and set it in the image Example of computing origin, scaling, directions from transformation matrix: https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Core/vtkMRMLVolumeNode.cxx#L420 How to create homogeneous transformation matrix from various ITK transforms: https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Core/vtkITKTransformConverter.h#L135 Andras From: Johnson, Hans J Sent: February 19, 2016 17:59 To: Hammond, Emily M; Insight Users Subject: Re: [ITK] [ITK-users] Apply rigid transform by changing image information Emily, Please review the following. https://github.com/BRAINSia/BRAINSTools/blob/master/BRAINSCommonLib/itkResampleInPlaceImageFilter.h This can do the translation and versor rotation parts of what you want, but currently requires isotropic 1mm scaling. Hopefully you could modify (and contribute back) an improvement that also incorporates the anisotropic scaleing component. Let me know if you want to work more closely on this. Hans -- From: Insight-users > on behalf of "Hammond, Emily M" > Date: Friday, February 19, 2016 at 3:43 PM To: Insight Users > Subject: [ITK-users] Apply rigid transform by changing image information Hello, Context: I am applying a rigid registration process to align two images. The transform allows for anisotropic scaling, a translation, and a versor rotation. I have perform the registration and checked my results by loading the resulting transform into 3D Slicer and applying it to the moving image. Problem: I am trying to apply the transform to the moving image without resampling, so just changing the image information. Essentially, I want to perform the equivalent of "Harden Transform" in Slicer. I have been following this example (http://www.itk.org/Doxygen/html/Examples_2RegistrationITKv3_2ChangeInformationImageFilter_8cxx-example.html#_a3) to change my image information. To apply the scaling, I simply multiplied the spacing by the corresponding scale factor. For translation, I added the translation to the origin. For applying the rotation, the example shows to multiply the image direction matrix by the versor rotation matrix. The new spacing, origin, and direction matrix are then input into the new change information image filter. I have done this, however, when using Slicer to load in the final image, the transform does not show to have been applied correctly. I have been saving my images as MetaImage files (.mhd) so the image information is saved in the header file. Can anyone please give me some advice on how to perform this task appropriately? Here is my code: // get image properties ImageType::PointType origin = image->GetOrigin(); ImageType::SpacingType spacing = image->GetSpacing(); ImageType::DirectionType direction = image->GetDirection(); // get transform parameters TransformType::TranslationType translation = transform->GetTranslation(); TransformType::ScaleVectorType scale = transform->GetScale(); TransformType::VersorType versor = transform->GetVersor(); // apply scaling and translation parameters to image for( int i = 0; i < 3; i++ ) { spacing[i] *= scale[i]; origin[i] += translation[i]; } // apply rotation to image ImageType::DirectionType newDirection = direction*versor.GetMatrix(); // allocate hardening filter typedef itk::ChangeInformationImageFilter< ImageType > HardenTransformFilter; HardenTransformFilter::Pointer harden = HardenTransformFilter::New(); harden->SetInput( image ); // set new parameters harden->SetOutputSpacing( spacing ); harden->SetOutputOrigin( origin ); harden->SetOutputDirection( newDirection ); // turn change flags on harden->ChangeSpacingOn(); harden->ChangeOriginOn(); harden->ChangeDirectionOn(); harden->Update(); Thanks in advance! Emily Hammond -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From artioml at post.bgu.ac.il Sun Feb 21 10:17:31 2016 From: artioml at post.bgu.ac.il (artioml) Date: Sun, 21 Feb 2016 08:17:31 -0700 (MST) Subject: [ITK] [ITK-users] BSpline transformation of Vector image Message-ID: <1456067851174-36816.post@n7.nabble.com> Hello, Is it possible to perform BSpline transformation of vector image? Or RGB image? Thank you. -- View this message in context: http://itk-users.7.n7.nabble.com/BSpline-transformation-of-Vector-image-tp36816.html Sent from the ITK - Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Sun Feb 21 13:41:16 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Sun, 21 Feb 2016 13:41:16 -0500 Subject: [ITK] BinaryMorphologicalOpening Filter compile error In-Reply-To: References: Message-ID: There were 3 fairly obvious mistakes. Attached are a diff file and a compilable source code. HTH, D?enan On Fri, Feb 19, 2016 at 2:06 PM, Kurt Sansom wrote: > This is one of my first attempts at using the ITK library, using some code > from someone elses masters thesis. > > I am getting the following type errors and and the subsequent code that I > am compiling on a mac: > > Thanks so much. > > */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Core/Common/include/itkImageToImageFilter.h:126:20: > **error: **type 'InputImageType' (aka 'unsigned char') cannot be* > > * used prior to '::' because it has no members* > > typedef typename InputImageType::Pointer InputImagePointer; > > * ^* > > */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/ImageFilterBase/include/itkBoxImageFilter.h:41:10: > note: *in instantiation of template class > > 'itk::ImageToImageFilter > >' requested here > > public ImageToImageFilter< TInputImage, TOutputImage > > > * ^* > > */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/ImageFilterBase/include/itkKernelImageFilter.h:41:10: > note: *in instantiation of template class > > 'itk::BoxImageFilter >' > requested here > > public BoxImageFilter< TInputImage, TOutputImage > > > * ^* > > */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryMorphologicalOpeningImageFilter.h:56:10: > note: *in > > instantiation of template class 'itk::KernelImageFilter char, itk::Image, > itk::BinaryBallStructuringElement > itk::NeighborhoodAllocator > >' requested here > > public KernelImageFilter< TInputImage, TOutputImage, TKernel > > > * ^* > > */Users/sansomk/code/cpp/us_seg/morph.cxx:63:3: note: *in instantiation > of template class 'itk::BinaryMorphologicalOpeningImageFilter > itk::Image, > itk::BinaryBallStructuringElement itk::NeighborhoodAllocator > >' requested here > > FilterType::Pointer filter = FilterType::New(); > > * ^* > > In file included from /Users/sansomk/code/cpp/us_seg/morph.cxx:12: > > In file included from > /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/ImageIntensity/include/itkRescaleIntensityImageFilter.h:21: > > In file included from > /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Core/Common/include/itkUnaryFunctorImageFilter.h:22: > > In file included from > /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Core/Common/include/itkInPlaceImageFilter.h:31: > > */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Core/Common/include/itkImageToImageFilter.h:127:20: > **error: **type 'InputImageType' (aka 'unsigned char') cannot be* > > * used prior to '::' because it has no members* > > typedef typename InputImageType::ConstPointer InputImageConstPointer; > > * ^* > > */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Core/Common/include/itkImageToImageFilter.h:128:20: > **error: **type 'InputImageType' (aka 'unsigned char') cannot be* > > * used prior to '::' because it has no members* > > typedef typename InputImageType::RegionType InputImageRegionType; > > * ^* > > */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Core/Common/include/itkImageToImageFilter.h:129:20: > **error: **type 'InputImageType' (aka 'unsigned char') cannot be* > > * used prior to '::' because it has no members* > > typedef typename InputImageType::PixelType InputImagePixelType; > > * ^* > > */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Core/Common/include/itkImageToImageFilter.h:133:23: > **error: **type 'unsigned char' cannot be used prior to '::'* > > * because it has no members* > > TInputImage::ImageDimension); > > * ^* > > */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Core/Common/include/itkMacro.h:763:73: > note: *expanded from macro 'itkStaticConstMacro' > > # define itkStaticConstMacro(name,type,value) static const type name = > value > > * ^* > > In file included from /Users/sansomk/code/cpp/us_seg/morph.cxx:13: > > In file included from > /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/MathematicalMorphology/include/itkBinaryBallStructuringElement.h:124: > > In file included from > /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/MathematicalMorphology/include/itkBinaryBallStructuringElement.hxx:22: > > In file included from > /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/MathematicalMorphology/include/itkFlatStructuringElement.h:246: > > In file included from > /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/MathematicalMorphology/include/itkFlatStructuringElement.hxx:40: > > In file included from > /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/MathematicalMorphology/include/itkVanHerkGilWermanDilateImageFilter.h:21: > > In file included from > /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/MathematicalMorphology/include/itkVanHerkGilWermanErodeDilateImageFilter.h:21: > > In file included from > /Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/ImageFilterBase/include/itkKernelImageFilter.h:21: > > */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/ImageFilterBase/include/itkBoxImageFilter.h:59:20: > **error: **type 'unsigned char' cannot be used prior to* > > * '::' because it has no members* > > typedef typename TInputImage::RegionType RegionType; > > * ^* > > */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/ImageFilterBase/include/itkKernelImageFilter.h:41:10: > note: *in instantiation of template class > > 'itk::BoxImageFilter >' > requested here > > public BoxImageFilter< TInputImage, TOutputImage > > > * ^* > > */Users/sansomk/build/ITK/ITKLatestRelease/Modules/Filtering/BinaryMathematicalMorphology/include/itkBinaryMorphologicalOpeningImageFilter.h:56:10: > note: *in > > instantiation of template class 'itk::KernelImageFilter char, itk::Image, > itk::BinaryBallStructuringElement > itk::NeighborhoodAllocator > >' requested here > > public KernelImageFilter< TInputImage, TOutputImage, TKernel > > > * ^* > > */Users/sansomk/code/cpp/us_seg/morph.cxx:63:3: note: *in instantiation > of template class 'itk::BinaryMorphologicalOpeningImageFilter > itk::Image, > itk::BinaryBallStructuringElement itk::NeighborhoodAllocator > >' requested here > > FilterType::Pointer filter = FilterType::New(); > > * ^* > > In file included from /Users/sansomk/code/cpp/us_seg/morph.cxx:13: > > here is the code: > > #if defined(MSCVER) > > #pragma warning ( disable : 4786 ) > > #endif > > > #ifdef _BORLANDC_ > > #define ITK_LEAN_AND_MEAN > > #endif > > > #include "itkImage.h" > > #include "itkImageFileReader.h" > > #include "itkImageFileWriter.h" > > #include "itkRescaleIntensityImageFilter.h" > > #include "itkBinaryBallStructuringElement.h" > > #include "itkBinaryMorphologicalClosingImageFilter.h" > > #include "itkBinaryMorphologicalOpeningImageFilter.h" > > > int main(int argc, char * argv[] ) { > > > if( argc < 5 ) { > > std::cerr << "Usage: " << std::endl; > > std::cerr << argv [0] << " inputImageFile outputImageFile radiusX(int)" > > << " radiusY(int) radiusZ(int) " << std::endl; > > return EXIT_FAILURE; > > } > > > > > > const unsigned int Dimension = 3; > > > > typedef unsigned char InputPixelType; > > typedef unsigned char OutputPixelType; > > > > typedef itk::Image< InputPixelType, Dimension > InputImageType; > > typedef itk::Image< OutputPixelType, Dimension > OutputImageType; > > > > typedef itk::ImageFileReader< InputImageType> ReaderType; > > typedef itk::ImageFileWriter< OutputImageType> WriterType; > > > > typedef itk::BinaryBallStructuringElement< InputPixelType, Dimension > > KernelType; > > > > typedef itk::BinaryMorphologicalOpeningImageFilter< InputPixelType, > > OutputImageType, > > KernelType > > FilterType; > > typedef itk::RescaleIntensityImageFilter OutputImageType> RescaleFilterType; > > > > > > // Read Image > > ReaderType::Pointer reader = ReaderType::New(); > > reader->SetFileName( argv[1] ); > > reader->Update(); > > > > //Create Kernel (structuring element) > > KernelType::RadiusType radius; > > radius[0] = atoi( argv[3] ); > > radius[1] = atoi( argv[4] ); > > radius[2] = atoi( argv[5] ); > > > > > > KernelType kernel; > > kernel.SetRadius( Dimension ); > > kernel.CreateStructuringElement(); > > > > // Create morphological filter > > FilterType::Pointer filter = FilterType::New(); > > filter->SetInput( reader ); > > filter->SetKernel( kernel ); > > filter->Update(); > > > > // Rescale for output > > RescaleFilterType::Pointer rescaler = RescaleFilterType::New(); > > rescaler->SetOutputMinimum( 0 ); > > rescaler->SetOutputMaximum( 255 ); > > rescaler->SetInput( filter->GetOutput() ); > > //rescaler->Update(); > > > > // Write output > > WriterType::Pointer writer = WriterType::New(); > > writer->SetFileName( argv[2] ); > > writer->SetInput( rescaler->GetOutput() ); > > writer->Update(); > > > > return EXIT_SUCCESS; > > } > > > > > -- > Kurt Sansom > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- diff --git "a/C:\\Misc\\Tester\\Source1.cpp" "b/C:\\Misc\\Tester\\tester.cpp" index b137d33..d690374 100644 --- "a/C:\\Misc\\Tester\\Source1.cpp" +++ "b/C:\\Misc\\Tester\\tester.cpp" @@ -37,7 +37,7 @@ int main(int argc, char * argv[]) { typedef itk::BinaryBallStructuringElement< InputPixelType, Dimension > KernelType; - typedef itk::BinaryMorphologicalOpeningImageFilter< InputPixelType, + typedef itk::BinaryMorphologicalOpeningImageFilter< InputImageType, OutputImageType, KernelType > FilterType; typedef itk::RescaleIntensityImageFilter RescaleFilterType; @@ -56,12 +56,12 @@ int main(int argc, char * argv[]) { KernelType kernel; - kernel.SetRadius(Dimension); + kernel.SetRadius(radius); kernel.CreateStructuringElement(); // Create morphological filter FilterType::Pointer filter = FilterType::New(); - filter->SetInput(reader); + filter->SetInput(reader->GetOutput()); filter->SetKernel(kernel); filter->Update(); @@ -80,4 +80,4 @@ int main(int argc, char * argv[]) { return EXIT_SUCCESS; -} +} \ No newline at end of file -------------- next part -------------- A non-text attachment was scrubbed... Name: tester.cpp Type: text/x-c++src Size: 2481 bytes Desc: not available URL: From matt.mccormick at kitware.com Sun Feb 21 19:27:33 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 21 Feb 2016 19:27:33 -0500 Subject: [ITK] [ITK-users] BSpline transformation of Vector image In-Reply-To: <1456067851174-36816.post@n7.nabble.com> References: <1456067851174-36816.post@n7.nabble.com> Message-ID: Hello, Yes, the transformation is not dependent on the pixel type. The Interpolator and ResampleImageFilter can handle a Vector or RGBPixel type. See this example as a reference: http://itk.org/ITKExamples/src/Filtering/ImageGrid/ResampleAVectorImage/Documentation.html HTH, Matt On Sun, Feb 21, 2016 at 10:17 AM, artioml wrote: > Hello, > > Is it possible to perform BSpline transformation of vector image? Or RGB > image? > > Thank you. > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/BSpline-transformation-of-Vector-image-tp36816.html > Sent from the ITK - Users mailing list archive at Nabble.com. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From kayarre at gmail.com Mon Feb 22 03:01:09 2016 From: kayarre at gmail.com (Kurt Sansom) Date: Mon, 22 Feb 2016 00:01:09 -0800 Subject: [ITK] ITK Ctest errors Message-ID: I have ITK and VTK built with shared libraries on OSX 10.11, and have DYLD_LIBRARY_PATH set to /VTK/build/lib:/ITK/build/lib But several tests fail with same kind of error.(see below) does anyone have any insight into what is causing this. I looked at using otool -L to look at what the library is trying to ling to but I didn't see anything weird or don't know enough to properly interpret. Thank you. ~Kurt 2783: Test command: /Users/sansomk/build/ITK/build/bin/itkTestDriver "--add-before-env" "PYTHONPATH" "/Users/sansomk/build/ITK/build/Wrapping/Generators/Python/Release" "--add-before-env" "PYTHONPATH" "/Users/sansomk/build/ITK/build/Wrapping/Generators/Python" "--add-before-env" "PYTHONPATH" "/Users/sansomk/build/ITK/build/lib/Release" "--add-before-env" "PYTHONPATH" "/Users/sansomk/build/ITK/build/lib" "--add-before-libpath" "/Users/sansomk/build/ITK/build/lib/Release" "--add-before-libpath" "/Users/sansomk/build/ITK/build/lib" "--add-before-libpath" "/Users/sansomk/build/ITK/build/bin/Release" "--add-before-libpath" "/Users/sansomk/build/ITK/build/bin" "--add-before-libpath" "/Users/sansomk/build/ITK/build" "arch" "-x86_64" "/Users/sansomk/anaconda/bin/python2.7" "/Users/sansomk/build/ITK/ITKLatestRelease/Examples/IO/test/../DicomSliceRead.py" "/Users/sansomk/build/ITK/build/ExternalData/Testing/Data/Input/dicom-sc_cs-1.dcm" "/Users/sansomk/build/ITK/build/Testing/Temporary/DicomSliceReadPythonOutput.png" "--compare" "/Users/sansomk/build/ITK/build/Testing/Temporary/DicomSliceReadPythonOutput.png" "/Users/sansomk/build/ITK/build/ExternalData/Examples/IO/test/Baseline/DicomSliceReadPythonOutputBaseline.png" 2783: Test timeout computed to be: 1500 2783: Traceback (most recent call last): 2783: File "/Users/sansomk/build/ITK/ITKLatestRelease/Examples/IO/test/../DicomSliceRead.py", line 36, in 2783: InputImageType = itk.Image.SS2 2783: File "/Users/sansomk/build/ITK/build/Wrapping/Generators/Python/itkLazy.py", line 42, in __getattribute__ 2783: itkBase.LoadModule(module, namespace) 2783: File "/Users/sansomk/build/ITK/build/Wrapping/Generators/Python/itkBase.py", line 128, in LoadModule 2783: module = loader.load(swigModuleName) 2783: File "/Users/sansomk/build/ITK/build/Wrapping/Generators/Python/itkBase.py", line 245, in load 2783: return imp.load_module(name, fp, pathname, description) 2783: File "/Users/sansomk/build/ITK/build/lib/ITKCommonPython.py", line 32, in 2783: _ITKCommonPython = swig_import_helper() 2783: File "/Users/sansomk/build/ITK/build/lib/ITKCommonPython.py", line 28, in swig_import_helper 2783: _mod = imp.load_module('_ITKCommonPython', fp, pathname, description) 2783: ImportError: dlopen(/Users/sansomk/build/ITK/build/lib/_ITKCommonPython.so, 2): Library not loaded: libvtkRenderingAnnotation-7.0.1.dylib 2783: Referenced from: /Users/sansomk/build/ITK/build/lib/_ITKCommonPython.so 2783: Reason: image not found 2783: itkTestDriver: Process exited with return value: 1 74/74 Test #2783: DicomSliceReadPythonTest ..................................***Failed 0.60 sec Does -- Kurt Sansom -------------- next part -------------- An HTML attachment was scrubbed... URL: From franciscolopezdelafranca at gmail.com Mon Feb 22 07:18:06 2016 From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca) Date: Mon, 22 Feb 2016 13:18:06 +0100 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <3F877AC4-BCD1-43FF-B8B3-7B30F9B6D30B@mail.nih.gov> Message-ID: Hi. In the end the crash came for my fault. I was creating the mask image in the wrong way. Sorry for the disturbances, and thank you very much everybody. Kind regards. /Francisco 2016-02-18 19:00 GMT+01:00 dzenanz [via ITK Insight Users] < ml-node+s2283740n7588516h31 at n2.nabble.com>: > /bigobj is an option for msvc, not mingw. > > But that is a different problem from crashing code. If you start a new > thread, somebody with MinGW experience might help you. > > On Thu, Feb 18, 2016 at 12:30 PM, Francisco Lopez de la Franca <[hidden > email] > wrote: > >> Yes. I use mingw (x86_64-w64-mingw32-g++.exe) and I set in CMAKE GUI the >> entry CMAKE_CXX_FLAGS to -bigobj and the result is "unrecognized option". >> >> >> 2016-02-18 15:25 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >> email] >: >> >>> Have you tried /bigobj >>> ? >>> Are you using MinGW? Visual Studio is now free >>> . >>> >>> HTH >>> >>> On Thu, Feb 18, 2016 at 6:37 AM, Francisco Lopez de la Franca <[hidden >>> email] > wrote: >>> >>>> Hi again, >>>> I've got ITK version 4.5.1 (a little bit old, I know), and after making >>>> the changes suggested by Dzenanz and recompiling ITK, the problem >>>> continues, that is, my code crashes at the same point. >>>> >>>> Then, I've downloaded the latest stable ITK version, ITK 4.9.0 and >>>> compiled from scratch and I get the following error: >>>> >>>> [ 98%] Building CXX object >>>> Modules/IO/TransformBase/src/CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.obj >>>> C:/MINGW/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: >>>> CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: too many >>>> sections (33106) >>>> C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Assembler messages: >>>> C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Fatal error: can't write >>>> CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: File too >>>> big >>>> >>>> After doing some "googling" and follow some of the instructions >>>> referred on the web, I've been unable to solve this. >>>> Has anyone met this problem and solved it? >>>> Thanks. >>>> KR. >>>> /Francisco >>>> >>>> 2016-02-16 22:13 GMT+01:00 Bradley Lowekamp [via ITK Insight Users] <[hidden >>>> email] >: >>>> >>>>> Hello, >>>>> >>>>> Please take a look at these changes: >>>>> >>>>> https://github.com/blowekamp/itkTextureAnalysis/commit/9654d74ea1d09f0677f1d1b93242cc94340591bf >>>>> >>>>> Brad >>>>> >>>>> On Feb 16, 2016, at 10:35 AM, D?enan Zuki? <[hidden email] >>>>> > wrote: >>>>> >>>>> I have set up a project using one of the tests from Brad's repository >>>>> (attached), and it works in debug mode both with his original code and with >>>>> your modified class, and crashes in release mode both with his original >>>>> code and with your modified class. I will now compile ITK in RelWithDebInfo >>>>> in an attempt to figure out where is the crash occurring. >>>>> >>>>> Regards, >>>>> D?enan >>>>> >>>>> On Tue, Feb 16, 2016 at 1:52 AM, Francisco Lopez de la Franca <[hidden >>>>> email] > wrote: >>>>> >>>>>> Excuse me Dzenanz, but that's not completely true, because I've >>>>>> tested Brad's class and it works right. >>>>>> The problem seems to be that when you add a new neighbor iterator to >>>>>> include just the mask points in the "histogram" then it is when the >>>>>> application crashes, and I donot understand why. >>>>>> If you just comment the 'maskIter' references you'll see that the >>>>>> application works. >>>>>> I've created a single threaded class based on the Brad's code and it >>>>>> works but it is twice slower, that is why I'm interesting on Brad's class >>>>>> (multi-threaded) to make it work. >>>>>> >>>>>> >>>>>> 2016-02-15 17:15 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>>>> email] >: >>>>>> >>>>>>> Hi Francisco, >>>>>>> >>>>>>> both your code and Brad's code run in debug mode (I did not wait for >>>>>>> the end), and both crash in release mode immediately on startup. Here is a >>>>>>> sample output: >>>>>>> >>>>>>> Progress input: 0000000002868970 >>>>>>> input: 0000000002868970 >>>>>>> _maskImage: 0000000002868970 >>>>>>> _maskImage: 0000000002868970 >>>>>>> input: 0000000002868970 >>>>>>> _maskImage: 0000000002868970 >>>>>>> iter.first: iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>>> [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>>> niter index: [5, 5, 210] >>>>>>> niter index: [5, 5, 140] >>>>>>> maskIter index: [5, 5, 140] >>>>>>> maskIter index: [5, 5, 210] >>>>>>> Before p3 >>>>>>> input: 0000000002868970 >>>>>>> _maskImage: 0000000002868970 >>>>>>> After p3: | 0niter index: [5, 5, 70] >>>>>>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>>> niter index: [5, 5, 5] >>>>>>> ? >>>>>>> maskIter index: [5, 5, 70] >>>>>>> After p4: ? >>>>>>> Before p3 >>>>>>> Before p3 >>>>>>> After p3: ?iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>>>> niter index: [5, 5, 140] >>>>>>> maskIter index: [5, 5, 140] >>>>>>> maskIter index: [5, 5, 5] >>>>>>> Before p3 >>>>>>> After p3: ? >>>>>>> After p3: ? >>>>>>> After p4: ? >>>>>>> After p4: ? >>>>>>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>>>> niter index: [5, 5, 5] >>>>>>> maskIter index: [5, 5, 5] >>>>>>> >>>>>>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>>>> Before p3 >>>>>>> Before p3 >>>>>>> After p4: ? >>>>>>> After p3: ? >>>>>>> After p4: ? >>>>>>> >>>>>>> Regards, >>>>>>> D?enan >>>>>>> >>>>>>> On Mon, Feb 15, 2016 at 1:36 AM, Francisco Lopez de la Franca <[hidden >>>>>>> email] > >>>>>>> wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> Here they are. >>>>>>>> KR. >>>>>>>> >>>>>>>> 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>>>>>> email] >: >>>>>>>> >>>>>>>>> Hi Francisco, >>>>>>>>> >>>>>>>>> do you mind attaching the modified files or pointing to your fork >>>>>>>>> of it on GitHub? >>>>>>>>> >>>>>>>>> Regards >>>>>>>>> >>>>>>>>> On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden >>>>>>>>> email] > >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Hi Dzenan, >>>>>>>>>> The original class is here: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >>>>>>>>>> >>>>>>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >>>>>>>>>> >>>>>>>>>> I've just added setInput and setMaskImage methods and modify some >>>>>>>>>> lines in >>>>>>>>>> the original class as I indicated in the yesterday mail within >>>>>>>>>> this thread. >>>>>>>>>> I'm running it on Windows, and there is no error at all, just a >>>>>>>>>> crash. I >>>>>>>>>> may have to include exceptions management. >>>>>>>>>> The crash occurs just when calling p3 = >>>>>>>>>> maskIter.GetPixel(iter->first) >>>>>>>>>> >>>>>>>>>> If you know why it could be or if you need more clarification, >>>>>>>>>> please let >>>>>>>>>> me know. >>>>>>>>>> Many thanks >>>>>>>>>> >>>>>>>>>> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >>>>>>>>>> [hidden email] >>>>>>>>>> >: >>>>>>>>>> >>>>>>>>>> > Hi Francisco, >>>>>>>>>> > >>>>>>>>>> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the >>>>>>>>>> error message >>>>>>>>>> > that goes along with the crash? In which file and line does it >>>>>>>>>> crash? >>>>>>>>>> > >>>>>>>>>> > Regards >>>>>>>>>> > >>>>>>>>>> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca >>>>>>>>>> <[hidden >>>>>>>>>> > email] > >>>>>>>>>> wrote: >>>>>>>>>> > >>>>>>>>>> >> Hi, >>>>>>>>>> >> Please, someone that could help me. I'm working in a >>>>>>>>>> pre-doctorate >>>>>>>>>> >> project and I need this class to work. >>>>>>>>>> >> I've read the chapter 13 in the ITK Software Guide on how to >>>>>>>>>> write a >>>>>>>>>> >> filter and now I see the fact of the threads due to >>>>>>>>>> inheritance of >>>>>>>>>> >> ImageToImageFilter. >>>>>>>>>> >> But, I keep on without understanding why the code crashes just >>>>>>>>>> when >>>>>>>>>> >> calling >>>>>>>>>> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >>>>>>>>>> >> It is just a call to read data, not to write. >>>>>>>>>> >> >>>>>>>>>> >> I guess somebody that had worked with creation of filters >>>>>>>>>> might see >>>>>>>>>> >> "easily" the problem, but not me. >>>>>>>>>> >> >>>>>>>>>> >> So, again, please, I need someone to help me with this because >>>>>>>>>> I'm stuck >>>>>>>>>> >> on this point. >>>>>>>>>> >> >>>>>>>>>> >> Thank you very much. >>>>>>>>>> >> KR. >>>>>>>>>> >> /Francisco >>>>>>>>>> >> >>>>>>>>>> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca >>>>>>>>>> <[hidden email] >>>>>>>>>> >> >: >>>>>>>>>> >> >>>>>>>>>> >>> Hi Bradley again. >>>>>>>>>> >>> I'm modifying your class in order to be able to set a mask >>>>>>>>>> image (a >>>>>>>>>> >>> binary image) to be used as a limit in the histogram >>>>>>>>>> calculations, I mean, >>>>>>>>>> >>> I set an input, a mask and the class should take into account >>>>>>>>>> to calculate >>>>>>>>>> >>> the histograms only the voxels that belong to the input and >>>>>>>>>> to the mask >>>>>>>>>> >>> image and having the value 1 in the mask image. >>>>>>>>>> >>> The changes seem to be easy but I don?t know why my tests are >>>>>>>>>> not >>>>>>>>>> >>> working. It seems that 2 threads are working at the same time >>>>>>>>>> and when I >>>>>>>>>> >>> added my mask iterator, the code crashes. >>>>>>>>>> >>> >>>>>>>>>> >>> *** Consider that the input and mask images are the same >>>>>>>>>> origin, spacing >>>>>>>>>> >>> and size. >>>>>>>>>> >>> >>>>>>>>>> >>> I attach the main changes I've done, and I would thank you a >>>>>>>>>> lot if you >>>>>>>>>> >>> don't mind having a look and help me to find what I'm doing >>>>>>>>>> wrong: >>>>>>>>>> >>> >>>>>>>>>> >>> template< class TImageType, class TOutputImage > >>>>>>>>>> >>> void >>>>>>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>>>>>> >::*SetInput*(InputImageType >>>>>>>>>> >>> *image) >>>>>>>>>> >>> { >>>>>>>>>> >>> // Process object is not const-correct so the const_cast is >>>>>>>>>> required >>>>>>>>>> >>> here >>>>>>>>>> >>> this->ProcessObject::SetNthInput( 0, >>>>>>>>>> >>> const_cast< >>>>>>>>>> InputImageType * >( >>>>>>>>>> >>> image ) ); >>>>>>>>>> >>> } >>>>>>>>>> >>> >>>>>>>>>> >>> template< class TImageType, class TOutputImage > >>>>>>>>>> >>> void >>>>>>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>>>>>> >::*SetMaskImage*(InputImageType >>>>>>>>>> >>> *image) >>>>>>>>>> >>> { >>>>>>>>>> >>> // Process object is not const-correct so the const_cast is >>>>>>>>>> required >>>>>>>>>> >>> here >>>>>>>>>> >>> this->ProcessObject::SetNthInput( 1, const_cast< >>>>>>>>>> InputImageType * >( >>>>>>>>>> >>> image ) ); >>>>>>>>>> >>> >>>>>>>>>> >>> _maskImage = image; // _maskImage is a private member >>>>>>>>>> >>> } >>>>>>>>>> >>> >>>>>>>>>> >>> In the *ThreadedGenerateData*(const RegionType& >>>>>>>>>> outputRegionForThread, >>>>>>>>>> >>> ThreadIdType threadId ) method: >>>>>>>>>> >>> { >>>>>>>>>> >>> >>>>>>>>>> >>> ... >>>>>>>>>> >>> >>>>>>>>>> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >>>>>>>>>> >>> { >>>>>>>>>> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >>>>>>>>>> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, >>>>>>>>>> *fit);* >>>>>>>>>> >>> OutputIterator outIter(output, *fit); >>>>>>>>>> >>> >>>>>>>>>> >>> OutputPixelType out; >>>>>>>>>> >>> NumericTraits::SetLength( out, >>>>>>>>>> >>> this->GetNumberOfOutputComponents() ); >>>>>>>>>> >>> >>>>>>>>>> >>> while( !nIter.IsAtEnd() ) >>>>>>>>>> >>> { >>>>>>>>>> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >>>>>>>>>> >>> >>>>>>>>>> >>> ... >>>>>>>>>> >>> >>>>>>>>>> >>> ++nIter; >>>>>>>>>> >>> ++outIter; >>>>>>>>>> >>> * ++maskIter;* >>>>>>>>>> >>> ... >>>>>>>>>> >>> >>>>>>>>>> >>> In the *FillHistogram *method: >>>>>>>>>> >>> { >>>>>>>>>> >>> >>>>>>>>>> >>> ... >>>>>>>>>> >>> >>>>>>>>>> >>> while( iter != m_CooccurenceOffsetVector.end() ) >>>>>>>>>> >>> { >>>>>>>>>> >>> >>>>>>>>>> >>> const PixelType p1 = niter.GetPixel(iter->first); >>>>>>>>>> >>> const PixelType p2 = niter.GetPixel(iter->second); >>>>>>>>>> >>> std::cout << "Before p3" << std::endl; >>>>>>>>>> >>> >>>>>>>>>> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); >>>>>>>>>> *std::cout >>>>>>>>>> >>> << "After p3: " << p3 << std::endl; >>>>>>>>>> >>> >>>>>>>>>> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >>>>>>>>>> >>> std::cout << "After p4: " << p4 << std::endl; >>>>>>>>>> >>> >>>>>>>>>> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 >>>>>>>>>> <= m_Max >>>>>>>>>> >>> *&& p3 == _insidePixelValue && p4 == >>>>>>>>>> _insidePixelValue* ) >>>>>>>>>> >>> // The point >>>>>>>>>> >>> { >>>>>>>>>> >>> >>>>>>>>>> >>> ... >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >>>>>>>>>> >>> >>>>>>>>>> >>> Thank you so much. >>>>>>>>>> >>> My kind regards. >>>>>>>>>> >>> /Paco >>>>>>>>>> >>> >>>>>>>>>> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca >>>>>>>>>> <[hidden email] >>>>>>>>>> >>> >: >>>>>>>>>> >>> >>>>>>>>>> >>>> Hello Bradley again. >>>>>>>>>> >>>> Sorry but I'd like to re-open this issue because I need your >>>>>>>>>> class but >>>>>>>>>> >>>> with some modification. >>>>>>>>>> >>>> I pass to tell you. >>>>>>>>>> >>>> >>>>>>>>>> >>>> As my tests with your external class were not good taking >>>>>>>>>> into account >>>>>>>>>> >>>> the performance, I wonder if you could create a variant of >>>>>>>>>> it, but in which >>>>>>>>>> >>>> I can set a mask image and your class just return the >>>>>>>>>> VectorImage with all >>>>>>>>>> >>>> the features for that region (the masked locations) as >>>>>>>>>> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >>>>>>>>>> >>>> I mean, to get the vector image with all the features but >>>>>>>>>> just >>>>>>>>>> >>>> calculate it for the regions belonging to the mask image. >>>>>>>>>> Positions not >>>>>>>>>> >>>> belonging to the mask region could have a pixel value of 0, >>>>>>>>>> for instance. >>>>>>>>>> >>>> >>>>>>>>>> >>>> I don?t know if it is very costly for you, but I would >>>>>>>>>> thank you so >>>>>>>>>> >>>> much. Otherwise, I could try it but I'd need your >>>>>>>>>> suggestions on how to do >>>>>>>>>> >>>> it. >>>>>>>>>> >>>> >>>>>>>>>> >>>> Thanks a lot. >>>>>>>>>> >>>> Best regards. >>>>>>>>>> >>>> >>>>>>>>>> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca >>>>>>>>>> <[hidden email] >>>>>>>>>> >>>> >: >>>>>>>>>> >>>> >>>>>>>>>> >>>>> Hello Bradley again, >>>>>>>>>> >>>>> I would like to ask you for a couple of favours. In the one >>>>>>>>>> hand, >>>>>>>>>> >>>>> could you please send me your 3D image so that I can test >>>>>>>>>> on it? And on the >>>>>>>>>> >>>>> other hand, could you test the example I have referenced in >>>>>>>>>> the previous >>>>>>>>>> >>>>> email with your image, not changing anything in the code, >>>>>>>>>> such as it is, >>>>>>>>>> >>>>> and tell me if the execution time is normal? >>>>>>>>>> >>>>> Thank you very much. >>>>>>>>>> >>>>> Regards, >>>>>>>>>> >>>>> /Francisco >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> PS: All my application trace is printed via standard 'cout' >>>>>>>>>> command, >>>>>>>>>> >>>>> not due to a debugging compilation mode. >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp >>>>>>>>>> <[hidden >>>>>>>>>> >>>>> email] < >>>>>>>>>> http:///user/SendEmail.jtp?type=node&node=7588477&i=4>> >>>>>>>>>> >>>>> escribi?: >>>>>>>>>> >>>>> >>>>>>>>>> >>>>>> Hello, >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Did you compile TextureFeatureImage in Release mode? >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> 1) The filter does not scale well with a large radius. And >>>>>>>>>> given by >>>>>>>>>> >>>>>> your initial report of print a very large number of offset >>>>>>>>>> you, it sounds >>>>>>>>>> >>>>>> like you are using a large radius with many offsets. I >>>>>>>>>> created a >>>>>>>>>> >>>>>> 224x224x300 unsigned short image and ran with the default >>>>>>>>>> offset and a >>>>>>>>>> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this >>>>>>>>>> filter is was ~10x >>>>>>>>>> >>>>>> faster than this example... things change though... >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> 2) I sounds like the boundaries/limits of the histogram >>>>>>>>>> may be >>>>>>>>>> >>>>>> clipping you values. I would inspect the co-occurance >>>>>>>>>> matrix. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> HTH, >>>>>>>>>> >>>>>> Brad >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca >>>>>>>>>> <[hidden >>>>>>>>>> >>>>>> email] < >>>>>>>>>> http:///user/SendEmail.jtp?type=node&node=7588477&i=5>> >>>>>>>>>> >>>>>> wrote: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> I've tested with itkTextureFeatureImageFilter, with >>>>>>>>>> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>>>>>>>> >>>>>> >>>>>>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures >>>>>>>>>> example, >>>>>>>>>> >>>>>> for a 3D image and here are my comments: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> 1. I had to interrupt the test after several hours and it >>>>>>>>>> kept on >>>>>>>>>> >>>>>> calculating. And this is for only a 3D image >>>>>>>>>> (224x224x300). I need to >>>>>>>>>> >>>>>> process around 35 images. >>>>>>>>>> >>>>>> 2. The result (texture features: entropy, energy, >>>>>>>>>> correlation, LH, >>>>>>>>>> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, >>>>>>>>>> 0, 7.83083e+247]. >>>>>>>>>> >>>>>> These values were not what I expected based on my >>>>>>>>>> experience on another >>>>>>>>>> >>>>>> application I developed, but in that case, I calculated >>>>>>>>>> the texture >>>>>>>>>> >>>>>> features for an image as a whole, not voxel by voxel. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Regards. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >>>>>>>>>> >>>>>> >: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>>> i yes i have tried radius = 3; >>>>>>>>>> >>>>>>> still no luck >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca >>>>>>>>>> [via ITK >>>>>>>>>> >>>>>>> Insight >>>>>>>>>> >>>>>>> Users] <[hidden email] >>>>>>>>>> >>>>>>> > >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> > Have you tried with a radius of 3 instead of 1? >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>>>>>>>> >>>>>>> > >>>>>>>>> >>: >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> >> hey Matt, >>>>>>>>>> >>>>>>> >> thanks for ur advice.. it did build successfully... >>>>>>>>>> but im not >>>>>>>>>> >>>>>>> able to run >>>>>>>>>> >>>>>>> >> the code for 2D png image... i tried to change the >>>>>>>>>> dimension to 2 >>>>>>>>>> >>>>>>> and >>>>>>>>>> >>>>>>> >> build >>>>>>>>>> >>>>>>> >> it which it did.. but when i run the code using the >>>>>>>>>> command >>>>>>>>>> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png >>>>>>>>>> putput.png >>>>>>>>>> >>>>>>> 1... i see >>>>>>>>>> >>>>>>> >> this output >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> offset: [-1, -1] [0, -1] >>>>>>>>>> >>>>>>> >> offset: [0, -1] [1, -1] >>>>>>>>>> >>>>>>> >> offset: [-1, 0] [0, 0] >>>>>>>>>> >>>>>>> >> offset: [0, 0] [1, 0] >>>>>>>>>> >>>>>>> >> offset: [-1, 1] [0, 1] >>>>>>>>>> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the >>>>>>>>>> program... if pls >>>>>>>>>> >>>>>>> tel me >>>>>>>>>> >>>>>>> >> how can i modify this code to work wid 2d image... >>>>>>>>>> forgive me if >>>>>>>>>> >>>>>>> my ques >>>>>>>>>> >>>>>>> >> are really silly im trying to learn something.. >>>>>>>>>> >>>>>>> >> regards >>>>>>>>>> >>>>>>> >> Vis >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via >>>>>>>>>> ITK >>>>>>>>>> >>>>>>> Insight Users] >>>>>>>>>> >>>>>>> >> < >>>>>>>>>> >>>>>>> >> [hidden email] < >>>>>>>>>> >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> > Hi, >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > The function: >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char >>>>>>>>>> *argv[]) >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > must be renamed to >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > main(int argc, char* argv[]) >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > HTH, >>>>>>>>>> >>>>>>> >> > Matt >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>>>>>>>> >>>>>>> >> > < >>>>>>>>>> http:///user/SendEmail.jtp?type=node&node=7587952&i=0>> wrote: >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > > hi all, >>>>>>>>>> >>>>>>> >> > > im trying to build the >>>>>>>>>> itkTextureFeatureImageFilterTest.cxx >>>>>>>>>> >>>>>>> code but >>>>>>>>>> >>>>>>> >> im >>>>>>>>>> >>>>>>> >> > not >>>>>>>>>> >>>>>>> >> > > able to it is showing the following error >>>>>>>>>> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>>>>>>>> >>>>>>> Configuration: >>>>>>>>>> >>>>>>> >> Debug >>>>>>>>>> >>>>>>> >> > x64 >>>>>>>>>> >>>>>>> >> > > ------ >>>>>>>>>> >>>>>>> >> > > 1> Checking Build System >>>>>>>>>> >>>>>>> >> > > 1> CMake does not need to re-run because >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>>>>>>>> >>>>>>> >> > is >>>>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>>>> >>>>>>> >> > > 2>------ Rebuild All started: Project: >>>>>>>>>> >>>>>>> >> itkTextureFeatureImageFilterTest, >>>>>>>>>> >>>>>>> >> > > Configuration: Debug x64 ------ >>>>>>>>>> >>>>>>> >> > > 2> Building Custom Rule >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>>>>> >>>>>>> >> > > 2> CMake does not need to re-run because >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >>>>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>>>>> >>>>>>> >> > is >>>>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>>>> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>>>>>>>> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>>>>>>>> >>>>>>> 'std::_Copy_impl': >>>>>>>>>> >>>>>>> >> > Function >>>>>>>>>> >>>>>>> >> > > call with parameters that may be unsafe - this >>>>>>>>>> call relies on >>>>>>>>>> >>>>>>> the >>>>>>>>>> >>>>>>> >> caller >>>>>>>>>> >>>>>>> >> > to >>>>>>>>>> >>>>>>> >> > > check that the passed values are correct. To >>>>>>>>>> disable this >>>>>>>>>> >>>>>>> warning, use >>>>>>>>>> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on >>>>>>>>>> how to use >>>>>>>>>> >>>>>>> Visual C++ >>>>>>>>>> >>>>>>> >> > > 'Checked Iterators' >>>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft >>>>>>>>>> Visual Studio >>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>>> >>>>>>> >> > > 2> >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>>>>>>>> >>>>>>> >> > see >>>>>>>>>> >>>>>>> >> > > reference to function template instantiation >>>>>>>>>> '_OutIt >>>>>>>>>> >>>>>>> std::copy>>>>>>>>> >>>>>>> >> > > unsigned char*,unsigned >>>>>>>>>> char*>(_InIt,_InIt,_OutIt)' being >>>>>>>>>> >>>>>>> compiled >>>>>>>>>> >>>>>>> >> > > 2> with >>>>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>>>> >>>>>>> >> > > 2> _OutIt=unsigned char *, >>>>>>>>>> >>>>>>> >> > > 2> _InIt=const unsigned char * >>>>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>>>> >>>>>>> >> > > 2> >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>>>>>>>> >>>>>>> >> > > while compiling class template member function >>>>>>>>>> 'void >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> itk::ImageFileReader::GenerateData(void)' >>>>>>>>>> >>>>>>> >> > > 2> with >>>>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>>>> >>>>>>> >> > > 2> >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > > : see reference to class template instantiation >>>>>>>>>> >>>>>>> >> > > 'itk::ImageFileReader' being compiled >>>>>>>>>> >>>>>>> >> > > 2> with >>>>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft >>>>>>>>>> Visual Studio >>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft >>>>>>>>>> Visual Studio >>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft >>>>>>>>>> Visual Studio >>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>>> >>>>>>> >> > > 2> Creating library >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > > and object >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: >>>>>>>>>> unresolved >>>>>>>>>> >>>>>>> external symbol >>>>>>>>>> >>>>>>> >> > main >>>>>>>>>> >>>>>>> >> > > referenced in function __tmainCRTStartup >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>>>>>>>> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>>>>>>>> >>>>>>> Configuration: Debug >>>>>>>>>> >>>>>>> >> > x64 >>>>>>>>>> >>>>>>> >> > > ------ >>>>>>>>>> >>>>>>> >> > > 3> Building Custom Rule >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>>>>> >>>>>>> >> > > 3> CMake does not need to re-run because >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >>>>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>>>>> >>>>>>> >> > is >>>>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>>>> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 >>>>>>>>>> skipped >>>>>>>>>> >>>>>>> ========== >>>>>>>>>> >>>>>>> >> > > im using the follwing CMakeList.txt >>>>>>>>>> >>>>>>> >> > > # This is the root ITK CMakeLists file. >>>>>>>>>> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>>>>>>>> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >>>>>>>>>> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>>>>>>>> >>>>>>> >> > > endif() >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > # This project is designed to be built outside the >>>>>>>>>> Insight >>>>>>>>>> >>>>>>> source >>>>>>>>>> >>>>>>> >> tree. >>>>>>>>>> >>>>>>> >> > > project(HelloWorld) >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > # Find ITK. >>>>>>>>>> >>>>>>> >> > > find_package(ITK REQUIRED) >>>>>>>>>> >>>>>>> >> > > include(${ITK_USE_FILE}) >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>>>>>>>> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> target_link_libraries(itkTextureFeatureImageFilterTest >>>>>>>>>> >>>>>>> >> ${ITK_LIBRARIES}) >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > please tel me wat the error is?? >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > -- >>>>>>>>>> >>>>>>> >> > > View this message in context: >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>>>>>>>> >>>>>>> >> > > Sent from the ITK Insight Users mailing list >>>>>>>>>> archive at >>>>>>>>>> >>>>>>> Nabble.com . >>>>>>>>>> >>>>>>> >> > > _____________________________________ >>>>>>>>>> >>>>>>> >> > > Powered by www.kitware.com >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > Visit other Kitware open-source projects at >>>>>>>>>> >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > Kitware offers ITK Training Courses, for more >>>>>>>>>> information >>>>>>>>>> >>>>>>> visit: >>>>>>>>>> >>>>>>> >> > > http://www.kitware.com/products/protraining.php >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > Please keep messages on-topic and check the ITK >>>>>>>>>> FAQ at: >>>>>>>>>> >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > Follow this link to subscribe/unsubscribe: >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>> >>>>>>> >> > _____________________________________ >>>>>>>>>> >>>>>>> >> > Powered by www.kitware.com >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > Visit other Kitware open-source projects at >>>>>>>>>> >>>>>>> >> > http://www.kitware.com/opensource/opensource.html >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > Kitware offers ITK Training Courses, for more >>>>>>>>>> information visit: >>>>>>>>>> >>>>>>> >> > http://www.kitware.com/products/protraining.php >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > Please keep messages on-topic and check the ITK FAQ >>>>>>>>>> at: >>>>>>>>>> >>>>>>> >> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > Follow this link to subscribe/unsubscribe: >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > ------------------------------ >>>>>>>>>> >>>>>>> >> > If you reply to this email, your message will be >>>>>>>>>> added to the >>>>>>>>>> >>>>>>> discussion >>>>>>>>>> >>>>>>> >> > below: >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587952.html >>>>>>>>>> >>>>>>> >> > To unsubscribe from [ITK-users] Texture pixel by >>>>>>>>>> pixel, click >>>>>>>>>> >>>>>>> here >>>>>>>>>> >>>>>>> >> > < > . >>>>>>>>>> >>>>>>> >> > NAML >>>>>>>>>> >>>>>>> >> > < >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> -- >>>>>>>>>> >>>>>>> >> View this message in context: >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587960.html >>>>>>>>>> >>>>>>> >> Sent from the ITK Insight Users mailing list archive at >>>>>>>>>> >>>>>>> Nabble.com . >>>>>>>>>> >>>>>>> >> _____________________________________ >>>>>>>>>> >>>>>>> >> Powered by www.kitware.com >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Visit other Kitware open-source projects at >>>>>>>>>> >>>>>>> >> http://www.kitware.com/opensource/opensource.html >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Kitware offers ITK Training Courses, for more >>>>>>>>>> information visit: >>>>>>>>>> >>>>>>> >> http://www.kitware.com/products/protraining.php >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>> >>>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Follow this link to subscribe/unsubscribe: >>>>>>>>>> >>>>>>> >> >>>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > _____________________________________ >>>>>>>>>> >>>>>>> > Powered by www.kitware.com >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > Visit other Kitware open-source projects at >>>>>>>>>> >>>>>>> > http://www.kitware.com/opensource/opensource.html >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > Kitware offers ITK Training Courses, for more >>>>>>>>>> information visit: >>>>>>>>>> >>>>>>> > http://www.kitware.com/products/protraining.php >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>> >>>>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > Follow this link to subscribe/unsubscribe: >>>>>>>>>> >>>>>>> > >>>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > ------------------------------ >>>>>>>>>> >>>>>>> > If you reply to this email, your message will be added >>>>>>>>>> to the >>>>>>>>>> >>>>>>> discussion >>>>>>>>>> >>>>>>> > below: >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> >>>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587961.html >>>>>>>>>> >>>>>>> > To unsubscribe from [ITK-users] Texture pixel by pixel, >>>>>>>>>> click here >>>>>>>>>> >>>>>>> > < > . >>>>>>>>>> >>>>>>> > NAML >>>>>>>>>> >>>>>>> > < >>>>>>>>>> >>>>>>> >>>>>>>>>> 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visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588516.html > To start a new topic under ITK Insight Users, email > ml-node+s2283740n2283740h75 at n2.nabble.com > To unsubscribe from ITK Insight Users, click here > > . > NAML > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Mon Feb 22 07:18:33 2016 From: franciscolopezdelafranca at gmail.com (=?UTF-8?Q?Francisco_L=C3=B3pez-Franca?=) Date: Mon, 22 Feb 2016 05:18:33 -0700 (MST) Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <3F877AC4-BCD1-43FF-B8B3-7B30F9B6D30B@mail.nih.gov> Message-ID: Hi. In the end the crash came for my fault. I was creating the mask image in the wrong way. Sorry for the disturbances, and thank you very much everybody. Kind regards. /Francisco 2016-02-18 19:00 GMT+01:00 dzenanz [via ITK Insight Users] < ml-node+s2283740n7588516h31 at n2.nabble.com>: > /bigobj is an option for msvc, not mingw. > > But that is a different problem from crashing code. If you start a new > thread, somebody with MinGW experience might help you. > > On Thu, Feb 18, 2016 at 12:30 PM, Francisco Lopez de la Franca <[hidden > email] > wrote: > >> Yes. I use mingw (x86_64-w64-mingw32-g++.exe) and I set in CMAKE GUI the >> entry CMAKE_CXX_FLAGS to -bigobj and the result is "unrecognized option". >> >> >> 2016-02-18 15:25 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >> email] >: >> >>> Have you tried /bigobj >>> ? >>> Are you using MinGW? Visual Studio is now free >>> . >>> >>> HTH >>> >>> On Thu, Feb 18, 2016 at 6:37 AM, Francisco Lopez de la Franca <[hidden >>> email] > wrote: >>> >>>> Hi again, >>>> I've got ITK version 4.5.1 (a little bit old, I know), and after making >>>> the changes suggested by Dzenanz and recompiling ITK, the problem >>>> continues, that is, my code crashes at the same point. >>>> >>>> Then, I've downloaded the latest stable ITK version, ITK 4.9.0 and >>>> compiled from scratch and I get the following error: >>>> >>>> [ 98%] Building CXX object >>>> Modules/IO/TransformBase/src/CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.obj >>>> C:/MINGW/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: >>>> CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: too many >>>> sections (33106) >>>> C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Assembler messages: >>>> C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Fatal error: can't write >>>> CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: File too >>>> big >>>> >>>> After doing some "googling" and follow some of the instructions >>>> referred on the web, I've been unable to solve this. >>>> Has anyone met this problem and solved it? >>>> Thanks. >>>> KR. >>>> /Francisco >>>> >>>> 2016-02-16 22:13 GMT+01:00 Bradley Lowekamp [via ITK Insight Users] <[hidden >>>> email] >: >>>> >>>>> Hello, >>>>> >>>>> Please take a look at these changes: >>>>> >>>>> https://github.com/blowekamp/itkTextureAnalysis/commit/9654d74ea1d09f0677f1d1b93242cc94340591bf >>>>> >>>>> Brad >>>>> >>>>> On Feb 16, 2016, at 10:35 AM, D?enan Zuki? <[hidden email] >>>>> > wrote: >>>>> >>>>> I have set up a project using one of the tests from Brad's repository >>>>> (attached), and it works in debug mode both with his original code and with >>>>> your modified class, and crashes in release mode both with his original >>>>> code and with your modified class. I will now compile ITK in RelWithDebInfo >>>>> in an attempt to figure out where is the crash occurring. >>>>> >>>>> Regards, >>>>> D?enan >>>>> >>>>> On Tue, Feb 16, 2016 at 1:52 AM, Francisco Lopez de la Franca <[hidden >>>>> email] > wrote: >>>>> >>>>>> Excuse me Dzenanz, but that's not completely true, because I've >>>>>> tested Brad's class and it works right. >>>>>> The problem seems to be that when you add a new neighbor iterator to >>>>>> include just the mask points in the "histogram" then it is when the >>>>>> application crashes, and I donot understand why. >>>>>> If you just comment the 'maskIter' references you'll see that the >>>>>> application works. >>>>>> I've created a single threaded class based on the Brad's code and it >>>>>> works but it is twice slower, that is why I'm interesting on Brad's class >>>>>> (multi-threaded) to make it work. >>>>>> >>>>>> >>>>>> 2016-02-15 17:15 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>>>> email] >: >>>>>> >>>>>>> Hi Francisco, >>>>>>> >>>>>>> both your code and Brad's code run in debug mode (I did not wait for >>>>>>> the end), and both crash in release mode immediately on startup. Here is a >>>>>>> sample output: >>>>>>> >>>>>>> Progress input: 0000000002868970 >>>>>>> input: 0000000002868970 >>>>>>> _maskImage: 0000000002868970 >>>>>>> _maskImage: 0000000002868970 >>>>>>> input: 0000000002868970 >>>>>>> _maskImage: 0000000002868970 >>>>>>> iter.first: iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>>> [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>>> niter index: [5, 5, 210] >>>>>>> niter index: [5, 5, 140] >>>>>>> maskIter index: [5, 5, 140] >>>>>>> maskIter index: [5, 5, 210] >>>>>>> Before p3 >>>>>>> input: 0000000002868970 >>>>>>> _maskImage: 0000000002868970 >>>>>>> After p3: | 0niter index: [5, 5, 70] >>>>>>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>>> niter index: [5, 5, 5] >>>>>>> ? >>>>>>> maskIter index: [5, 5, 70] >>>>>>> After p4: ? >>>>>>> Before p3 >>>>>>> Before p3 >>>>>>> After p3: ?iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>>>> niter index: [5, 5, 140] >>>>>>> maskIter index: [5, 5, 140] >>>>>>> maskIter index: [5, 5, 5] >>>>>>> Before p3 >>>>>>> After p3: ? >>>>>>> After p3: ? >>>>>>> After p4: ? >>>>>>> After p4: ? >>>>>>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>>>> niter index: [5, 5, 5] >>>>>>> maskIter index: [5, 5, 5] >>>>>>> >>>>>>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>>>> Before p3 >>>>>>> Before p3 >>>>>>> After p4: ? >>>>>>> After p3: ? >>>>>>> After p4: ? >>>>>>> >>>>>>> Regards, >>>>>>> D?enan >>>>>>> >>>>>>> On Mon, Feb 15, 2016 at 1:36 AM, Francisco Lopez de la Franca <[hidden >>>>>>> email] > >>>>>>> wrote: >>>>>>> >>>>>>>> Hi, >>>>>>>> Here they are. >>>>>>>> KR. >>>>>>>> >>>>>>>> 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>>>>>> email] >: >>>>>>>> >>>>>>>>> Hi Francisco, >>>>>>>>> >>>>>>>>> do you mind attaching the modified files or pointing to your fork >>>>>>>>> of it on GitHub? >>>>>>>>> >>>>>>>>> Regards >>>>>>>>> >>>>>>>>> On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden >>>>>>>>> email] > >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Hi Dzenan, >>>>>>>>>> The original class is here: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >>>>>>>>>> >>>>>>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >>>>>>>>>> >>>>>>>>>> I've just added setInput and setMaskImage methods and modify some >>>>>>>>>> lines in >>>>>>>>>> the original class as I indicated in the yesterday mail within >>>>>>>>>> this thread. >>>>>>>>>> I'm running it on Windows, and there is no error at all, just a >>>>>>>>>> crash. I >>>>>>>>>> may have to include exceptions management. >>>>>>>>>> The crash occurs just when calling p3 = >>>>>>>>>> maskIter.GetPixel(iter->first) >>>>>>>>>> >>>>>>>>>> If you know why it could be or if you need more clarification, >>>>>>>>>> please let >>>>>>>>>> me know. >>>>>>>>>> Many thanks >>>>>>>>>> >>>>>>>>>> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >>>>>>>>>> [hidden email] >>>>>>>>>> >: >>>>>>>>>> >>>>>>>>>> > Hi Francisco, >>>>>>>>>> > >>>>>>>>>> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the >>>>>>>>>> error message >>>>>>>>>> > that goes along with the crash? In which file and line does it >>>>>>>>>> crash? >>>>>>>>>> > >>>>>>>>>> > Regards >>>>>>>>>> > >>>>>>>>>> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca >>>>>>>>>> <[hidden >>>>>>>>>> > email] > >>>>>>>>>> wrote: >>>>>>>>>> > >>>>>>>>>> >> Hi, >>>>>>>>>> >> Please, someone that could help me. I'm working in a >>>>>>>>>> pre-doctorate >>>>>>>>>> >> project and I need this class to work. >>>>>>>>>> >> I've read the chapter 13 in the ITK Software Guide on how to >>>>>>>>>> write a >>>>>>>>>> >> filter and now I see the fact of the threads due to >>>>>>>>>> inheritance of >>>>>>>>>> >> ImageToImageFilter. >>>>>>>>>> >> But, I keep on without understanding why the code crashes just >>>>>>>>>> when >>>>>>>>>> >> calling >>>>>>>>>> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >>>>>>>>>> >> It is just a call to read data, not to write. >>>>>>>>>> >> >>>>>>>>>> >> I guess somebody that had worked with creation of filters >>>>>>>>>> might see >>>>>>>>>> >> "easily" the problem, but not me. >>>>>>>>>> >> >>>>>>>>>> >> So, again, please, I need someone to help me with this because >>>>>>>>>> I'm stuck >>>>>>>>>> >> on this point. >>>>>>>>>> >> >>>>>>>>>> >> Thank you very much. >>>>>>>>>> >> KR. >>>>>>>>>> >> /Francisco >>>>>>>>>> >> >>>>>>>>>> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca >>>>>>>>>> <[hidden email] >>>>>>>>>> >> >: >>>>>>>>>> >> >>>>>>>>>> >>> Hi Bradley again. >>>>>>>>>> >>> I'm modifying your class in order to be able to set a mask >>>>>>>>>> image (a >>>>>>>>>> >>> binary image) to be used as a limit in the histogram >>>>>>>>>> calculations, I mean, >>>>>>>>>> >>> I set an input, a mask and the class should take into account >>>>>>>>>> to calculate >>>>>>>>>> >>> the histograms only the voxels that belong to the input and >>>>>>>>>> to the mask >>>>>>>>>> >>> image and having the value 1 in the mask image. >>>>>>>>>> >>> The changes seem to be easy but I don?t know why my tests are >>>>>>>>>> not >>>>>>>>>> >>> working. It seems that 2 threads are working at the same time >>>>>>>>>> and when I >>>>>>>>>> >>> added my mask iterator, the code crashes. >>>>>>>>>> >>> >>>>>>>>>> >>> *** Consider that the input and mask images are the same >>>>>>>>>> origin, spacing >>>>>>>>>> >>> and size. >>>>>>>>>> >>> >>>>>>>>>> >>> I attach the main changes I've done, and I would thank you a >>>>>>>>>> lot if you >>>>>>>>>> >>> don't mind having a look and help me to find what I'm doing >>>>>>>>>> wrong: >>>>>>>>>> >>> >>>>>>>>>> >>> template< class TImageType, class TOutputImage > >>>>>>>>>> >>> void >>>>>>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>>>>>> >::*SetInput*(InputImageType >>>>>>>>>> >>> *image) >>>>>>>>>> >>> { >>>>>>>>>> >>> // Process object is not const-correct so the const_cast is >>>>>>>>>> required >>>>>>>>>> >>> here >>>>>>>>>> >>> this->ProcessObject::SetNthInput( 0, >>>>>>>>>> >>> const_cast< >>>>>>>>>> InputImageType * >( >>>>>>>>>> >>> image ) ); >>>>>>>>>> >>> } >>>>>>>>>> >>> >>>>>>>>>> >>> template< class TImageType, class TOutputImage > >>>>>>>>>> >>> void >>>>>>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>>>>>> >::*SetMaskImage*(InputImageType >>>>>>>>>> >>> *image) >>>>>>>>>> >>> { >>>>>>>>>> >>> // Process object is not const-correct so the const_cast is >>>>>>>>>> required >>>>>>>>>> >>> here >>>>>>>>>> >>> this->ProcessObject::SetNthInput( 1, const_cast< >>>>>>>>>> InputImageType * >( >>>>>>>>>> >>> image ) ); >>>>>>>>>> >>> >>>>>>>>>> >>> _maskImage = image; // _maskImage is a private member >>>>>>>>>> >>> } >>>>>>>>>> >>> >>>>>>>>>> >>> In the *ThreadedGenerateData*(const RegionType& >>>>>>>>>> outputRegionForThread, >>>>>>>>>> >>> ThreadIdType threadId ) method: >>>>>>>>>> >>> { >>>>>>>>>> >>> >>>>>>>>>> >>> ... >>>>>>>>>> >>> >>>>>>>>>> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >>>>>>>>>> >>> { >>>>>>>>>> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >>>>>>>>>> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, >>>>>>>>>> *fit);* >>>>>>>>>> >>> OutputIterator outIter(output, *fit); >>>>>>>>>> >>> >>>>>>>>>> >>> OutputPixelType out; >>>>>>>>>> >>> NumericTraits::SetLength( out, >>>>>>>>>> >>> this->GetNumberOfOutputComponents() ); >>>>>>>>>> >>> >>>>>>>>>> >>> while( !nIter.IsAtEnd() ) >>>>>>>>>> >>> { >>>>>>>>>> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >>>>>>>>>> >>> >>>>>>>>>> >>> ... >>>>>>>>>> >>> >>>>>>>>>> >>> ++nIter; >>>>>>>>>> >>> ++outIter; >>>>>>>>>> >>> * ++maskIter;* >>>>>>>>>> >>> ... >>>>>>>>>> >>> >>>>>>>>>> >>> In the *FillHistogram *method: >>>>>>>>>> >>> { >>>>>>>>>> >>> >>>>>>>>>> >>> ... >>>>>>>>>> >>> >>>>>>>>>> >>> while( iter != m_CooccurenceOffsetVector.end() ) >>>>>>>>>> >>> { >>>>>>>>>> >>> >>>>>>>>>> >>> const PixelType p1 = niter.GetPixel(iter->first); >>>>>>>>>> >>> const PixelType p2 = niter.GetPixel(iter->second); >>>>>>>>>> >>> std::cout << "Before p3" << std::endl; >>>>>>>>>> >>> >>>>>>>>>> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); >>>>>>>>>> *std::cout >>>>>>>>>> >>> << "After p3: " << p3 << std::endl; >>>>>>>>>> >>> >>>>>>>>>> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >>>>>>>>>> >>> std::cout << "After p4: " << p4 << std::endl; >>>>>>>>>> >>> >>>>>>>>>> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 >>>>>>>>>> <= m_Max >>>>>>>>>> >>> *&& p3 == _insidePixelValue && p4 == >>>>>>>>>> _insidePixelValue* ) >>>>>>>>>> >>> // The point >>>>>>>>>> >>> { >>>>>>>>>> >>> >>>>>>>>>> >>> ... >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >>>>>>>>>> >>> >>>>>>>>>> >>> Thank you so much. >>>>>>>>>> >>> My kind regards. >>>>>>>>>> >>> /Paco >>>>>>>>>> >>> >>>>>>>>>> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca >>>>>>>>>> <[hidden email] >>>>>>>>>> >>> >: >>>>>>>>>> >>> >>>>>>>>>> >>>> Hello Bradley again. >>>>>>>>>> >>>> Sorry but I'd like to re-open this issue because I need your >>>>>>>>>> class but >>>>>>>>>> >>>> with some modification. >>>>>>>>>> >>>> I pass to tell you. >>>>>>>>>> >>>> >>>>>>>>>> >>>> As my tests with your external class were not good taking >>>>>>>>>> into account >>>>>>>>>> >>>> the performance, I wonder if you could create a variant of >>>>>>>>>> it, but in which >>>>>>>>>> >>>> I can set a mask image and your class just return the >>>>>>>>>> VectorImage with all >>>>>>>>>> >>>> the features for that region (the masked locations) as >>>>>>>>>> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >>>>>>>>>> >>>> I mean, to get the vector image with all the features but >>>>>>>>>> just >>>>>>>>>> >>>> calculate it for the regions belonging to the mask image. >>>>>>>>>> Positions not >>>>>>>>>> >>>> belonging to the mask region could have a pixel value of 0, >>>>>>>>>> for instance. >>>>>>>>>> >>>> >>>>>>>>>> >>>> I don?t know if it is very costly for you, but I would >>>>>>>>>> thank you so >>>>>>>>>> >>>> much. Otherwise, I could try it but I'd need your >>>>>>>>>> suggestions on how to do >>>>>>>>>> >>>> it. >>>>>>>>>> >>>> >>>>>>>>>> >>>> Thanks a lot. >>>>>>>>>> >>>> Best regards. >>>>>>>>>> >>>> >>>>>>>>>> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca >>>>>>>>>> <[hidden email] >>>>>>>>>> >>>> >: >>>>>>>>>> >>>> >>>>>>>>>> >>>>> Hello Bradley again, >>>>>>>>>> >>>>> I would like to ask you for a couple of favours. In the one >>>>>>>>>> hand, >>>>>>>>>> >>>>> could you please send me your 3D image so that I can test >>>>>>>>>> on it? And on the >>>>>>>>>> >>>>> other hand, could you test the example I have referenced in >>>>>>>>>> the previous >>>>>>>>>> >>>>> email with your image, not changing anything in the code, >>>>>>>>>> such as it is, >>>>>>>>>> >>>>> and tell me if the execution time is normal? >>>>>>>>>> >>>>> Thank you very much. >>>>>>>>>> >>>>> Regards, >>>>>>>>>> >>>>> /Francisco >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> PS: All my application trace is printed via standard 'cout' >>>>>>>>>> command, >>>>>>>>>> >>>>> not due to a debugging compilation mode. >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> >>>>>>>>>> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp >>>>>>>>>> <[hidden >>>>>>>>>> >>>>> email] < >>>>>>>>>> http:///user/SendEmail.jtp?type=node&node=7588477&i=4>> >>>>>>>>>> >>>>> escribi?: >>>>>>>>>> >>>>> >>>>>>>>>> >>>>>> Hello, >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Did you compile TextureFeatureImage in Release mode? >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> 1) The filter does not scale well with a large radius. And >>>>>>>>>> given by >>>>>>>>>> >>>>>> your initial report of print a very large number of offset >>>>>>>>>> you, it sounds >>>>>>>>>> >>>>>> like you are using a large radius with many offsets. I >>>>>>>>>> created a >>>>>>>>>> >>>>>> 224x224x300 unsigned short image and ran with the default >>>>>>>>>> offset and a >>>>>>>>>> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this >>>>>>>>>> filter is was ~10x >>>>>>>>>> >>>>>> faster than this example... things change though... >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> 2) I sounds like the boundaries/limits of the histogram >>>>>>>>>> may be >>>>>>>>>> >>>>>> clipping you values. I would inspect the co-occurance >>>>>>>>>> matrix. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> HTH, >>>>>>>>>> >>>>>> Brad >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca >>>>>>>>>> <[hidden >>>>>>>>>> >>>>>> email] < >>>>>>>>>> http:///user/SendEmail.jtp?type=node&node=7588477&i=5>> >>>>>>>>>> >>>>>> wrote: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> I've tested with itkTextureFeatureImageFilter, with >>>>>>>>>> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>>>>>>>> >>>>>> >>>>>>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures >>>>>>>>>> example, >>>>>>>>>> >>>>>> for a 3D image and here are my comments: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> 1. I had to interrupt the test after several hours and it >>>>>>>>>> kept on >>>>>>>>>> >>>>>> calculating. And this is for only a 3D image >>>>>>>>>> (224x224x300). I need to >>>>>>>>>> >>>>>> process around 35 images. >>>>>>>>>> >>>>>> 2. The result (texture features: entropy, energy, >>>>>>>>>> correlation, LH, >>>>>>>>>> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, >>>>>>>>>> 0, 7.83083e+247]. >>>>>>>>>> >>>>>> These values were not what I expected based on my >>>>>>>>>> experience on another >>>>>>>>>> >>>>>> application I developed, but in that case, I calculated >>>>>>>>>> the texture >>>>>>>>>> >>>>>> features for an image as a whole, not voxel by voxel. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> Regards. >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >>>>>>>>>> >>>>>> >: >>>>>>>>>> >>>>>> >>>>>>>>>> >>>>>>> i yes i have tried radius = 3; >>>>>>>>>> >>>>>>> still no luck >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca >>>>>>>>>> [via ITK >>>>>>>>>> >>>>>>> Insight >>>>>>>>>> >>>>>>> Users] <[hidden email] >>>>>>>>>> >>>>>>> > >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>> >>>>>>>>>> >>>>>>> > Have you tried with a radius of 3 instead of 1? >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>>>>>>>> >>>>>>> > >>>>>>>>> >>: >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> >> hey Matt, >>>>>>>>>> >>>>>>> >> thanks for ur advice.. it did build successfully... >>>>>>>>>> but im not >>>>>>>>>> >>>>>>> able to run >>>>>>>>>> >>>>>>> >> the code for 2D png image... i tried to change the >>>>>>>>>> dimension to 2 >>>>>>>>>> >>>>>>> and >>>>>>>>>> >>>>>>> >> build >>>>>>>>>> >>>>>>> >> it which it did.. but when i run the code using the >>>>>>>>>> command >>>>>>>>>> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png >>>>>>>>>> putput.png >>>>>>>>>> >>>>>>> 1... i see >>>>>>>>>> >>>>>>> >> this output >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> offset: [-1, -1] [0, -1] >>>>>>>>>> >>>>>>> >> offset: [0, -1] [1, -1] >>>>>>>>>> >>>>>>> >> offset: [-1, 0] [0, 0] >>>>>>>>>> >>>>>>> >> offset: [0, 0] [1, 0] >>>>>>>>>> >>>>>>> >> offset: [-1, 1] [0, 1] >>>>>>>>>> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the >>>>>>>>>> program... if pls >>>>>>>>>> >>>>>>> tel me >>>>>>>>>> >>>>>>> >> how can i modify this code to work wid 2d image... >>>>>>>>>> forgive me if >>>>>>>>>> >>>>>>> my ques >>>>>>>>>> >>>>>>> >> are really silly im trying to learn something.. >>>>>>>>>> >>>>>>> >> regards >>>>>>>>>> >>>>>>> >> Vis >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via >>>>>>>>>> ITK >>>>>>>>>> >>>>>>> Insight Users] >>>>>>>>>> >>>>>>> >> < >>>>>>>>>> >>>>>>> >> [hidden email] < >>>>>>>>>> >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>> >>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> > Hi, >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > The function: >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char >>>>>>>>>> *argv[]) >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > must be renamed to >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > main(int argc, char* argv[]) >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > HTH, >>>>>>>>>> >>>>>>> >> > Matt >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>>>>>>>> >>>>>>> >> > < >>>>>>>>>> http:///user/SendEmail.jtp?type=node&node=7587952&i=0>> wrote: >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > > hi all, >>>>>>>>>> >>>>>>> >> > > im trying to build the >>>>>>>>>> itkTextureFeatureImageFilterTest.cxx >>>>>>>>>> >>>>>>> code but >>>>>>>>>> >>>>>>> >> im >>>>>>>>>> >>>>>>> >> > not >>>>>>>>>> >>>>>>> >> > > able to it is showing the following error >>>>>>>>>> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>>>>>>>> >>>>>>> Configuration: >>>>>>>>>> >>>>>>> >> Debug >>>>>>>>>> >>>>>>> >> > x64 >>>>>>>>>> >>>>>>> >> > > ------ >>>>>>>>>> >>>>>>> >> > > 1> Checking Build System >>>>>>>>>> >>>>>>> >> > > 1> CMake does not need to re-run because >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>>>>>>>> >>>>>>> >> > is >>>>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>>>> >>>>>>> >> > > 2>------ Rebuild All started: Project: >>>>>>>>>> >>>>>>> >> itkTextureFeatureImageFilterTest, >>>>>>>>>> >>>>>>> >> > > Configuration: Debug x64 ------ >>>>>>>>>> >>>>>>> >> > > 2> Building Custom Rule >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>>>>> >>>>>>> >> > > 2> CMake does not need to re-run because >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >>>>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>>>>> >>>>>>> >> > is >>>>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>>>> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>>>>>>>> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>>>>>>>> >>>>>>> 'std::_Copy_impl': >>>>>>>>>> >>>>>>> >> > Function >>>>>>>>>> >>>>>>> >> > > call with parameters that may be unsafe - this >>>>>>>>>> call relies on >>>>>>>>>> >>>>>>> the >>>>>>>>>> >>>>>>> >> caller >>>>>>>>>> >>>>>>> >> > to >>>>>>>>>> >>>>>>> >> > > check that the passed values are correct. To >>>>>>>>>> disable this >>>>>>>>>> >>>>>>> warning, use >>>>>>>>>> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on >>>>>>>>>> how to use >>>>>>>>>> >>>>>>> Visual C++ >>>>>>>>>> >>>>>>> >> > > 'Checked Iterators' >>>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft >>>>>>>>>> Visual Studio >>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>>> >>>>>>> >> > > 2> >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>>>>>>>> >>>>>>> >> > see >>>>>>>>>> >>>>>>> >> > > reference to function template instantiation >>>>>>>>>> '_OutIt >>>>>>>>>> >>>>>>> std::copy>>>>>>>>> >>>>>>> >> > > unsigned char*,unsigned >>>>>>>>>> char*>(_InIt,_InIt,_OutIt)' being >>>>>>>>>> >>>>>>> compiled >>>>>>>>>> >>>>>>> >> > > 2> with >>>>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>>>> >>>>>>> >> > > 2> _OutIt=unsigned char *, >>>>>>>>>> >>>>>>> >> > > 2> _InIt=const unsigned char * >>>>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>>>> >>>>>>> >> > > 2> >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>>>>>>>> >>>>>>> >> > > while compiling class template member function >>>>>>>>>> 'void >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> itk::ImageFileReader::GenerateData(void)' >>>>>>>>>> >>>>>>> >> > > 2> with >>>>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>>>> >>>>>>> >> > > 2> >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > > : see reference to class template instantiation >>>>>>>>>> >>>>>>> >> > > 'itk::ImageFileReader' being compiled >>>>>>>>>> >>>>>>> >> > > 2> with >>>>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft >>>>>>>>>> Visual Studio >>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft >>>>>>>>>> Visual Studio >>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft >>>>>>>>>> Visual Studio >>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >>>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>>> >>>>>>> >> > > 2> Creating library >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > > and object >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: >>>>>>>>>> unresolved >>>>>>>>>> >>>>>>> external symbol >>>>>>>>>> >>>>>>> >> > main >>>>>>>>>> >>>>>>> >> > > referenced in function __tmainCRTStartup >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>>>>>>>> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>>>>>>>> >>>>>>> Configuration: Debug >>>>>>>>>> >>>>>>> >> > x64 >>>>>>>>>> >>>>>>> >> > > ------ >>>>>>>>>> >>>>>>> >> > > 3> Building Custom Rule >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>>>>> >>>>>>> >> > > 3> CMake does not need to re-run because >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >>>>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>>>>> >>>>>>> >> > is >>>>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>>>> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 >>>>>>>>>> skipped >>>>>>>>>> >>>>>>> ========== >>>>>>>>>> >>>>>>> >> > > im using the follwing CMakeList.txt >>>>>>>>>> >>>>>>> >> > > # This is the root ITK CMakeLists file. >>>>>>>>>> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>>>>>>>> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >>>>>>>>>> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>>>>>>>> >>>>>>> >> > > endif() >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > # This project is designed to be built outside the >>>>>>>>>> Insight >>>>>>>>>> >>>>>>> source >>>>>>>>>> >>>>>>> >> tree. >>>>>>>>>> >>>>>>> >> > > project(HelloWorld) >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > # Find ITK. >>>>>>>>>> >>>>>>> >> > > find_package(ITK REQUIRED) >>>>>>>>>> >>>>>>> >> > > include(${ITK_USE_FILE}) >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>>>>>>>> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> target_link_libraries(itkTextureFeatureImageFilterTest >>>>>>>>>> >>>>>>> >> ${ITK_LIBRARIES}) >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > please tel me wat the error is?? >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > -- >>>>>>>>>> >>>>>>> >> > > View this message in context: >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>>>>>>>> >>>>>>> >> > > Sent from the ITK Insight Users mailing list >>>>>>>>>> archive at >>>>>>>>>> >>>>>>> Nabble.com . >>>>>>>>>> >>>>>>> >> > > _____________________________________ >>>>>>>>>> >>>>>>> >> > > Powered by www.kitware.com >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > Visit other Kitware open-source projects at >>>>>>>>>> >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > Kitware offers ITK Training Courses, for more >>>>>>>>>> information >>>>>>>>>> >>>>>>> visit: >>>>>>>>>> >>>>>>> >> > > http://www.kitware.com/products/protraining.php >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > Please keep messages on-topic and check the ITK >>>>>>>>>> FAQ at: >>>>>>>>>> >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> >>>>>>> >> > > Follow this link to subscribe/unsubscribe: >>>>>>>>>> >>>>>>> >> > > >>>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>> >>>>>>> >> > _____________________________________ >>>>>>>>>> >>>>>>> >> > Powered by www.kitware.com >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > Visit other Kitware open-source projects at >>>>>>>>>> >>>>>>> >> > http://www.kitware.com/opensource/opensource.html >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > Kitware offers ITK Training Courses, for more >>>>>>>>>> information visit: >>>>>>>>>> >>>>>>> >> > http://www.kitware.com/products/protraining.php >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > Please keep messages on-topic and check the ITK FAQ >>>>>>>>>> at: >>>>>>>>>> >>>>>>> >> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > Follow this link to subscribe/unsubscribe: >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > ------------------------------ >>>>>>>>>> >>>>>>> >> > If you reply to this email, your message will be >>>>>>>>>> added to the >>>>>>>>>> >>>>>>> discussion >>>>>>>>>> >>>>>>> >> > below: >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587952.html >>>>>>>>>> >>>>>>> >> > To unsubscribe from [ITK-users] Texture pixel by >>>>>>>>>> pixel, click >>>>>>>>>> >>>>>>> here >>>>>>>>>> >>>>>>> >> > < > . >>>>>>>>>> >>>>>>> >> > NAML >>>>>>>>>> >>>>>>> >> > < >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> > >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> -- >>>>>>>>>> >>>>>>> >> View this message in context: >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >>>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587960.html >>>>>>>>>> >>>>>>> >> Sent from the ITK Insight Users mailing list archive at >>>>>>>>>> >>>>>>> Nabble.com . >>>>>>>>>> >>>>>>> >> _____________________________________ >>>>>>>>>> >>>>>>> >> Powered by www.kitware.com >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Visit other Kitware open-source projects at >>>>>>>>>> >>>>>>> >> http://www.kitware.com/opensource/opensource.html >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Kitware offers ITK Training Courses, for more >>>>>>>>>> information visit: >>>>>>>>>> >>>>>>> >> http://www.kitware.com/products/protraining.php >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>> >>>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> >> Follow this link to subscribe/unsubscribe: >>>>>>>>>> >>>>>>> >> >>>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>> >>>>>>> >> >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > _____________________________________ >>>>>>>>>> >>>>>>> > Powered by www.kitware.com >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > Visit other Kitware open-source projects at >>>>>>>>>> >>>>>>> > http://www.kitware.com/opensource/opensource.html >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > Kitware offers ITK Training Courses, for more >>>>>>>>>> information visit: >>>>>>>>>> >>>>>>> > http://www.kitware.com/products/protraining.php >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>> >>>>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > Follow this link to subscribe/unsubscribe: >>>>>>>>>> >>>>>>> > >>>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > ------------------------------ >>>>>>>>>> >>>>>>> > If you reply to this email, your message will be added >>>>>>>>>> to the >>>>>>>>>> >>>>>>> discussion >>>>>>>>>> >>>>>>> > below: >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> > >>>>>>>>>> >>>>>>> >>>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587961.html >>>>>>>>>> >>>>>>> > To unsubscribe from [ITK-users] Texture pixel by pixel, >>>>>>>>>> click here >>>>>>>>>> >>>>>>> > < > . >>>>>>>>>> >>>>>>> > NAML >>>>>>>>>> >>>>>>> > < >>>>>>>>>> >>>>>>> >>>>>>>>>> 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Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>>>> >>>>> ------------------------------ >>>>> If you reply to this email, your message will be added to the >>>>> discussion below: >>>>> >>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588505.html >>>>> To start a new topic under ITK Insight Users, email [hidden email] >>>>> >>>>> To unsubscribe from ITK Insight Users, click here. >>>>> NAML >>>>> >>>>> >>>> >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information 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http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588513.html >>> To start a new topic under ITK Insight Users, email [hidden email] >>> >>> To unsubscribe from ITK Insight Users, click here. >>> NAML >>> >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588516.html > To start a new topic under ITK Insight Users, email > ml-node+s2283740n2283740h75 at n2.nabble.com > To unsubscribe from ITK Insight Users, click here > > . > NAML > > -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588529.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Mon Feb 22 07:20:20 2016 From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca) Date: Mon, 22 Feb 2016 13:20:20 +0100 Subject: [ITK] [ITK-users] Compilation error when building ITK 4.9.0 with MinGW In-Reply-To: References: Message-ID: I've achieved to compile ITK 4.9.0 through MS Visual Studio 2010, but not with MinGW. Thanks everybody. Kind regards. /Francisco 2016-02-19 23:56 GMT+01:00 Francisco Lopez de la Franca < franciscolopezdelafranca at gmail.com>: > Hello Matt, > I had already tested the -Wa,-mbig-obj options in CMAKE_CXX_FLAGS and in > CMAKE_C_FLAGS and the answer was: > > C:/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: > unrecognized option `-mbig-obj' > > So, I'm stuck at this point, and I'm thinking to change from Mingw to > Visual Studio or another one. But it is very strange that ITK wasn't be > prepared to be compiled via MinGW. > > Thanks for answering and if you have any suggestion, it wiil be very well > received. > > /Francisco > > > 2016-02-19 18:00 GMT+01:00 Matt McCormick : > >> Hi Franscisco, >> >> According to this thread: >> >> https://cmake.org/pipermail/insight-users/2015-September/052511.html >> >> adding the flags >> >> -Wa,-mbig-obj >> >> helps at least with the build error. Does it help in your case? >> >> Thanks, >> Matt >> >> On Thu, Feb 18, 2016 at 6:22 PM, Francisco Lopez de la Franca >> wrote: >> > Hi, >> > I've downloaded the last stable ITK version, 4.9.0, for Windows and >> compile >> > it by using MinGW-64. >> > When the compilation reaches almost the 100%, it gives the error: >> > >> > [ 98%] Building CXX object >> > >> Modules/IO/TransformBase/src/CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.obj >> > >> C:/MINGW/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: >> > CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: too >> many >> > sections (33106) >> > C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Assembler messages: >> > C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Fatal error: can't write >> > CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: File >> too >> > big >> > >> > I've been searching for a solution on the web for several hours and all >> the >> > attempts to solve it have not fix it. >> > >> > Has anyone ever faced this problem and fix it? >> > >> > Thanks a lot. >> > Best regards. >> > /Francisco >> > >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-users >> > >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Mon Feb 22 08:42:02 2016 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 22 Feb 2016 08:42:02 -0500 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <3F877AC4-BCD1-43FF-B8B3-7B30F9B6D30B@mail.nih.gov> Message-ID: Francisco, Glad to hear that you figured out the problem with your code. Were you able to try out the change to add Mask support I committed to the github repository? Does this meet you masking needs and improve your performance? Please consider studying the difference between your change any my change and the performance implications. Enjoy, Brad > On Feb 22, 2016, at 7:18 AM, Francisco Lopez de la Franca wrote: > > Hi. > In the end the crash came for my fault. I was creating the mask image in the wrong way. Sorry for the disturbances, and thank you very much everybody. > Kind regards. > /Francisco > > 2016-02-18 19:00 GMT+01:00 dzenanz [via ITK Insight Users] >: > /bigobj is an option for msvc, not mingw. > > But that is a different problem from crashing code. If you start a new thread, somebody with MinGW experience might help you. > > On Thu, Feb 18, 2016 at 12:30 PM, Francisco Lopez de la Franca <[hidden email] > wrote: > Yes. I use mingw (x86_64-w64-mingw32-g++.exe) and I set in CMAKE GUI the entry CMAKE_CXX_FLAGS to -bigobj and the result is "unrecognized option". > > > 2016-02-18 15:25 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden email] >: > Have you tried /bigobj ? Are you using MinGW? Visual Studio is now free . > > HTH > > On Thu, Feb 18, 2016 at 6:37 AM, Francisco Lopez de la Franca <[hidden email] > wrote: > Hi again, > I've got ITK version 4.5.1 (a little bit old, I know), and after making the changes suggested by Dzenanz and recompiling ITK, the problem continues, that is, my code crashes at the same point. > > Then, I've downloaded the latest stable ITK version, ITK 4.9.0 and compiled from scratch and I get the following error: > > [ 98%] Building CXX object Modules/IO/TransformBase/src/CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.obj > C:/MINGW/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: too many sections (33106) > C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Assembler messages: > C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Fatal error: can't write CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: File too big > > After doing some "googling" and follow some of the instructions referred on the web, I've been unable to solve this. > Has anyone met this problem and solved it? > Thanks. > KR. > /Francisco > > 2016-02-16 22:13 GMT+01:00 Bradley Lowekamp [via ITK Insight Users] <[hidden email] >: > Hello, > > Please take a look at these changes: > https://github.com/blowekamp/itkTextureAnalysis/commit/9654d74ea1d09f0677f1d1b93242cc94340591bf > > Brad > >> On Feb 16, 2016, at 10:35 AM, D?enan Zuki? <[hidden email] > wrote: >> >> I have set up a project using one of the tests from Brad's repository (attached), and it works in debug mode both with his original code and with your modified class, and crashes in release mode both with his original code and with your modified class. I will now compile ITK in RelWithDebInfo in an attempt to figure out where is the crash occurring. >> >> Regards, >> D?enan >> >> On Tue, Feb 16, 2016 at 1:52 AM, Francisco Lopez de la Franca <[hidden email] > wrote: >> Excuse me Dzenanz, but that's not completely true, because I've tested Brad's class and it works right. >> The problem seems to be that when you add a new neighbor iterator to include just the mask points in the "histogram" then it is when the application crashes, and I donot understand why. >> If you just comment the 'maskIter' references you'll see that the application works. >> I've created a single threaded class based on the Brad's code and it works but it is twice slower, that is why I'm interesting on Brad's class (multi-threaded) to make it work. >> >> >> 2016-02-15 17:15 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden email] >: >> Hi Francisco, >> >> both your code and Brad's code run in debug mode (I did not wait for the end), and both crash in release mode immediately on startup. Here is a sample output: >> >> Progress input: 0000000002868970 >> input: 0000000002868970 >> _maskImage: 0000000002868970 >> _maskImage: 0000000002868970 >> input: 0000000002868970 >> _maskImage: 0000000002868970 >> iter.first: iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >> [-5, -5, -5] iter.second: [-4, -5, -5] >> niter index: [5, 5, 210] >> niter index: [5, 5, 140] >> maskIter index: [5, 5, 140] >> maskIter index: [5, 5, 210] >> Before p3 >> input: 0000000002868970 >> _maskImage: 0000000002868970 >> After p3: | 0niter index: [5, 5, 70] >> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >> niter index: [5, 5, 5] >> ? >> maskIter index: [5, 5, 70] >> After p4: ? >> Before p3 >> Before p3 >> After p3: ?iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >> niter index: [5, 5, 140] >> maskIter index: [5, 5, 140] >> maskIter index: [5, 5, 5] >> Before p3 >> After p3: ? >> After p3: ? >> After p4: ? >> After p4: ? >> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >> niter index: [5, 5, 5] >> maskIter index: [5, 5, 5] >> >> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >> Before p3 >> Before p3 >> After p4: ? >> After p3: ? >> After p4: ? >> >> Regards, >> D?enan >> >> On Mon, Feb 15, 2016 at 1:36 AM, Francisco Lopez de la Franca <[hidden email] > wrote: >> Hi, >> Here they are. >> KR. >> >> 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden email] >: >> Hi Francisco, >> >> do you mind attaching the modified files or pointing to your fork of it on GitHub? >> >> Regards >> >> On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden email] > wrote: >> Hi Dzenan, >> The original class is here: >> >> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >> >> I've just added setInput and setMaskImage methods and modify some lines in >> the original class as I indicated in the yesterday mail within this thread. >> I'm running it on Windows, and there is no error at all, just a crash. I >> may have to include exceptions management. >> The crash occurs just when calling p3 = maskIter.GetPixel(iter->first) >> >> If you know why it could be or if you need more clarification, please let >> me know. >> Many thanks >> >> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >> [hidden email] >: >> >> > Hi Francisco, >> > >> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the error message >> > that goes along with the crash? In which file and line does it crash? >> > >> > Regards >> > >> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca <[hidden >> > email] >> wrote: >> > >> >> Hi, >> >> Please, someone that could help me. I'm working in a pre-doctorate >> >> project and I need this class to work. >> >> I've read the chapter 13 in the ITK Software Guide on how to write a >> >> filter and now I see the fact of the threads due to inheritance of >> >> ImageToImageFilter. >> >> But, I keep on without understanding why the code crashes just when >> >> calling >> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >> >> It is just a call to read data, not to write. >> >> >> >> I guess somebody that had worked with creation of filters might see >> >> "easily" the problem, but not me. >> >> >> >> So, again, please, I need someone to help me with this because I'm stuck >> >> on this point. >> >> >> >> Thank you very much. >> >> KR. >> >> /Francisco >> >> >> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden email] >> >> >>: >> >> >> >>> Hi Bradley again. >> >>> I'm modifying your class in order to be able to set a mask image (a >> >>> binary image) to be used as a limit in the histogram calculations, I mean, >> >>> I set an input, a mask and the class should take into account to calculate >> >>> the histograms only the voxels that belong to the input and to the mask >> >>> image and having the value 1 in the mask image. >> >>> The changes seem to be easy but I don?t know why my tests are not >> >>> working. It seems that 2 threads are working at the same time and when I >> >>> added my mask iterator, the code crashes. >> >>> >> >>> *** Consider that the input and mask images are the same origin, spacing >> >>> and size. >> >>> >> >>> I attach the main changes I've done, and I would thank you a lot if you >> >>> don't mind having a look and help me to find what I'm doing wrong: >> >>> >> >>> template< class TImageType, class TOutputImage > >> >>> void >> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >::*SetInput*(InputImageType >> >>> *image) >> >>> { >> >>> // Process object is not const-correct so the const_cast is required >> >>> here >> >>> this->ProcessObject::SetNthInput( 0, >> >>> const_cast< InputImageType * >( >> >>> image ) ); >> >>> } >> >>> >> >>> template< class TImageType, class TOutputImage > >> >>> void >> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >::*SetMaskImage*(InputImageType >> >>> *image) >> >>> { >> >>> // Process object is not const-correct so the const_cast is required >> >>> here >> >>> this->ProcessObject::SetNthInput( 1, const_cast< InputImageType * >( >> >>> image ) ); >> >>> >> >>> _maskImage = image; // _maskImage is a private member >> >>> } >> >>> >> >>> In the *ThreadedGenerateData*(const RegionType& outputRegionForThread, >> >>> ThreadIdType threadId ) method: >> >>> { >> >>> >> >>> ... >> >>> >> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit ) >> >>> { >> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, *fit);* >> >>> OutputIterator outIter(output, *fit); >> >>> >> >>> OutputPixelType out; >> >>> NumericTraits::SetLength( out, >> >>> this->GetNumberOfOutputComponents() ); >> >>> >> >>> while( !nIter.IsAtEnd() ) >> >>> { >> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >> >>> >> >>> ... >> >>> >> >>> ++nIter; >> >>> ++outIter; >> >>> * ++maskIter;* >> >>> ... >> >>> >> >>> In the *FillHistogram *method: >> >>> { >> >>> >> >>> ... >> >>> >> >>> while( iter != m_CooccurenceOffsetVector.end() ) >> >>> { >> >>> >> >>> const PixelType p1 = niter.GetPixel(iter->first); >> >>> const PixelType p2 = niter.GetPixel(iter->second); >> >>> std::cout << "Before p3" << std::endl; >> >>> >> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); *std::cout >> >>> << "After p3: " << p3 << std::endl; >> >>> >> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); * >> >>> std::cout << "After p4: " << p4 << std::endl; >> >>> >> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= m_Max >> >>> *&& p3 == _insidePixelValue && p4 == _insidePixelValue* ) >> >>> // The point >> >>> { >> >>> >> >>> ... >> >>> >> >>> >> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >> >>> >> >>> Thank you so much. >> >>> My kind regards. >> >>> /Paco >> >>> >> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca <[hidden email] >> >>> >>: >> >>> >> >>>> Hello Bradley again. >> >>>> Sorry but I'd like to re-open this issue because I need your class but >> >>>> with some modification. >> >>>> I pass to tell you. >> >>>> >> >>>> As my tests with your external class were not good taking into account >> >>>> the performance, I wonder if you could create a variant of it, but in which >> >>>> I can set a mask image and your class just return the VectorImage with all >> >>>> the features for that region (the masked locations) as >> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >> >>>> I mean, to get the vector image with all the features but just >> >>>> calculate it for the regions belonging to the mask image. Positions not >> >>>> belonging to the mask region could have a pixel value of 0, for instance. >> >>>> >> >>>> I don?t know if it is very costly for you, but I would thank you so >> >>>> much. Otherwise, I could try it but I'd need your suggestions on how to do >> >>>> it. >> >>>> >> >>>> Thanks a lot. >> >>>> Best regards. >> >>>> >> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca <[hidden email] >> >>>> >>: >> >>>> >> >>>>> Hello Bradley again, >> >>>>> I would like to ask you for a couple of favours. In the one hand, >> >>>>> could you please send me your 3D image so that I can test on it? And on the >> >>>>> other hand, could you test the example I have referenced in the previous >> >>>>> email with your image, not changing anything in the code, such as it is, >> >>>>> and tell me if the execution time is normal? >> >>>>> Thank you very much. >> >>>>> Regards, >> >>>>> /Francisco >> >>>>> >> >>>>> PS: All my application trace is printed via standard 'cout' command, >> >>>>> not due to a debugging compilation mode. >> >>>>> >> >>>>> >> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp <[hidden >> >>>>> email] >> >> >>>>> escribi?: >> >>>>> >> >>>>>> Hello, >> >>>>>> >> >>>>>> Did you compile TextureFeatureImage in Release mode? >> >>>>>> >> >>>>>> 1) The filter does not scale well with a large radius. And given by >> >>>>>> your initial report of print a very large number of offset you, it sounds >> >>>>>> like you are using a large radius with many offsets. I created a >> >>>>>> 224x224x300 unsigned short image and ran with the default offset and a >> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this filter is was ~10x >> >>>>>> faster than this example... things change though... >> >>>>>> >> >>>>>> >> >>>>>> 2) I sounds like the boundaries/limits of the histogram may be >> >>>>>> clipping you values. I would inspect the co-occurance matrix. >> >>>>>> >> >>>>>> >> >>>>>> HTH, >> >>>>>> Brad >> >>>>>> >> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca <[hidden >> >>>>>> email] >> >> >>>>>> wrote: >> >>>>>> >> >>>>>> I've tested with itkTextureFeatureImageFilter, with >> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >> >>>>>>http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures example, >> >>>>>> for a 3D image and here are my comments: >> >>>>>> >> >>>>>> >> >>>>>> 1. I had to interrupt the test after several hours and it kept on >> >>>>>> calculating. And this is for only a 3D image (224x224x300). I need to >> >>>>>> process around 35 images. >> >>>>>> 2. The result (texture features: entropy, energy, correlation, LH, >> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, 7.83083e+247]. >> >>>>>> These values were not what I expected based on my experience on another >> >>>>>> application I developed, but in that case, I calculated the texture >> >>>>>> features for an image as a whole, not voxel by voxel. >> >>>>>> >> >>>>>> Regards. >> >>>>>> >> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >> >>>>>> >>: >> >>>>>> >> >>>>>>> i yes i have tried radius = 3; >> >>>>>>> still no luck >> >>>>>>> >> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca [via ITK >> >>>>>>> Insight >> >>>>>>> Users] <[hidden email] >> >>>>>>> >> wrote: >> >>>>>>> >> >>>>>>> > Have you tried with a radius of 3 instead of 1? >> >>>>>>> > >> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >> >>>>>>> > >>: >> >>>>>>> > >> >>>>>>> >> hey Matt, >> >>>>>>> >> thanks for ur advice.. it did build successfully... but im not >> >>>>>>> able to run >> >>>>>>> >> the code for 2D png image... i tried to change the dimension to 2 >> >>>>>>> and >> >>>>>>> >> build >> >>>>>>> >> it which it did.. but when i run the code using the command >> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png putput.png >> >>>>>>> 1... i see >> >>>>>>> >> this output >> >>>>>>> >> >> >>>>>>> >> offset: [-1, -1] [0, -1] >> >>>>>>> >> offset: [0, -1] [1, -1] >> >>>>>>> >> offset: [-1, 0] [0, 0] >> >>>>>>> >> offset: [0, 0] [1, 0] >> >>>>>>> >> offset: [-1, 1] [0, 1] >> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... if pls >> >>>>>>> tel me >> >>>>>>> >> how can i modify this code to work wid 2d image... forgive me if >> >>>>>>> my ques >> >>>>>>> >> are really silly im trying to learn something.. >> >>>>>>> >> regards >> >>>>>>> >> Vis >> >>>>>>> >> >> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK >> >>>>>>> Insight Users] >> >>>>>>> >> < >> >>>>>>> >> [hidden email] < >> >>>>>>>http:///user/SendEmail.jtp?type=node&node=7587961&i=1 >> >> >>>>>>> >> wrote: >> >>>>>>> >> >> >>>>>>> >> > Hi, >> >>>>>>> >> > >> >>>>>>> >> > The function: >> >>>>>>> >> > >> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char *argv[]) >> >>>>>>> >> > >> >>>>>>> >> > must be renamed to >> >>>>>>> >> > >> >>>>>>> >> > main(int argc, char* argv[]) >> >>>>>>> >> > >> >>>>>>> >> > HTH, >> >>>>>>> >> > Matt >> >>>>>>> >> > >> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >> >>>>>>> >> > >> wrote: >> >>>>>>> >> > >> >>>>>>> >> > > hi all, >> >>>>>>> >> > > im trying to build the itkTextureFeatureImageFilterTest.cxx >> >>>>>>> code but >> >>>>>>> >> im >> >>>>>>> >> > not >> >>>>>>> >> > > able to it is showing the following error >> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >> >>>>>>> Configuration: >> >>>>>>> >> Debug >> >>>>>>> >> > x64 >> >>>>>>> >> > > ------ >> >>>>>>> >> > > 1> Checking Build System >> >>>>>>> >> > > 1> CMake does not need to re-run because >> >>>>>>> >> > > >> >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >> >>>>>>> >> > is >> >>>>>>> >> > > up-to-date. >> >>>>>>> >> > > 2>------ Rebuild All started: Project: >> >>>>>>> >> itkTextureFeatureImageFilterTest, >> >>>>>>> >> > > Configuration: Debug x64 ------ >> >>>>>>> >> > > 2> Building Custom Rule >> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >> >>>>>>> >> > > 2> CMake does not need to re-run because >> >>>>>>> >> > > >> >>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >> >>>>>>> >> > is >> >>>>>>> >> > > up-to-date. >> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >> >>>>>>> 'std::_Copy_impl': >> >>>>>>> >> > Function >> >>>>>>> >> > > call with parameters that may be unsafe - this call relies on >> >>>>>>> the >> >>>>>>> >> caller >> >>>>>>> >> > to >> >>>>>>> >> > > check that the passed values are correct. To disable this >> >>>>>>> warning, use >> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to use >> >>>>>>> Visual C++ >> >>>>>>> >> > > 'Checked Iterators' >> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >> >>>>>>> 'std::_Copy_impl' >> >>>>>>> >> > > 2> >> >>>>>>> >> > > >> >>>>>>> >> >> >>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >> >>>>>>> >> > see >> >>>>>>> >> > > reference to function template instantiation '_OutIt >> >>>>>>> std::copy> >>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' being >> >>>>>>> compiled >> >>>>>>> >> > > 2> with >> >>>>>>> >> > > 2> [ >> >>>>>>> >> > > 2> _OutIt=unsigned char *, >> >>>>>>> >> > > 2> _InIt=const unsigned char * >> >>>>>>> >> > > 2> ] >> >>>>>>> >> > > 2> >> >>>>>>> >> > > >> >>>>>>> >> >> >>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >> >>>>>>> >> > > while compiling class template member function 'void >> >>>>>>> >> > > itk::ImageFileReader::GenerateData(void)' >> >>>>>>> >> > > 2> with >> >>>>>>> >> > > 2> [ >> >>>>>>> >> > > 2> TOutputImage=InputImageType >> >>>>>>> >> > > 2> ] >> >>>>>>> >> > > 2> >> >>>>>>> >> > > >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >> >>>>>>> >> > >> >>>>>>> >> > > : see reference to class template instantiation >> >>>>>>> >> > > 'itk::ImageFileReader' being compiled >> >>>>>>> >> > > 2> with >> >>>>>>> >> > > 2> [ >> >>>>>>> >> > > 2> TOutputImage=InputImageType >> >>>>>>> >> > > 2> ] >> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >> >>>>>>> 'std::_Copy_impl' >> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >> >>>>>>> 'std::_Copy_impl' >> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft Visual Studio >> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of >> >>>>>>> 'std::_Copy_impl' >> >>>>>>> >> > > 2> Creating library >> >>>>>>> >> > > >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >> >>>>>>> >> > >> >>>>>>> >> > > and object >> >>>>>>> >> > > >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >> >>>>>>> >> > >> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved >> >>>>>>> external symbol >> >>>>>>> >> > main >> >>>>>>> >> > > referenced in function __tmainCRTStartup >> >>>>>>> >> > > >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >> >>>>>>> >> > >> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >> >>>>>>> Configuration: Debug >> >>>>>>> >> > x64 >> >>>>>>> >> > > ------ >> >>>>>>> >> > > 3> Building Custom Rule >> >>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >> >>>>>>> >> > > 3> CMake does not need to re-run because >> >>>>>>> >> > > >> >>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >> >>>>>>> >> > is >> >>>>>>> >> > > up-to-date. >> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 skipped >> >>>>>>> ========== >> >>>>>>> >> > > im using the follwing CMakeList.txt >> >>>>>>> >> > > # This is the root ITK CMakeLists file. >> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >> >>>>>>> >> > > endif() >> >>>>>>> >> > > >> >>>>>>> >> > > >> >>>>>>> >> > > # This project is designed to be built outside the Insight >> >>>>>>> source >> >>>>>>> >> tree. >> >>>>>>> >> > > project(HelloWorld) >> >>>>>>> >> > > >> >>>>>>> >> > > # Find ITK. >> >>>>>>> >> > > find_package(ITK REQUIRED) >> >>>>>>> >> > > include(${ITK_USE_FILE}) >> >>>>>>> >> > > >> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >> >>>>>>> >> > > >> >>>>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest >> >>>>>>> >> ${ITK_LIBRARIES}) >> >>>>>>> >> > > >> >>>>>>> >> > > please tel me wat the error is?? >> >>>>>>> >> > > >> >>>>>>> >> > > >> >>>>>>> >> > > >> >>>>>>> >> > > -- >> >>>>>>> >> > > View this message in context: >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>>http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >> >>>>>>> >> > > Sent from the ITK Insight Users mailing list archive at >> >>>>>>>Nabble.com . >> >>>>>>> >> > > _____________________________________ >> >>>>>>> >> > > Powered bywww.kitware.com >> >>>>>>> >> > > >> >>>>>>> >> > > Visit other Kitware open-source projects at >> >>>>>>> >> > >http://www.kitware.com/opensource/opensource.html >> >>>>>>> >> > > >> >>>>>>> >> > > Kitware offers ITK Training Courses, for more information >> >>>>>>> visit: >> >>>>>>> >> > >http://www.kitware.com/products/protraining.php >> >>>>>>> >> > > >> >>>>>>> >> > > Please keep messages on-topic and check the ITK FAQ at: >> >>>>>>> >> > >http://www.itk.org/Wiki/ITK_FAQ >> >>>>>>> >> > > >> >>>>>>> >> > > Follow this link to subscribe/unsubscribe: >> >>>>>>> >> > >http://public.kitware.com/mailman/listinfo/insight-users >> >>>>>>> >> > _____________________________________ >> >>>>>>> >> > Powered bywww.kitware.com >> >>>>>>> >> > >> >>>>>>> >> > Visit other Kitware open-source projects at >> >>>>>>> >> >http://www.kitware.com/opensource/opensource.html >> >>>>>>> >> > >> >>>>>>> >> > Kitware offers ITK Training Courses, for more information visit: >> >>>>>>> >> >http://www.kitware.com/products/protraining.php >> >>>>>>> >> > >> >>>>>>> >> > Please keep messages on-topic and check the ITK FAQ at: >> >>>>>>> >> >http://www.itk.org/Wiki/ITK_FAQ >> >>>>>>> >> > >> >>>>>>> >> > Follow this link to subscribe/unsubscribe: >> >>>>>>> >> >http://public.kitware.com/mailman/listinfo/insight-users >> >>>>>>> >> > >> >>>>>>> >> > >> >>>>>>> >> > ------------------------------ >> >>>>>>> >> > If you reply to this email, your message will be added to the >> >>>>>>> discussion >> >>>>>>> >> > below: >> >>>>>>> >> > >> >>>>>>> >> > >> >>>>>>> >> >> >>>>>>>http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587952.html >> >>>>>>> >> > To unsubscribe from [ITK-users] Texture pixel by pixel, click >> >>>>>>> here >> >>>>>>> >> > < > . >> >>>>>>> >> > NAML >> >>>>>>> >> > < >> >>>>>>> >> >> 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at >> >>>>>>> >>http://www.kitware.com/opensource/opensource.html >> >>>>>>> >> >> >>>>>>> >> Kitware offers ITK Training Courses, for more information visit: >> >>>>>>> >>http://www.kitware.com/products/protraining.php >> >>>>>>> >> >> >>>>>>> >> Please keep messages on-topic and check the ITK FAQ at: >> >>>>>>> >>http://www.itk.org/Wiki/ITK_FAQ >> >>>>>>> >> >> >>>>>>> >> Follow this link to subscribe/unsubscribe: >> >>>>>>> >>http://public.kitware.com/mailman/listinfo/insight-users >> >>>>>>> >> >> >>>>>>> > >> >>>>>>> > >> >>>>>>> > _____________________________________ >> >>>>>>> > Powered bywww.kitware.com >> >>>>>>> > >> >>>>>>> > Visit other Kitware open-source projects at >> >>>>>>> >http://www.kitware.com/opensource/opensource.html >> >>>>>>> > >> >>>>>>> > Kitware offers ITK Training Courses, for more information visit: >> >>>>>>> >http://www.kitware.com/products/protraining.php >> >>>>>>> > >> >>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >> >>>>>>> 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>>>>>>> >> >>>>>>> Kitware offers ITK Training Courses, for more information visit: >> >>>>>>>http://www.kitware.com/products/protraining.php >> >>>>>>> >> >>>>>>> Please keep messages on-topic and check the ITK FAQ at: >> >>>>>>>http://www.itk.org/Wiki/ITK_FAQ >> >>>>>>> >> >>>>>>> Follow this link to subscribe/unsubscribe: >> >>>>>>>http://public.kitware.com/mailman/listinfo/insight-users >> >>>>>>> >> >>>>>> >> >>>>>> _____________________________________ >> >>>>>> Powered bywww.kitware.com >> >>>>>> >> >>>>>> Visit other Kitware open-source projects at >> >>>>>>http://www.kitware.com/opensource/opensource.html >> >>>>>> >> >>>>>> Kitware offers ITK Training Courses, for more information visit: >> >>>>>>http://www.kitware.com/products/protraining.php >> >>>>>> >> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >> >>>>>>http://www.itk.org/Wiki/ITK_FAQ >> >>>>>> >> >>>>>> Follow this link to subscribe/unsubscribe: >> >>>>>>http://public.kitware.com/mailman/listinfo/insight-users >> >>>>>> >> >>>>>> >> >>>>>> >> >>>> >> >>> >> >> >> >> _____________________________________ >> >> Powered bywww.kitware.com >> >> >> >> Visit other Kitware open-source projects at >> >>http://www.kitware.com/opensource/opensource.html >> >> >> >> Kitware offers ITK Training Courses, for more information visit: >> >>http://www.kitware.com/products/protraining.php >> >> >> >> Please keep messages on-topic and check the ITK FAQ at: >> >>http://www.itk.org/Wiki/ITK_FAQ >> >> >> >> Follow this link to subscribe/unsubscribe: >> >>http://public.kitware.com/mailman/listinfo/insight-users >> >> >> >> >> > >> > _____________________________________ >> > Powered bywww.kitware.com >> > >> > Visit other Kitware open-source projects at >> >http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> >http://www.kitware.com/products/protraining.php >> > >> > Please keep 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URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Mon Feb 22 08:49:44 2016 From: franciscolopezdelafranca at gmail.com (Francisco Lopez de la Franca) Date: Mon, 22 Feb 2016 14:49:44 +0100 Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <3F877AC4-BCD1-43FF-B8B3-7B30F9B6D30B@mail.nih.gov> Message-ID: Hi Brad, Of course I tried out the mask support you provide to the github repository. In fact, if I donot make use of the mask image, the processing of a 3D image takes 10 minutes aproximately. By using the mask image, it takes 75 seconds on a Intel Core2. What I do with the 3D image is to extract all its blobs and within a loop dealing with each one and calculating their texture features with your class. So, I'm very glad that finally I've got what I needed and the performance is very good. Thank you so much. /Francisco 2016-02-22 14:42 GMT+01:00 Bradley Lowekamp [via ITK Insight Users] < ml-node+s2283740n7588531h96 at n2.nabble.com>: > Francisco, > > Glad to hear that you figured out the problem with your code. > > Were you able to try out the change to add Mask support I committed to the > github repository? Does this meet you masking needs and improve your > performance? > > Please consider studying the difference between your change any my change > and the performance implications. > > Enjoy, > Brad > > On Feb 22, 2016, at 7:18 AM, Francisco Lopez de la Franca <[hidden email] > > wrote: > > Hi. > In the end the crash came for my fault. I was creating the mask image in > the wrong way. Sorry for the disturbances, and thank you very much > everybody. > Kind regards. > /Francisco > > 2016-02-18 19:00 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden email] > >: > >> /bigobj is an option for msvc, not mingw. >> >> But that is a different problem from crashing code. If you start a new >> thread, somebody with MinGW experience might help you. >> >> On Thu, Feb 18, 2016 at 12:30 PM, Francisco Lopez de la Franca <[hidden >> email] > wrote: >> >>> Yes. I use mingw (x86_64-w64-mingw32-g++.exe) and I set in CMAKE GUI the >>> entry CMAKE_CXX_FLAGS to -bigobj and the result is "unrecognized option". >>> >>> >>> 2016-02-18 15:25 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>> email] >: >>> >>>> Have you tried /bigobj >>>> ? >>>> Are you using MinGW? Visual Studio is now free >>>> . >>>> >>>> HTH >>>> >>>> On Thu, Feb 18, 2016 at 6:37 AM, Francisco Lopez de la Franca <[hidden >>>> email] > wrote: >>>> >>>>> Hi again, >>>>> I've got ITK version 4.5.1 (a little bit old, I know), and after >>>>> making the changes suggested by Dzenanz and recompiling ITK, the problem >>>>> continues, that is, my code crashes at the same point. >>>>> >>>>> Then, I've downloaded the latest stable ITK version, ITK 4.9.0 and >>>>> compiled from scratch and I get the following error: >>>>> >>>>> [ 98%] Building CXX object >>>>> Modules/IO/TransformBase/src/CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.obj >>>>> C:/MINGW/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: >>>>> CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: too many >>>>> sections (33106) >>>>> C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Assembler messages: >>>>> C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Fatal error: can't >>>>> write CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: >>>>> File too big >>>>> >>>>> After doing some "googling" and follow some of the instructions >>>>> referred on the web, I've been unable to solve this. >>>>> Has anyone met this problem and solved it? >>>>> Thanks. >>>>> KR. >>>>> /Francisco >>>>> >>>>> 2016-02-16 22:13 GMT+01:00 Bradley Lowekamp [via ITK Insight Users] <[hidden >>>>> email] >: >>>>> >>>>>> Hello, >>>>>> >>>>>> Please take a look at these changes: >>>>>> >>>>>> https://github.com/blowekamp/itkTextureAnalysis/commit/9654d74ea1d09f0677f1d1b93242cc94340591bf >>>>>> >>>>>> Brad >>>>>> >>>>>> On Feb 16, 2016, at 10:35 AM, D?enan Zuki? <[hidden email] >>>>>> > wrote: >>>>>> >>>>>> I have set up a project using one of the tests from Brad's repository >>>>>> (attached), and it works in debug mode both with his original code and with >>>>>> your modified class, and crashes in release mode both with his original >>>>>> code and with your modified class. I will now compile ITK in RelWithDebInfo >>>>>> in an attempt to figure out where is the crash occurring. >>>>>> >>>>>> Regards, >>>>>> D?enan >>>>>> >>>>>> On Tue, Feb 16, 2016 at 1:52 AM, Francisco Lopez de la Franca <[hidden >>>>>> email] > wrote: >>>>>> >>>>>>> Excuse me Dzenanz, but that's not completely true, because I've >>>>>>> tested Brad's class and it works right. >>>>>>> The problem seems to be that when you add a new neighbor iterator to >>>>>>> include just the mask points in the "histogram" then it is when the >>>>>>> application crashes, and I donot understand why. >>>>>>> If you just comment the 'maskIter' references you'll see that the >>>>>>> application works. >>>>>>> I've created a single threaded class based on the Brad's code and it >>>>>>> works but it is twice slower, that is why I'm interesting on Brad's class >>>>>>> (multi-threaded) to make it work. >>>>>>> >>>>>>> >>>>>>> 2016-02-15 17:15 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>>>>> email] >: >>>>>>> >>>>>>>> Hi Francisco, >>>>>>>> >>>>>>>> both your code and Brad's code run in debug mode (I did not wait >>>>>>>> for the end), and both crash in release mode immediately on startup. Here >>>>>>>> is a sample output: >>>>>>>> >>>>>>>> Progress input: 0000000002868970 >>>>>>>> input: 0000000002868970 >>>>>>>> _maskImage: 0000000002868970 >>>>>>>> _maskImage: 0000000002868970 >>>>>>>> input: 0000000002868970 >>>>>>>> _maskImage: 0000000002868970 >>>>>>>> iter.first: iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>>>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>>>> [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>>>> niter index: [5, 5, 210] >>>>>>>> niter index: [5, 5, 140] >>>>>>>> maskIter index: [5, 5, 140] >>>>>>>> maskIter index: [5, 5, 210] >>>>>>>> Before p3 >>>>>>>> input: 0000000002868970 >>>>>>>> _maskImage: 0000000002868970 >>>>>>>> After p3: | 0niter index: [5, 5, 70] >>>>>>>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>>>> niter index: [5, 5, 5] >>>>>>>> ? >>>>>>>> maskIter index: [5, 5, 70] >>>>>>>> After p4: ? >>>>>>>> Before p3 >>>>>>>> Before p3 >>>>>>>> After p3: ?iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>>>>> niter index: [5, 5, 140] >>>>>>>> maskIter index: [5, 5, 140] >>>>>>>> maskIter index: [5, 5, 5] >>>>>>>> Before p3 >>>>>>>> After p3: ? >>>>>>>> After p3: ? >>>>>>>> After p4: ? >>>>>>>> After p4: ? >>>>>>>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>>>>> niter index: [5, 5, 5] >>>>>>>> maskIter index: [5, 5, 5] >>>>>>>> >>>>>>>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>>>>> Before p3 >>>>>>>> Before p3 >>>>>>>> After p4: ? >>>>>>>> After p3: ? >>>>>>>> After p4: ? >>>>>>>> >>>>>>>> Regards, >>>>>>>> D?enan >>>>>>>> >>>>>>>> On Mon, Feb 15, 2016 at 1:36 AM, Francisco Lopez de la Franca <[hidden >>>>>>>> email] > >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> Here they are. >>>>>>>>> KR. >>>>>>>>> >>>>>>>>> 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>>>>>>> email] >: >>>>>>>>> >>>>>>>>>> Hi Francisco, >>>>>>>>>> >>>>>>>>>> do you mind attaching the modified files or pointing to your fork >>>>>>>>>> of it on GitHub? >>>>>>>>>> >>>>>>>>>> Regards >>>>>>>>>> >>>>>>>>>> On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden >>>>>>>>>> email] > >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> Hi Dzenan, >>>>>>>>>>> The original class is here: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >>>>>>>>>>> >>>>>>>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >>>>>>>>>>> >>>>>>>>>>> I've just added setInput and setMaskImage methods and modify >>>>>>>>>>> some lines in >>>>>>>>>>> the original class as I indicated in the yesterday mail within >>>>>>>>>>> this thread. >>>>>>>>>>> I'm running it on Windows, and there is no error at all, just a >>>>>>>>>>> crash. I >>>>>>>>>>> may have to include exceptions management. >>>>>>>>>>> The crash occurs just when calling p3 = >>>>>>>>>>> maskIter.GetPixel(iter->first) >>>>>>>>>>> >>>>>>>>>>> If you know why it could be or if you need more clarification, >>>>>>>>>>> please let >>>>>>>>>>> me know. >>>>>>>>>>> Many thanks >>>>>>>>>>> >>>>>>>>>>> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >>>>>>>>>>> [hidden email] >>>>>>>>>>> >: >>>>>>>>>>> >>>>>>>>>>> > Hi Francisco, >>>>>>>>>>> > >>>>>>>>>>> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the >>>>>>>>>>> error message >>>>>>>>>>> > that goes along with the crash? In which file and line does it >>>>>>>>>>> crash? >>>>>>>>>>> > >>>>>>>>>>> > Regards >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca >>>>>>>>>>> <[hidden >>>>>>>>>>> > email] >>>>>>>>>> >> wrote: >>>>>>>>>>> > >>>>>>>>>>> >> Hi, >>>>>>>>>>> >> Please, someone that could help me. I'm working in a >>>>>>>>>>> pre-doctorate >>>>>>>>>>> >> project and I need this class to work. >>>>>>>>>>> >> I've read the chapter 13 in the ITK Software Guide on how to >>>>>>>>>>> write a >>>>>>>>>>> >> filter and now I see the fact of the threads due to >>>>>>>>>>> inheritance of >>>>>>>>>>> >> ImageToImageFilter. >>>>>>>>>>> >> But, I keep on without understanding why the code crashes >>>>>>>>>>> just when >>>>>>>>>>> >> calling >>>>>>>>>>> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >>>>>>>>>>> >> It is just a call to read data, not to write. >>>>>>>>>>> >> >>>>>>>>>>> >> I guess somebody that had worked with creation of filters >>>>>>>>>>> might see >>>>>>>>>>> >> "easily" the problem, but not me. >>>>>>>>>>> >> >>>>>>>>>>> >> So, again, please, I need someone to help me with this >>>>>>>>>>> because I'm stuck >>>>>>>>>>> >> on this point. >>>>>>>>>>> >> >>>>>>>>>>> >> Thank you very much. >>>>>>>>>>> >> KR. >>>>>>>>>>> >> /Francisco >>>>>>>>>>> >> >>>>>>>>>>> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca >>>>>>>>>>> <[hidden email] >>>>>>>>>>> >> >>>>>>>>>> >>: >>>>>>>>>>> >> >>>>>>>>>>> >>> Hi Bradley again. >>>>>>>>>>> >>> I'm modifying your class in order to be able to set a mask >>>>>>>>>>> image (a >>>>>>>>>>> >>> binary image) to be used as a limit in the histogram >>>>>>>>>>> calculations, I mean, >>>>>>>>>>> >>> I set an input, a mask and the class should take into >>>>>>>>>>> account to calculate >>>>>>>>>>> >>> the histograms only the voxels that belong to the input and >>>>>>>>>>> to the mask >>>>>>>>>>> >>> image and having the value 1 in the mask image. >>>>>>>>>>> >>> The changes seem to be easy but I don?t know why my tests >>>>>>>>>>> are not >>>>>>>>>>> >>> working. It seems that 2 threads are working at the same >>>>>>>>>>> time and when I >>>>>>>>>>> >>> added my mask iterator, the code crashes. >>>>>>>>>>> >>> >>>>>>>>>>> >>> *** Consider that the input and mask images are the same >>>>>>>>>>> origin, spacing >>>>>>>>>>> >>> and size. >>>>>>>>>>> >>> >>>>>>>>>>> >>> I attach the main changes I've done, and I would thank you a >>>>>>>>>>> lot if you >>>>>>>>>>> >>> don't mind having a look and help me to find what I'm doing >>>>>>>>>>> wrong: >>>>>>>>>>> >>> >>>>>>>>>>> >>> template< class TImageType, class TOutputImage > >>>>>>>>>>> >>> void >>>>>>>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>>>>>>> >::*SetInput*(InputImageType >>>>>>>>>>> >>> *image) >>>>>>>>>>> >>> { >>>>>>>>>>> >>> // Process object is not const-correct so the const_cast >>>>>>>>>>> is required >>>>>>>>>>> >>> here >>>>>>>>>>> >>> this->ProcessObject::SetNthInput( 0, >>>>>>>>>>> >>> const_cast< >>>>>>>>>>> InputImageType * >( >>>>>>>>>>> >>> image ) ); >>>>>>>>>>> >>> } >>>>>>>>>>> >>> >>>>>>>>>>> >>> template< class TImageType, class TOutputImage > >>>>>>>>>>> >>> void >>>>>>>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>>>>>>> >::*SetMaskImage*(InputImageType >>>>>>>>>>> >>> *image) >>>>>>>>>>> >>> { >>>>>>>>>>> >>> // Process object is not const-correct so the const_cast >>>>>>>>>>> is required >>>>>>>>>>> >>> here >>>>>>>>>>> >>> this->ProcessObject::SetNthInput( 1, const_cast< >>>>>>>>>>> InputImageType * >( >>>>>>>>>>> >>> image ) ); >>>>>>>>>>> >>> >>>>>>>>>>> >>> _maskImage = image; // _maskImage is a private member >>>>>>>>>>> >>> } >>>>>>>>>>> >>> >>>>>>>>>>> >>> In the *ThreadedGenerateData*(const RegionType& >>>>>>>>>>> outputRegionForThread, >>>>>>>>>>> >>> ThreadIdType threadId ) method: >>>>>>>>>>> >>> { >>>>>>>>>>> >>> >>>>>>>>>>> >>> ... >>>>>>>>>>> >>> >>>>>>>>>>> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit >>>>>>>>>>> ) >>>>>>>>>>> >>> { >>>>>>>>>>> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >>>>>>>>>>> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, >>>>>>>>>>> *fit);* >>>>>>>>>>> >>> OutputIterator outIter(output, *fit); >>>>>>>>>>> >>> >>>>>>>>>>> >>> OutputPixelType out; >>>>>>>>>>> >>> NumericTraits::SetLength( out, >>>>>>>>>>> >>> this->GetNumberOfOutputComponents() ); >>>>>>>>>>> >>> >>>>>>>>>>> >>> while( !nIter.IsAtEnd() ) >>>>>>>>>>> >>> { >>>>>>>>>>> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >>>>>>>>>>> >>> >>>>>>>>>>> >>> ... >>>>>>>>>>> >>> >>>>>>>>>>> >>> ++nIter; >>>>>>>>>>> >>> ++outIter; >>>>>>>>>>> >>> * ++maskIter;* >>>>>>>>>>> >>> ... >>>>>>>>>>> >>> >>>>>>>>>>> >>> In the *FillHistogram *method: >>>>>>>>>>> >>> { >>>>>>>>>>> >>> >>>>>>>>>>> >>> ... >>>>>>>>>>> >>> >>>>>>>>>>> >>> while( iter != m_CooccurenceOffsetVector.end() ) >>>>>>>>>>> >>> { >>>>>>>>>>> >>> >>>>>>>>>>> >>> const PixelType p1 = niter.GetPixel(iter->first); >>>>>>>>>>> >>> const PixelType p2 = niter.GetPixel(iter->second); >>>>>>>>>>> >>> std::cout << "Before p3" << std::endl; >>>>>>>>>>> >>> >>>>>>>>>>> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); >>>>>>>>>>> *std::cout >>>>>>>>>>> >>> << "After p3: " << p3 << std::endl; >>>>>>>>>>> >>> >>>>>>>>>>> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); >>>>>>>>>>> * >>>>>>>>>>> >>> std::cout << "After p4: " << p4 << std::endl; >>>>>>>>>>> >>> >>>>>>>>>>> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 >>>>>>>>>>> <= m_Max >>>>>>>>>>> >>> *&& p3 == _insidePixelValue && p4 == >>>>>>>>>>> _insidePixelValue* ) >>>>>>>>>>> >>> // The point >>>>>>>>>>> >>> { >>>>>>>>>>> >>> >>>>>>>>>>> >>> ... >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thank you so much. >>>>>>>>>>> >>> My kind regards. >>>>>>>>>>> >>> /Paco >>>>>>>>>>> >>> >>>>>>>>>>> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca >>>>>>>>>>> <[hidden email] >>>>>>>>>>> >>> >>>>>>>>>> >>: >>>>>>>>>>> >>> >>>>>>>>>>> >>>> Hello Bradley again. >>>>>>>>>>> >>>> Sorry but I'd like to re-open this issue because I need >>>>>>>>>>> your class but >>>>>>>>>>> >>>> with some modification. >>>>>>>>>>> >>>> I pass to tell you. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> As my tests with your external class were not good taking >>>>>>>>>>> into account >>>>>>>>>>> >>>> the performance, I wonder if you could create a variant of >>>>>>>>>>> it, but in which >>>>>>>>>>> >>>> I can set a mask image and your class just return the >>>>>>>>>>> VectorImage with all >>>>>>>>>>> >>>> the features for that region (the masked locations) as >>>>>>>>>>> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >>>>>>>>>>> >>>> I mean, to get the vector image with all the features but >>>>>>>>>>> just >>>>>>>>>>> >>>> calculate it for the regions belonging to the mask image. >>>>>>>>>>> Positions not >>>>>>>>>>> >>>> belonging to the mask region could have a pixel value of 0, >>>>>>>>>>> for instance. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> I don?t know if it is very costly for you, but I would >>>>>>>>>>> thank you so >>>>>>>>>>> >>>> much. Otherwise, I could try it but I'd need your >>>>>>>>>>> suggestions on how to do >>>>>>>>>>> >>>> it. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Thanks a lot. >>>>>>>>>>> >>>> Best regards. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca >>>>>>>>>>> <[hidden email] >>>>>>>>>>> >>>> >>>>>>>>>> >>: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>>> Hello Bradley again, >>>>>>>>>>> >>>>> I would like to ask you for a couple of favours. In the >>>>>>>>>>> one hand, >>>>>>>>>>> >>>>> could you please send me your 3D image so that I can test >>>>>>>>>>> on it? And on the >>>>>>>>>>> >>>>> other hand, could you test the example I have referenced >>>>>>>>>>> in the previous >>>>>>>>>>> >>>>> email with your image, not changing anything in the code, >>>>>>>>>>> such as it is, >>>>>>>>>>> >>>>> and tell me if the execution time is normal? >>>>>>>>>>> >>>>> Thank you very much. >>>>>>>>>>> >>>>> Regards, >>>>>>>>>>> >>>>> /Francisco >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> PS: All my application trace is printed via standard >>>>>>>>>>> 'cout' command, >>>>>>>>>>> >>>>> not due to a debugging compilation mode. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp >>>>>>>>>>> <[hidden >>>>>>>>>>> >>>>> email] < >>>>>>>>>>> http:///user/SendEmail.jtp?type=node&node=7588477&i=4 >>>>>>>>>>> >> >>>>>>>>>>> >>>>> escribi?: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>>> Hello, >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Did you compile TextureFeatureImage in Release mode? >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> 1) The filter does not scale well with a large radius. >>>>>>>>>>> And given by >>>>>>>>>>> >>>>>> your initial report of print a very large number of >>>>>>>>>>> offset you, it sounds >>>>>>>>>>> >>>>>> like you are using a large radius with many offsets. I >>>>>>>>>>> created a >>>>>>>>>>> >>>>>> 224x224x300 unsigned short image and ran with the default >>>>>>>>>>> offset and a >>>>>>>>>>> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this >>>>>>>>>>> filter is was ~10x >>>>>>>>>>> >>>>>> faster than this example... things change though... >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> 2) I sounds like the boundaries/limits of the histogram >>>>>>>>>>> may be >>>>>>>>>>> >>>>>> clipping you values. I would inspect the co-occurance >>>>>>>>>>> matrix. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> HTH, >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca >>>>>>>>>>> <[hidden >>>>>>>>>>> >>>>>> email] < >>>>>>>>>>> http:///user/SendEmail.jtp?type=node&node=7588477&i=5 >>>>>>>>>>> >> >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I've tested with itkTextureFeatureImageFilter, with >>>>>>>>>>> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>>>>>>>>> >>>>>> >>>>>>>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures >>>>>>>>>>> example, >>>>>>>>>>> >>>>>> for a 3D image and here are my comments: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> 1. I had to interrupt the test after several hours and it >>>>>>>>>>> kept on >>>>>>>>>>> >>>>>> calculating. And this is for only a 3D image >>>>>>>>>>> (224x224x300). I need to >>>>>>>>>>> >>>>>> process around 35 images. >>>>>>>>>>> >>>>>> 2. The result (texture features: entropy, energy, >>>>>>>>>>> correlation, LH, >>>>>>>>>>> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, >>>>>>>>>>> 0, 7.83083e+247]. >>>>>>>>>>> >>>>>> These values were not what I expected based on my >>>>>>>>>>> experience on another >>>>>>>>>>> >>>>>> application I developed, but in that case, I calculated >>>>>>>>>>> the texture >>>>>>>>>>> >>>>>> features for an image as a whole, not voxel by voxel. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Regards. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >>>>>>>>>>> >>>>>> >>>>>>>>>> >>: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>>> i yes i have tried radius = 3; >>>>>>>>>>> >>>>>>> still no luck >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca >>>>>>>>>>> [via ITK >>>>>>>>>>> >>>>>>> Insight >>>>>>>>>>> >>>>>>> Users] <[hidden email] >>>>>>>>>>> >>>>>>> >>>>>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> > Have you tried with a radius of 3 instead of 1? >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>>>>>>>>> >>>>>>> > >>>>>>>>>> >>: >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> >> hey Matt, >>>>>>>>>>> >>>>>>> >> thanks for ur advice.. it did build successfully... >>>>>>>>>>> but im not >>>>>>>>>>> >>>>>>> able to run >>>>>>>>>>> >>>>>>> >> the code for 2D png image... i tried to change the >>>>>>>>>>> dimension to 2 >>>>>>>>>>> >>>>>>> and >>>>>>>>>>> >>>>>>> >> build >>>>>>>>>>> >>>>>>> >> it which it did.. but when i run the code using the >>>>>>>>>>> command >>>>>>>>>>> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png >>>>>>>>>>> putput.png >>>>>>>>>>> >>>>>>> 1... i see >>>>>>>>>>> >>>>>>> >> this output >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> offset: [-1, -1] [0, -1] >>>>>>>>>>> >>>>>>> >> offset: [0, -1] [1, -1] >>>>>>>>>>> >>>>>>> >> offset: [-1, 0] [0, 0] >>>>>>>>>>> >>>>>>> >> offset: [0, 0] [1, 0] >>>>>>>>>>> >>>>>>> >> offset: [-1, 1] [0, 1] >>>>>>>>>>> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the >>>>>>>>>>> program... if pls >>>>>>>>>>> >>>>>>> tel me >>>>>>>>>>> >>>>>>> >> how can i modify this code to work wid 2d image... >>>>>>>>>>> forgive me if >>>>>>>>>>> >>>>>>> my ques >>>>>>>>>>> >>>>>>> >> are really silly im trying to learn something.. >>>>>>>>>>> >>>>>>> >> regards >>>>>>>>>>> >>>>>>> >> Vis >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 >>>>>>>>>>> [via ITK >>>>>>>>>>> >>>>>>> Insight Users] >>>>>>>>>>> >>>>>>> >> < >>>>>>>>>>> >>>>>>> >> [hidden email] < >>>>>>>>>>> >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1 >>>>>>>>>>> >> >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> > Hi, >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > The function: >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char >>>>>>>>>>> *argv[]) >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > must be renamed to >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > main(int argc, char* argv[]) >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > HTH, >>>>>>>>>>> >>>>>>> >> > Matt >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>>>>>>>>> >>>>>>> >> > < >>>>>>>>>>> http:///user/SendEmail.jtp?type=node&node=7587952&i=0 >>>>>>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > > hi all, >>>>>>>>>>> >>>>>>> >> > > im trying to build the >>>>>>>>>>> itkTextureFeatureImageFilterTest.cxx >>>>>>>>>>> >>>>>>> code but >>>>>>>>>>> >>>>>>> >> im >>>>>>>>>>> >>>>>>> >> > not >>>>>>>>>>> >>>>>>> >> > > able to it is showing the following error >>>>>>>>>>> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>>>>>>>>> >>>>>>> Configuration: >>>>>>>>>>> >>>>>>> >> Debug >>>>>>>>>>> >>>>>>> >> > x64 >>>>>>>>>>> >>>>>>> >> > > ------ >>>>>>>>>>> >>>>>>> >> > > 1> Checking Build System >>>>>>>>>>> >>>>>>> >> > > 1> CMake does not need to re-run because >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >>>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>>>>>>>>> >>>>>>> >> > is >>>>>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>>>>> >>>>>>> >> > > 2>------ Rebuild All started: Project: >>>>>>>>>>> >>>>>>> >> itkTextureFeatureImageFilterTest, >>>>>>>>>>> >>>>>>> >> > > Configuration: Debug x64 ------ >>>>>>>>>>> >>>>>>> >> > > 2> Building Custom Rule >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>>>>>> >>>>>>> >> > > 2> CMake does not need to re-run because >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >>>>>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>>>>>> >>>>>>> >> > is >>>>>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>>>>> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>>>>>>>>> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>>>>>>>>> >>>>>>> 'std::_Copy_impl': >>>>>>>>>>> >>>>>>> >> > Function >>>>>>>>>>> >>>>>>> >> > > call with parameters that may be unsafe - this >>>>>>>>>>> call relies on >>>>>>>>>>> >>>>>>> the >>>>>>>>>>> >>>>>>> >> caller >>>>>>>>>>> >>>>>>> >> > to >>>>>>>>>>> >>>>>>> >> > > check that the passed values are correct. To >>>>>>>>>>> disable this >>>>>>>>>>> >>>>>>> warning, use >>>>>>>>>>> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on >>>>>>>>>>> how to use >>>>>>>>>>> >>>>>>> Visual C++ >>>>>>>>>>> >>>>>>> >> > > 'Checked Iterators' >>>>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft >>>>>>>>>>> Visual Studio >>>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration >>>>>>>>>>> of >>>>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>>>> >>>>>>> >> > > 2> >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>>>>>>>>> >>>>>>> >> > see >>>>>>>>>>> >>>>>>> >> > > reference to function template instantiation >>>>>>>>>>> '_OutIt >>>>>>>>>>> >>>>>>> std::copy>>>>>>>>>> >>>>>>> >> > > unsigned char*,unsigned >>>>>>>>>>> char*>(_InIt,_InIt,_OutIt)' being >>>>>>>>>>> >>>>>>> compiled >>>>>>>>>>> >>>>>>> >> > > 2> with >>>>>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>>>>> >>>>>>> >> > > 2> _OutIt=unsigned char *, >>>>>>>>>>> >>>>>>> >> > > 2> _InIt=const unsigned char * >>>>>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>>>>> >>>>>>> >> > > 2> >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>>>>>>>>> >>>>>>> >> > > while compiling class template member function >>>>>>>>>>> 'void >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> itk::ImageFileReader::GenerateData(void)' >>>>>>>>>>> >>>>>>> >> > > 2> with >>>>>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>>>>> >>>>>>> >> > > 2> >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > > : see reference to class template instantiation >>>>>>>>>>> >>>>>>> >> > > 'itk::ImageFileReader' being >>>>>>>>>>> compiled >>>>>>>>>>> >>>>>>> >> > > 2> with >>>>>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft >>>>>>>>>>> Visual Studio >>>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration >>>>>>>>>>> of >>>>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft >>>>>>>>>>> Visual Studio >>>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration >>>>>>>>>>> of >>>>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft >>>>>>>>>>> Visual Studio >>>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration >>>>>>>>>>> of >>>>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>>>> >>>>>>> >> > > 2> Creating library >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > > and object >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: >>>>>>>>>>> unresolved >>>>>>>>>>> >>>>>>> external symbol >>>>>>>>>>> >>>>>>> >> > main >>>>>>>>>>> >>>>>>> >> > > referenced in function __tmainCRTStartup >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>>>>>>>>> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>>>>>>>>> >>>>>>> Configuration: Debug >>>>>>>>>>> >>>>>>> >> > x64 >>>>>>>>>>> >>>>>>> >> > > ------ >>>>>>>>>>> >>>>>>> >> > > 3> Building Custom Rule >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>>>>>> >>>>>>> >> > > 3> CMake does not need to re-run because >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >>>>>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>>>>>> >>>>>>> >> > is >>>>>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>>>>> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 >>>>>>>>>>> skipped >>>>>>>>>>> >>>>>>> ========== >>>>>>>>>>> >>>>>>> >> > > im using the follwing CMakeList.txt >>>>>>>>>>> >>>>>>> >> > > # This is the root ITK CMakeLists file. >>>>>>>>>>> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>>>>>>>>> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >>>>>>>>>>> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>>>>>>>>> >>>>>>> >> > > endif() >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > # This project is designed to be built outside >>>>>>>>>>> the Insight >>>>>>>>>>> >>>>>>> source >>>>>>>>>>> >>>>>>> >> tree. >>>>>>>>>>> >>>>>>> >> > > project(HelloWorld) >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > # Find ITK. >>>>>>>>>>> >>>>>>> >> > > find_package(ITK REQUIRED) >>>>>>>>>>> >>>>>>> >> > > include(${ITK_USE_FILE}) >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>>>>>>>>> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> target_link_libraries(itkTextureFeatureImageFilterTest >>>>>>>>>>> >>>>>>> >> ${ITK_LIBRARIES}) >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > please tel me wat the error is?? >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > -- >>>>>>>>>>> >>>>>>> >> > > View this message in context: >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>>>>>>>>> >>>>>>> >> > > Sent from the ITK Insight Users mailing list >>>>>>>>>>> archive at >>>>>>>>>>> >>>>>>> Nabble.com . >>>>>>>>>>> >>>>>>> >> > > _____________________________________ >>>>>>>>>>> >>>>>>> >> > > Powered by www.kitware.com >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > Visit other Kitware open-source projects at >>>>>>>>>>> >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > Kitware offers ITK Training Courses, for more >>>>>>>>>>> information >>>>>>>>>>> >>>>>>> visit: >>>>>>>>>>> >>>>>>> >> > > http://www.kitware.com/products/protraining.php >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > Please keep messages on-topic and check the ITK >>>>>>>>>>> FAQ at: >>>>>>>>>>> >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > Follow this 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_____________________________________ >>>>>>>>>>> >>>>>>> >> Powered by www.kitware.com >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Visit other Kitware open-source projects at >>>>>>>>>>> >>>>>>> >> http://www.kitware.com/opensource/opensource.html >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Kitware offers ITK Training Courses, for more >>>>>>>>>>> information visit: >>>>>>>>>>> >>>>>>> >> http://www.kitware.com/products/protraining.php >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Please keep messages on-topic and check the ITK FAQ >>>>>>>>>>> at: >>>>>>>>>>> >>>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Follow this link to subscribe/unsubscribe: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > _____________________________________ >>>>>>>>>>> >>>>>>> > Powered by www.kitware.com >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Visit other Kitware open-source projects at >>>>>>>>>>> >>>>>>> > http://www.kitware.com/opensource/opensource.html >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Kitware offers ITK Training Courses, for more >>>>>>>>>>> information visit: >>>>>>>>>>> >>>>>>> > http://www.kitware.com/products/protraining.php >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>>> >>>>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Follow this link to subscribe/unsubscribe: >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > ------------------------------ >>>>>>>>>>> >>>>>>> > If you reply to this email, your message will be added >>>>>>>>>>> to the >>>>>>>>>>> >>>>>>> discussion >>>>>>>>>>> >>>>>>> > below: >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> >>>>>>>>>>> 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>>>>>> >>>>>>>>>>> >>>>>> _____________________________________ >>>>>>>>>>> >>>>>> Powered by www.kitware.com >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>>>>>>> >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Kitware offers ITK Training Courses, for more information >>>>>>>>>>> visit: >>>>>>>>>>> >>>>>> http://www.kitware.com/products/protraining.php >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>>> >>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>>>>> >>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>> >>>>>>>>>>> >>> >>>>>>>>>>> >> >>>>>>>>>>> >> _____________________________________ >>>>>>>>>>> >> Powered by www.kitware.com >>>>>>>>>>> >> >>>>>>>>>>> >> Visit other Kitware 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_____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> ------------------------------ >> If you reply to this email, your message will be added to the discussion >> below: >> >> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588516.html >> To start a new topic under ITK Insight Users, email [hidden email] >> >> To unsubscribe from ITK Insight Users, click here. >> NAML >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > 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http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588531.html > To start a new topic under ITK Insight Users, email > ml-node+s2283740n2283740h75 at n2.nabble.com > To unsubscribe from ITK Insight Users, click here > > . > NAML > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From franciscolopezdelafranca at gmail.com Mon Feb 22 08:49:46 2016 From: franciscolopezdelafranca at gmail.com (=?UTF-8?Q?Francisco_L=C3=B3pez-Franca?=) Date: Mon, 22 Feb 2016 06:49:46 -0700 (MST) Subject: [ITK] [ITK-users] Texture pixel by pixel In-Reply-To: References: <3F877AC4-BCD1-43FF-B8B3-7B30F9B6D30B@mail.nih.gov> Message-ID: Hi Brad, Of course I tried out the mask support you provide to the github repository. In fact, if I donot make use of the mask image, the processing of a 3D image takes 10 minutes aproximately. By using the mask image, it takes 75 seconds on a Intel Core2. What I do with the 3D image is to extract all its blobs and within a loop dealing with each one and calculating their texture features with your class. So, I'm very glad that finally I've got what I needed and the performance is very good. Thank you so much. /Francisco 2016-02-22 14:42 GMT+01:00 Bradley Lowekamp [via ITK Insight Users] < ml-node+s2283740n7588531h96 at n2.nabble.com>: > Francisco, > > Glad to hear that you figured out the problem with your code. > > Were you able to try out the change to add Mask support I committed to the > github repository? Does this meet you masking needs and improve your > performance? > > Please consider studying the difference between your change any my change > and the performance implications. > > Enjoy, > Brad > > On Feb 22, 2016, at 7:18 AM, Francisco Lopez de la Franca <[hidden email] > > wrote: > > Hi. > In the end the crash came for my fault. I was creating the mask image in > the wrong way. Sorry for the disturbances, and thank you very much > everybody. > Kind regards. > /Francisco > > 2016-02-18 19:00 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden email] > >: > >> /bigobj is an option for msvc, not mingw. >> >> But that is a different problem from crashing code. If you start a new >> thread, somebody with MinGW experience might help you. >> >> On Thu, Feb 18, 2016 at 12:30 PM, Francisco Lopez de la Franca <[hidden >> email] > wrote: >> >>> Yes. I use mingw (x86_64-w64-mingw32-g++.exe) and I set in CMAKE GUI the >>> entry CMAKE_CXX_FLAGS to -bigobj and the result is "unrecognized option". >>> >>> >>> 2016-02-18 15:25 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>> email] >: >>> >>>> Have you tried /bigobj >>>> ? >>>> Are you using MinGW? Visual Studio is now free >>>> . >>>> >>>> HTH >>>> >>>> On Thu, Feb 18, 2016 at 6:37 AM, Francisco Lopez de la Franca <[hidden >>>> email] > wrote: >>>> >>>>> Hi again, >>>>> I've got ITK version 4.5.1 (a little bit old, I know), and after >>>>> making the changes suggested by Dzenanz and recompiling ITK, the problem >>>>> continues, that is, my code crashes at the same point. >>>>> >>>>> Then, I've downloaded the latest stable ITK version, ITK 4.9.0 and >>>>> compiled from scratch and I get the following error: >>>>> >>>>> [ 98%] Building CXX object >>>>> Modules/IO/TransformBase/src/CMakeFiles/ITKIOTransformBase.dir/itkTransformFactoryBase.cxx.obj >>>>> C:/MINGW/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/4.8.2/../../../../x86_64-w64-mingw32/bin/as.exe: >>>>> CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: too many >>>>> sections (33106) >>>>> C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Assembler messages: >>>>> C:\Users\User~1\AppData\Local\Temp\ccrJIGis.s: Fatal error: can't >>>>> write CMakeFiles\ITKIOTransformBase.dir\itkTransformFactoryBase.cxx.obj: >>>>> File too big >>>>> >>>>> After doing some "googling" and follow some of the instructions >>>>> referred on the web, I've been unable to solve this. >>>>> Has anyone met this problem and solved it? >>>>> Thanks. >>>>> KR. >>>>> /Francisco >>>>> >>>>> 2016-02-16 22:13 GMT+01:00 Bradley Lowekamp [via ITK Insight Users] <[hidden >>>>> email] >: >>>>> >>>>>> Hello, >>>>>> >>>>>> Please take a look at these changes: >>>>>> >>>>>> https://github.com/blowekamp/itkTextureAnalysis/commit/9654d74ea1d09f0677f1d1b93242cc94340591bf >>>>>> >>>>>> Brad >>>>>> >>>>>> On Feb 16, 2016, at 10:35 AM, D?enan Zuki? <[hidden email] >>>>>> > wrote: >>>>>> >>>>>> I have set up a project using one of the tests from Brad's repository >>>>>> (attached), and it works in debug mode both with his original code and with >>>>>> your modified class, and crashes in release mode both with his original >>>>>> code and with your modified class. I will now compile ITK in RelWithDebInfo >>>>>> in an attempt to figure out where is the crash occurring. >>>>>> >>>>>> Regards, >>>>>> D?enan >>>>>> >>>>>> On Tue, Feb 16, 2016 at 1:52 AM, Francisco Lopez de la Franca <[hidden >>>>>> email] > wrote: >>>>>> >>>>>>> Excuse me Dzenanz, but that's not completely true, because I've >>>>>>> tested Brad's class and it works right. >>>>>>> The problem seems to be that when you add a new neighbor iterator to >>>>>>> include just the mask points in the "histogram" then it is when the >>>>>>> application crashes, and I donot understand why. >>>>>>> If you just comment the 'maskIter' references you'll see that the >>>>>>> application works. >>>>>>> I've created a single threaded class based on the Brad's code and it >>>>>>> works but it is twice slower, that is why I'm interesting on Brad's class >>>>>>> (multi-threaded) to make it work. >>>>>>> >>>>>>> >>>>>>> 2016-02-15 17:15 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>>>>> email] >: >>>>>>> >>>>>>>> Hi Francisco, >>>>>>>> >>>>>>>> both your code and Brad's code run in debug mode (I did not wait >>>>>>>> for the end), and both crash in release mode immediately on startup. Here >>>>>>>> is a sample output: >>>>>>>> >>>>>>>> Progress input: 0000000002868970 >>>>>>>> input: 0000000002868970 >>>>>>>> _maskImage: 0000000002868970 >>>>>>>> _maskImage: 0000000002868970 >>>>>>>> input: 0000000002868970 >>>>>>>> _maskImage: 0000000002868970 >>>>>>>> iter.first: iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>>>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>>>> [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>>>> niter index: [5, 5, 210] >>>>>>>> niter index: [5, 5, 140] >>>>>>>> maskIter index: [5, 5, 140] >>>>>>>> maskIter index: [5, 5, 210] >>>>>>>> Before p3 >>>>>>>> input: 0000000002868970 >>>>>>>> _maskImage: 0000000002868970 >>>>>>>> After p3: | 0niter index: [5, 5, 70] >>>>>>>> iter.first: [-5, -5, -5] iter.second: [-4, -5, -5] >>>>>>>> niter index: [5, 5, 5] >>>>>>>> ? >>>>>>>> maskIter index: [5, 5, 70] >>>>>>>> After p4: ? >>>>>>>> Before p3 >>>>>>>> Before p3 >>>>>>>> After p3: ?iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>>>>> niter index: [5, 5, 140] >>>>>>>> maskIter index: [5, 5, 140] >>>>>>>> maskIter index: [5, 5, 5] >>>>>>>> Before p3 >>>>>>>> After p3: ? >>>>>>>> After p3: ? >>>>>>>> After p4: ? >>>>>>>> After p4: ? >>>>>>>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>>>>> niter index: [5, 5, 5] >>>>>>>> maskIter index: [5, 5, 5] >>>>>>>> >>>>>>>> iter.first: [-4, -5, -5] iter.second: [-3, -5, -5] >>>>>>>> Before p3 >>>>>>>> Before p3 >>>>>>>> After p4: ? >>>>>>>> After p3: ? >>>>>>>> After p4: ? >>>>>>>> >>>>>>>> Regards, >>>>>>>> D?enan >>>>>>>> >>>>>>>> On Mon, Feb 15, 2016 at 1:36 AM, Francisco Lopez de la Franca <[hidden >>>>>>>> email] > >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi, >>>>>>>>> Here they are. >>>>>>>>> KR. >>>>>>>>> >>>>>>>>> 2016-02-12 16:22 GMT+01:00 dzenanz [via ITK Insight Users] <[hidden >>>>>>>>> email] >: >>>>>>>>> >>>>>>>>>> Hi Francisco, >>>>>>>>>> >>>>>>>>>> do you mind attaching the modified files or pointing to your fork >>>>>>>>>> of it on GitHub? >>>>>>>>>> >>>>>>>>>> Regards >>>>>>>>>> >>>>>>>>>> On Thu, Feb 11, 2016 at 12:08 PM, Francisco L?pez-Franca <[hidden >>>>>>>>>> email] > >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> Hi Dzenan, >>>>>>>>>>> The original class is here: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h >>>>>>>>>>> >>>>>>>>>>> https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx >>>>>>>>>>> >>>>>>>>>>> I've just added setInput and setMaskImage methods and modify >>>>>>>>>>> some lines in >>>>>>>>>>> the original class as I indicated in the yesterday mail within >>>>>>>>>>> this thread. >>>>>>>>>>> I'm running it on Windows, and there is no error at all, just a >>>>>>>>>>> crash. I >>>>>>>>>>> may have to include exceptions management. >>>>>>>>>>> The crash occurs just when calling p3 = >>>>>>>>>>> maskIter.GetPixel(iter->first) >>>>>>>>>>> >>>>>>>>>>> If you know why it could be or if you need more clarification, >>>>>>>>>>> please let >>>>>>>>>>> me know. >>>>>>>>>>> Many thanks >>>>>>>>>>> >>>>>>>>>>> 2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] < >>>>>>>>>>> [hidden email] >>>>>>>>>>> >: >>>>>>>>>>> >>>>>>>>>>> > Hi Francisco, >>>>>>>>>>> > >>>>>>>>>>> > "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the >>>>>>>>>>> error message >>>>>>>>>>> > that goes along with the crash? In which file and line does it >>>>>>>>>>> crash? >>>>>>>>>>> > >>>>>>>>>>> > Regards >>>>>>>>>>> > >>>>>>>>>>> > On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca >>>>>>>>>>> <[hidden >>>>>>>>>>> > email] >>>>>>>>>> >> wrote: >>>>>>>>>>> > >>>>>>>>>>> >> Hi, >>>>>>>>>>> >> Please, someone that could help me. I'm working in a >>>>>>>>>>> pre-doctorate >>>>>>>>>>> >> project and I need this class to work. >>>>>>>>>>> >> I've read the chapter 13 in the ITK Software Guide on how to >>>>>>>>>>> write a >>>>>>>>>>> >> filter and now I see the fact of the threads due to >>>>>>>>>>> inheritance of >>>>>>>>>>> >> ImageToImageFilter. >>>>>>>>>>> >> But, I keep on without understanding why the code crashes >>>>>>>>>>> just when >>>>>>>>>>> >> calling >>>>>>>>>>> >> *const PixelType p3 = maskIter.GetPixel(iter->first);* >>>>>>>>>>> >> It is just a call to read data, not to write. >>>>>>>>>>> >> >>>>>>>>>>> >> I guess somebody that had worked with creation of filters >>>>>>>>>>> might see >>>>>>>>>>> >> "easily" the problem, but not me. >>>>>>>>>>> >> >>>>>>>>>>> >> So, again, please, I need someone to help me with this >>>>>>>>>>> because I'm stuck >>>>>>>>>>> >> on this point. >>>>>>>>>>> >> >>>>>>>>>>> >> Thank you very much. >>>>>>>>>>> >> KR. >>>>>>>>>>> >> /Francisco >>>>>>>>>>> >> >>>>>>>>>>> >> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca >>>>>>>>>>> <[hidden email] >>>>>>>>>>> >> >>>>>>>>>> >>: >>>>>>>>>>> >> >>>>>>>>>>> >>> Hi Bradley again. >>>>>>>>>>> >>> I'm modifying your class in order to be able to set a mask >>>>>>>>>>> image (a >>>>>>>>>>> >>> binary image) to be used as a limit in the histogram >>>>>>>>>>> calculations, I mean, >>>>>>>>>>> >>> I set an input, a mask and the class should take into >>>>>>>>>>> account to calculate >>>>>>>>>>> >>> the histograms only the voxels that belong to the input and >>>>>>>>>>> to the mask >>>>>>>>>>> >>> image and having the value 1 in the mask image. >>>>>>>>>>> >>> The changes seem to be easy but I don?t know why my tests >>>>>>>>>>> are not >>>>>>>>>>> >>> working. It seems that 2 threads are working at the same >>>>>>>>>>> time and when I >>>>>>>>>>> >>> added my mask iterator, the code crashes. >>>>>>>>>>> >>> >>>>>>>>>>> >>> *** Consider that the input and mask images are the same >>>>>>>>>>> origin, spacing >>>>>>>>>>> >>> and size. >>>>>>>>>>> >>> >>>>>>>>>>> >>> I attach the main changes I've done, and I would thank you a >>>>>>>>>>> lot if you >>>>>>>>>>> >>> don't mind having a look and help me to find what I'm doing >>>>>>>>>>> wrong: >>>>>>>>>>> >>> >>>>>>>>>>> >>> template< class TImageType, class TOutputImage > >>>>>>>>>>> >>> void >>>>>>>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>>>>>>> >::*SetInput*(InputImageType >>>>>>>>>>> >>> *image) >>>>>>>>>>> >>> { >>>>>>>>>>> >>> // Process object is not const-correct so the const_cast >>>>>>>>>>> is required >>>>>>>>>>> >>> here >>>>>>>>>>> >>> this->ProcessObject::SetNthInput( 0, >>>>>>>>>>> >>> const_cast< >>>>>>>>>>> InputImageType * >( >>>>>>>>>>> >>> image ) ); >>>>>>>>>>> >>> } >>>>>>>>>>> >>> >>>>>>>>>>> >>> template< class TImageType, class TOutputImage > >>>>>>>>>>> >>> void >>>>>>>>>>> >>> TextureFeatureImageFilterV2< TImageType, TOutputImage >>>>>>>>>>> >::*SetMaskImage*(InputImageType >>>>>>>>>>> >>> *image) >>>>>>>>>>> >>> { >>>>>>>>>>> >>> // Process object is not const-correct so the const_cast >>>>>>>>>>> is required >>>>>>>>>>> >>> here >>>>>>>>>>> >>> this->ProcessObject::SetNthInput( 1, const_cast< >>>>>>>>>>> InputImageType * >( >>>>>>>>>>> >>> image ) ); >>>>>>>>>>> >>> >>>>>>>>>>> >>> _maskImage = image; // _maskImage is a private member >>>>>>>>>>> >>> } >>>>>>>>>>> >>> >>>>>>>>>>> >>> In the *ThreadedGenerateData*(const RegionType& >>>>>>>>>>> outputRegionForThread, >>>>>>>>>>> >>> ThreadIdType threadId ) method: >>>>>>>>>>> >>> { >>>>>>>>>>> >>> >>>>>>>>>>> >>> ... >>>>>>>>>>> >>> >>>>>>>>>>> >>> for ( fit = faceList.begin(); fit != faceList.end(); ++fit >>>>>>>>>>> ) >>>>>>>>>>> >>> { >>>>>>>>>>> >>> NeighborhoodIteratorType nIter( radius, input, *fit ); >>>>>>>>>>> >>> *NeighborhoodIteratorType maskIter( radius, _maskImage, >>>>>>>>>>> *fit);* >>>>>>>>>>> >>> OutputIterator outIter(output, *fit); >>>>>>>>>>> >>> >>>>>>>>>>> >>> OutputPixelType out; >>>>>>>>>>> >>> NumericTraits::SetLength( out, >>>>>>>>>>> >>> this->GetNumberOfOutputComponents() ); >>>>>>>>>>> >>> >>>>>>>>>>> >>> while( !nIter.IsAtEnd() ) >>>>>>>>>>> >>> { >>>>>>>>>>> >>> this->FillHistogram( *histogram, nIter, *maskIter *); >>>>>>>>>>> >>> >>>>>>>>>>> >>> ... >>>>>>>>>>> >>> >>>>>>>>>>> >>> ++nIter; >>>>>>>>>>> >>> ++outIter; >>>>>>>>>>> >>> * ++maskIter;* >>>>>>>>>>> >>> ... >>>>>>>>>>> >>> >>>>>>>>>>> >>> In the *FillHistogram *method: >>>>>>>>>>> >>> { >>>>>>>>>>> >>> >>>>>>>>>>> >>> ... >>>>>>>>>>> >>> >>>>>>>>>>> >>> while( iter != m_CooccurenceOffsetVector.end() ) >>>>>>>>>>> >>> { >>>>>>>>>>> >>> >>>>>>>>>>> >>> const PixelType p1 = niter.GetPixel(iter->first); >>>>>>>>>>> >>> const PixelType p2 = niter.GetPixel(iter->second); >>>>>>>>>>> >>> std::cout << "Before p3" << std::endl; >>>>>>>>>>> >>> >>>>>>>>>>> >>> * const PixelType p3 = maskIter.GetPixel(iter->first); >>>>>>>>>>> *std::cout >>>>>>>>>>> >>> << "After p3: " << p3 << std::endl; >>>>>>>>>>> >>> >>>>>>>>>>> >>> * const PixelType p4 = maskIter.GetPixel(iter->second); >>>>>>>>>>> * >>>>>>>>>>> >>> std::cout << "After p4: " << p4 << std::endl; >>>>>>>>>>> >>> >>>>>>>>>>> >>> if ( p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 >>>>>>>>>>> <= m_Max >>>>>>>>>>> >>> *&& p3 == _insidePixelValue && p4 == >>>>>>>>>>> _insidePixelValue* ) >>>>>>>>>>> >>> // The point >>>>>>>>>>> >>> { >>>>>>>>>>> >>> >>>>>>>>>>> >>> ... >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.* >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thank you so much. >>>>>>>>>>> >>> My kind regards. >>>>>>>>>>> >>> /Paco >>>>>>>>>>> >>> >>>>>>>>>>> >>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca >>>>>>>>>>> <[hidden email] >>>>>>>>>>> >>> >>>>>>>>>> >>: >>>>>>>>>>> >>> >>>>>>>>>>> >>>> Hello Bradley again. >>>>>>>>>>> >>>> Sorry but I'd like to re-open this issue because I need >>>>>>>>>>> your class but >>>>>>>>>>> >>>> with some modification. >>>>>>>>>>> >>>> I pass to tell you. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> As my tests with your external class were not good taking >>>>>>>>>>> into account >>>>>>>>>>> >>>> the performance, I wonder if you could create a variant of >>>>>>>>>>> it, but in which >>>>>>>>>>> >>>> I can set a mask image and your class just return the >>>>>>>>>>> VectorImage with all >>>>>>>>>>> >>>> the features for that region (the masked locations) as >>>>>>>>>>> >>>> itk::ScalarImageToTextureFeaturesFilter class does. >>>>>>>>>>> >>>> I mean, to get the vector image with all the features but >>>>>>>>>>> just >>>>>>>>>>> >>>> calculate it for the regions belonging to the mask image. >>>>>>>>>>> Positions not >>>>>>>>>>> >>>> belonging to the mask region could have a pixel value of 0, >>>>>>>>>>> for instance. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> I don?t know if it is very costly for you, but I would >>>>>>>>>>> thank you so >>>>>>>>>>> >>>> much. Otherwise, I could try it but I'd need your >>>>>>>>>>> suggestions on how to do >>>>>>>>>>> >>>> it. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> Thanks a lot. >>>>>>>>>>> >>>> Best regards. >>>>>>>>>>> >>>> >>>>>>>>>>> >>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca >>>>>>>>>>> <[hidden email] >>>>>>>>>>> >>>> >>>>>>>>>> >>: >>>>>>>>>>> >>>> >>>>>>>>>>> >>>>> Hello Bradley again, >>>>>>>>>>> >>>>> I would like to ask you for a couple of favours. In the >>>>>>>>>>> one hand, >>>>>>>>>>> >>>>> could you please send me your 3D image so that I can test >>>>>>>>>>> on it? And on the >>>>>>>>>>> >>>>> other hand, could you test the example I have referenced >>>>>>>>>>> in the previous >>>>>>>>>>> >>>>> email with your image, not changing anything in the code, >>>>>>>>>>> such as it is, >>>>>>>>>>> >>>>> and tell me if the execution time is normal? >>>>>>>>>>> >>>>> Thank you very much. >>>>>>>>>>> >>>>> Regards, >>>>>>>>>>> >>>>> /Francisco >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> PS: All my application trace is printed via standard >>>>>>>>>>> 'cout' command, >>>>>>>>>>> >>>>> not due to a debugging compilation mode. >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>> El mi?rcoles, 30 de septiembre de 2015, Bradley Lowekamp >>>>>>>>>>> <[hidden >>>>>>>>>>> >>>>> email] < >>>>>>>>>>> http:///user/SendEmail.jtp?type=node&node=7588477&i=4 >>>>>>>>>>> >> >>>>>>>>>>> >>>>> escribi?: >>>>>>>>>>> >>>>> >>>>>>>>>>> >>>>>> Hello, >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Did you compile TextureFeatureImage in Release mode? >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> 1) The filter does not scale well with a large radius. >>>>>>>>>>> And given by >>>>>>>>>>> >>>>>> your initial report of print a very large number of >>>>>>>>>>> offset you, it sounds >>>>>>>>>>> >>>>>> like you are using a large radius with many offsets. I >>>>>>>>>>> created a >>>>>>>>>>> >>>>>> 224x224x300 unsigned short image and ran with the default >>>>>>>>>>> offset and a >>>>>>>>>>> >>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this >>>>>>>>>>> filter is was ~10x >>>>>>>>>>> >>>>>> faster than this example... things change though... >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> 2) I sounds like the boundaries/limits of the histogram >>>>>>>>>>> may be >>>>>>>>>>> >>>>>> clipping you values. I would inspect the co-occurance >>>>>>>>>>> matrix. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> HTH, >>>>>>>>>>> >>>>>> Brad >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca >>>>>>>>>>> <[hidden >>>>>>>>>>> >>>>>> email] < >>>>>>>>>>> http:///user/SendEmail.jtp?type=node&node=7588477&i=5 >>>>>>>>>>> >> >>>>>>>>>>> >>>>>> wrote: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> I've tested with itkTextureFeatureImageFilter, with >>>>>>>>>>> >>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the >>>>>>>>>>> >>>>>> >>>>>>>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures >>>>>>>>>>> example, >>>>>>>>>>> >>>>>> for a 3D image and here are my comments: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> 1. I had to interrupt the test after several hours and it >>>>>>>>>>> kept on >>>>>>>>>>> >>>>>> calculating. And this is for only a 3D image >>>>>>>>>>> (224x224x300). I need to >>>>>>>>>>> >>>>>> process around 35 images. >>>>>>>>>>> >>>>>> 2. The result (texture features: entropy, energy, >>>>>>>>>>> correlation, LH, >>>>>>>>>>> >>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, >>>>>>>>>>> 0, 7.83083e+247]. >>>>>>>>>>> >>>>>> These values were not what I expected based on my >>>>>>>>>>> experience on another >>>>>>>>>>> >>>>>> application I developed, but in that case, I calculated >>>>>>>>>>> the texture >>>>>>>>>>> >>>>>> features for an image as a whole, not voxel by voxel. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> Regards. >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email] >>>>>>>>>>> >>>>>> >>>>>>>>>> >>: >>>>>>>>>>> >>>>>> >>>>>>>>>>> >>>>>>> i yes i have tried radius = 3; >>>>>>>>>>> >>>>>>> still no luck >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco L?pez-Franca >>>>>>>>>>> [via ITK >>>>>>>>>>> >>>>>>> Insight >>>>>>>>>>> >>>>>>> Users] <[hidden email] >>>>>>>>>>> >>>>>>> >>>>>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >>>>>>>>>>> >>>>>>> > Have you tried with a radius of 3 instead of 1? >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email] >>>>>>>>>>> >>>>>>> > >>>>>>>>>> >>: >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> >> hey Matt, >>>>>>>>>>> >>>>>>> >> thanks for ur advice.. it did build successfully... >>>>>>>>>>> but im not >>>>>>>>>>> >>>>>>> able to run >>>>>>>>>>> >>>>>>> >> the code for 2D png image... i tried to change the >>>>>>>>>>> dimension to 2 >>>>>>>>>>> >>>>>>> and >>>>>>>>>>> >>>>>>> >> build >>>>>>>>>>> >>>>>>> >> it which it did.. but when i run the code using the >>>>>>>>>>> command >>>>>>>>>>> >>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png >>>>>>>>>>> putput.png >>>>>>>>>>> >>>>>>> 1... i see >>>>>>>>>>> >>>>>>> >> this output >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> offset: [-1, -1] [0, -1] >>>>>>>>>>> >>>>>>> >> offset: [0, -1] [1, -1] >>>>>>>>>>> >>>>>>> >> offset: [-1, 0] [0, 0] >>>>>>>>>>> >>>>>>> >> offset: [0, 0] [1, 0] >>>>>>>>>>> >>>>>>> >> offset: [-1, 1] [0, 1] >>>>>>>>>>> >>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the >>>>>>>>>>> program... if pls >>>>>>>>>>> >>>>>>> tel me >>>>>>>>>>> >>>>>>> >> how can i modify this code to work wid 2d image... >>>>>>>>>>> forgive me if >>>>>>>>>>> >>>>>>> my ques >>>>>>>>>>> >>>>>>> >> are really silly im trying to learn something.. >>>>>>>>>>> >>>>>>> >> regards >>>>>>>>>>> >>>>>>> >> Vis >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 >>>>>>>>>>> [via ITK >>>>>>>>>>> >>>>>>> Insight Users] >>>>>>>>>>> >>>>>>> >> < >>>>>>>>>>> >>>>>>> >> [hidden email] < >>>>>>>>>>> >>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1 >>>>>>>>>>> >> >>>>>>>>>>> >>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> > Hi, >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > The function: >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > itkTextureFeatureImageFilterTest(int argc, char >>>>>>>>>>> *argv[]) >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > must be renamed to >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > main(int argc, char* argv[]) >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > HTH, >>>>>>>>>>> >>>>>>> >> > Matt >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email] >>>>>>>>>>> >>>>>>> >> > < >>>>>>>>>>> http:///user/SendEmail.jtp?type=node&node=7587952&i=0 >>>>>>>>>>> >> wrote: >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > > hi all, >>>>>>>>>>> >>>>>>> >> > > im trying to build the >>>>>>>>>>> itkTextureFeatureImageFilterTest.cxx >>>>>>>>>>> >>>>>>> code but >>>>>>>>>>> >>>>>>> >> im >>>>>>>>>>> >>>>>>> >> > not >>>>>>>>>>> >>>>>>> >> > > able to it is showing the following error >>>>>>>>>>> >>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK, >>>>>>>>>>> >>>>>>> Configuration: >>>>>>>>>>> >>>>>>> >> Debug >>>>>>>>>>> >>>>>>> >> > x64 >>>>>>>>>>> >>>>>>> >> > > ------ >>>>>>>>>>> >>>>>>> >> > > 1> Checking Build System >>>>>>>>>>> >>>>>>> >> > > 1> CMake does not need to re-run because >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >>>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp >>>>>>>>>>> >>>>>>> >> > is >>>>>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>>>>> >>>>>>> >> > > 2>------ Rebuild All started: Project: >>>>>>>>>>> >>>>>>> >> itkTextureFeatureImageFilterTest, >>>>>>>>>>> >>>>>>> >> > > Configuration: Debug x64 ------ >>>>>>>>>>> >>>>>>> >> > > 2> Building Custom Rule >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>>>>>> >>>>>>> >> > > 2> CMake does not need to re-run because >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >>>>>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>>>>>> >>>>>>> >> > is >>>>>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>>>>> >>>>>>> >> > > 2> itkTextureFeatureImageFilterTest.cxx >>>>>>>>>>> >>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio >>>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996: >>>>>>>>>>> >>>>>>> 'std::_Copy_impl': >>>>>>>>>>> >>>>>>> >> > Function >>>>>>>>>>> >>>>>>> >> > > call with parameters that may be unsafe - this >>>>>>>>>>> call relies on >>>>>>>>>>> >>>>>>> the >>>>>>>>>>> >>>>>>> >> caller >>>>>>>>>>> >>>>>>> >> > to >>>>>>>>>>> >>>>>>> >> > > check that the passed values are correct. To >>>>>>>>>>> disable this >>>>>>>>>>> >>>>>>> warning, use >>>>>>>>>>> >>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on >>>>>>>>>>> how to use >>>>>>>>>>> >>>>>>> Visual C++ >>>>>>>>>>> >>>>>>> >> > > 'Checked Iterators' >>>>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft >>>>>>>>>>> Visual Studio >>>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration >>>>>>>>>>> of >>>>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>>>> >>>>>>> >> > > 2> >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) : >>>>>>>>>>> >>>>>>> >> > see >>>>>>>>>>> >>>>>>> >> > > reference to function template instantiation >>>>>>>>>>> '_OutIt >>>>>>>>>>> >>>>>>> std::copy>>>>>>>>>> >>>>>>> >> > > unsigned char*,unsigned >>>>>>>>>>> char*>(_InIt,_InIt,_OutIt)' being >>>>>>>>>>> >>>>>>> compiled >>>>>>>>>>> >>>>>>> >> > > 2> with >>>>>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>>>>> >>>>>>> >> > > 2> _OutIt=unsigned char *, >>>>>>>>>>> >>>>>>> >> > > 2> _InIt=const unsigned char * >>>>>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>>>>> >>>>>>> >> > > 2> >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) : >>>>>>>>>>> >>>>>>> >> > > while compiling class template member function >>>>>>>>>>> 'void >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> itk::ImageFileReader::GenerateData(void)' >>>>>>>>>>> >>>>>>> >> > > 2> with >>>>>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>>>>> >>>>>>> >> > > 2> >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47) >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > > : see reference to class template instantiation >>>>>>>>>>> >>>>>>> >> > > 'itk::ImageFileReader' being >>>>>>>>>>> compiled >>>>>>>>>>> >>>>>>> >> > > 2> with >>>>>>>>>>> >>>>>>> >> > > 2> [ >>>>>>>>>>> >>>>>>> >> > > 2> TOutputImage=InputImageType >>>>>>>>>>> >>>>>>> >> > > 2> ] >>>>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft >>>>>>>>>>> Visual Studio >>>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration >>>>>>>>>>> of >>>>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft >>>>>>>>>>> Visual Studio >>>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration >>>>>>>>>>> of >>>>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>>>> >>>>>>> >> > > 2> C:\Program Files (x86)\Microsoft >>>>>>>>>>> Visual Studio >>>>>>>>>>> >>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration >>>>>>>>>>> of >>>>>>>>>>> >>>>>>> 'std::_Copy_impl' >>>>>>>>>>> >>>>>>> >> > > 2> Creating library >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > > and object >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: >>>>>>>>>>> unresolved >>>>>>>>>>> >>>>>>> external symbol >>>>>>>>>>> >>>>>>> >> > main >>>>>>>>>>> >>>>>>> >> > > referenced in function __tmainCRTStartup >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals >>>>>>>>>>> >>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD, >>>>>>>>>>> >>>>>>> Configuration: Debug >>>>>>>>>>> >>>>>>> >> > x64 >>>>>>>>>>> >>>>>>> >> > > ------ >>>>>>>>>>> >>>>>>> >> > > 3> Building Custom Rule >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt >>>>>>>>>>> >>>>>>> >> > > 3> CMake does not need to re-run because >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >>>>>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp >>>>>>>>>>> >>>>>>> >> > is >>>>>>>>>>> >>>>>>> >> > > up-to-date. >>>>>>>>>>> >>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 >>>>>>>>>>> skipped >>>>>>>>>>> >>>>>>> ========== >>>>>>>>>>> >>>>>>> >> > > im using the follwing CMakeList.txt >>>>>>>>>>> >>>>>>> >> > > # This is the root ITK CMakeLists file. >>>>>>>>>>> >>>>>>> >> > > cmake_minimum_required(VERSION 2.4) >>>>>>>>>>> >>>>>>> >> > > if(COMMAND CMAKE_POLICY) >>>>>>>>>>> >>>>>>> >> > > cmake_policy(SET CMP0003 NEW) >>>>>>>>>>> >>>>>>> >> > > endif() >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > # This project is designed to be built outside >>>>>>>>>>> the Insight >>>>>>>>>>> >>>>>>> source >>>>>>>>>>> >>>>>>> >> tree. >>>>>>>>>>> >>>>>>> >> > > project(HelloWorld) >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > # Find ITK. >>>>>>>>>>> >>>>>>> >> > > find_package(ITK REQUIRED) >>>>>>>>>>> >>>>>>> >> > > include(${ITK_USE_FILE}) >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest >>>>>>>>>>> >>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx ) >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> target_link_libraries(itkTextureFeatureImageFilterTest >>>>>>>>>>> >>>>>>> >> ${ITK_LIBRARIES}) >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > please tel me wat the error is?? >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > -- >>>>>>>>>>> >>>>>>> >> > > View this message in context: >>>>>>>>>>> >>>>>>> >> > >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >>>>>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html >>>>>>>>>>> >>>>>>> >> > > Sent from the ITK Insight Users mailing list >>>>>>>>>>> archive at >>>>>>>>>>> >>>>>>> Nabble.com . >>>>>>>>>>> >>>>>>> >> > > _____________________________________ >>>>>>>>>>> >>>>>>> >> > > Powered by www.kitware.com >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > Visit other Kitware open-source projects at >>>>>>>>>>> >>>>>>> >> > > http://www.kitware.com/opensource/opensource.html >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > Kitware offers ITK Training Courses, for more >>>>>>>>>>> information >>>>>>>>>>> >>>>>>> visit: >>>>>>>>>>> >>>>>>> >> > > http://www.kitware.com/products/protraining.php >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > Please keep messages on-topic and check the ITK >>>>>>>>>>> FAQ at: >>>>>>>>>>> >>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>>> >>>>>>> >> > > >>>>>>>>>>> >>>>>>> >> > > Follow this 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_____________________________________ >>>>>>>>>>> >>>>>>> >> Powered by www.kitware.com >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Visit other Kitware open-source projects at >>>>>>>>>>> >>>>>>> >> http://www.kitware.com/opensource/opensource.html >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Kitware offers ITK Training Courses, for more >>>>>>>>>>> information visit: >>>>>>>>>>> >>>>>>> >> http://www.kitware.com/products/protraining.php >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Please keep messages on-topic and check the ITK FAQ >>>>>>>>>>> at: >>>>>>>>>>> >>>>>>> >> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> >> Follow this link to subscribe/unsubscribe: >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>>> >>>>>>> >> >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > _____________________________________ >>>>>>>>>>> >>>>>>> > Powered by www.kitware.com >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Visit other Kitware open-source projects at >>>>>>>>>>> >>>>>>> > http://www.kitware.com/opensource/opensource.html >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Kitware offers ITK Training Courses, for more >>>>>>>>>>> information visit: >>>>>>>>>>> >>>>>>> > http://www.kitware.com/products/protraining.php >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Please keep messages on-topic and check the ITK FAQ at: >>>>>>>>>>> >>>>>>> > http://www.itk.org/Wiki/ITK_FAQ >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > Follow this link to subscribe/unsubscribe: >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > ------------------------------ >>>>>>>>>>> >>>>>>> > If you reply to this email, your message will be added >>>>>>>>>>> to the >>>>>>>>>>> >>>>>>> discussion >>>>>>>>>>> >>>>>>> > below: >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> > >>>>>>>>>>> >>>>>>> >>>>>>>>>>> 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_____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> ------------------------------ >> If you reply to this email, your message will be added to the discussion >> below: >> >> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588516.html >> To start a new topic under ITK Insight Users, email [hidden email] >> >> To unsubscribe from ITK Insight Users, click here. >> NAML >> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588531.html > To start a new topic under ITK Insight Users, email > ml-node+s2283740n2283740h75 at n2.nabble.com > To unsubscribe from ITK Insight Users, click here > > . > NAML > > -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7588532.html Sent from the ITK Insight Users mailing list archive at Nabble.com. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Mon Feb 22 09:24:46 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 22 Feb 2016 09:24:46 -0500 Subject: [ITK] ITK Ctest errors In-Reply-To: References: Message-ID: Hi Kurt, Does libvtkRenderingAnnotation-7.0.1.dylib exist in /VTK/build/lib/ ? Thanks, Matt On Mon, Feb 22, 2016 at 3:01 AM, Kurt Sansom wrote: > I have ITK and VTK built with shared libraries on OSX 10.11, and have > DYLD_LIBRARY_PATH set to > > /VTK/build/lib:/ITK/build/lib > > But several tests fail with same kind of error.(see below) does anyone > have any insight into what is causing this. I looked at using otool -L to > look at what the library is trying to ling to but I didn't see anything > weird or don't know enough to properly interpret. > > Thank you. > > ~Kurt > > > 2783: Test command: /Users/sansomk/build/ITK/build/bin/itkTestDriver > "--add-before-env" "PYTHONPATH" > "/Users/sansomk/build/ITK/build/Wrapping/Generators/Python/Release" > "--add-before-env" "PYTHONPATH" > "/Users/sansomk/build/ITK/build/Wrapping/Generators/Python" > "--add-before-env" "PYTHONPATH" > "/Users/sansomk/build/ITK/build/lib/Release" "--add-before-env" > "PYTHONPATH" "/Users/sansomk/build/ITK/build/lib" "--add-before-libpath" > "/Users/sansomk/build/ITK/build/lib/Release" "--add-before-libpath" > "/Users/sansomk/build/ITK/build/lib" "--add-before-libpath" > "/Users/sansomk/build/ITK/build/bin/Release" "--add-before-libpath" > "/Users/sansomk/build/ITK/build/bin" "--add-before-libpath" > "/Users/sansomk/build/ITK/build" "arch" "-x86_64" > "/Users/sansomk/anaconda/bin/python2.7" > "/Users/sansomk/build/ITK/ITKLatestRelease/Examples/IO/test/../DicomSliceRead.py" > "/Users/sansomk/build/ITK/build/ExternalData/Testing/Data/Input/dicom-sc_cs-1.dcm" > "/Users/sansomk/build/ITK/build/Testing/Temporary/DicomSliceReadPythonOutput.png" > "--compare" > "/Users/sansomk/build/ITK/build/Testing/Temporary/DicomSliceReadPythonOutput.png" > "/Users/sansomk/build/ITK/build/ExternalData/Examples/IO/test/Baseline/DicomSliceReadPythonOutputBaseline.png" > > 2783: Test timeout computed to be: 1500 > > 2783: Traceback (most recent call last): > > 2783: File > "/Users/sansomk/build/ITK/ITKLatestRelease/Examples/IO/test/../DicomSliceRead.py", > line 36, in > > 2783: InputImageType = itk.Image.SS2 > > 2783: File > "/Users/sansomk/build/ITK/build/Wrapping/Generators/Python/itkLazy.py", > line 42, in __getattribute__ > > 2783: itkBase.LoadModule(module, namespace) > > 2783: File > "/Users/sansomk/build/ITK/build/Wrapping/Generators/Python/itkBase.py", > line 128, in LoadModule > > 2783: module = loader.load(swigModuleName) > > 2783: File > "/Users/sansomk/build/ITK/build/Wrapping/Generators/Python/itkBase.py", > line 245, in load > > 2783: return imp.load_module(name, fp, pathname, description) > > 2783: File "/Users/sansomk/build/ITK/build/lib/ITKCommonPython.py", line > 32, in > > 2783: _ITKCommonPython = swig_import_helper() > > 2783: File "/Users/sansomk/build/ITK/build/lib/ITKCommonPython.py", line > 28, in swig_import_helper > > 2783: _mod = imp.load_module('_ITKCommonPython', fp, pathname, > description) > > 2783: ImportError: > dlopen(/Users/sansomk/build/ITK/build/lib/_ITKCommonPython.so, 2): Library > not loaded: libvtkRenderingAnnotation-7.0.1.dylib > > 2783: Referenced from: > /Users/sansomk/build/ITK/build/lib/_ITKCommonPython.so > > 2783: Reason: image not found > > 2783: itkTestDriver: Process exited with return value: 1 > > 74/74 Test #2783: DicomSliceReadPythonTest > ..................................***Failed 0.60 sec > > Does > -- > Kurt Sansom > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at insightsoftwareconsortium.org Mon Feb 22 09:39:04 2016 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 22 Feb 2016 09:39:04 -0500 (EST) Subject: [ITK] [ITK-users] New Submission: A Multi-atlas Approach for the Automatic Segmentation of Multiple Structures in Head and Neck CT Images Message-ID: <20160222143904.60C233D6207F@insight-journal.org> Hello, A new submission has been added to the MIDAS Journal. Title: A Multi-atlas Approach for the Automatic Segmentation of Multiple Structures in Head and Neck CT Images Authors: Chen A., Dawant B. Abstract: A multi-atlas approach is proposed for the automatic segmentation of nine different structures in a set of head and neck CT images for radiotherapy. The approach takes advantage of a training dataset of 25 images to build average head and neck atlases of high-quality. By registering patient images with the atlases at the global level, structures of interest are aligned approximately in space, which allowed multi-atlas-based segmentations and correlation-based label fusion to be performed at the local level in the following steps. Qualitative and quantitative evaluations are performed on a set of 15 testing images. As shown by the results, mandible, brainstem and parotid glands are segmented accurately (mean volume DSC>0.8). The segmentation accuracy for the optic nerves is also improved over previously reported results (mean DSC above 0.61 compared with 0.52 for previous results). Download and review this publication at: http://hdl.handle.net/10380/3540 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Feb 22 09:39:43 2016 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 22 Feb 2016 09:39:43 -0500 (EST) Subject: [ITK] [ITK-users] New Submission: Head and Neck Auto Segmentation Challenge based on Non-Local Generative Models Message-ID: <20160222143943.DD15E3D6220D@insight-journal.org> Hello, A new submission has been added to the MIDAS Journal. Title: Head and Neck Auto Segmentation Challenge based on Non-Local Generative Models Authors: Orbes Arteaga M., Cardenas Pe??a D., Castellanos Dominguez G. Abstract: We have presented a novel patch label fusion method based on a generative probabilistic approach for weighting the label votes of the neighborhood patches. Additionally a 3D sliding Gaussian window is used to combine the multiples estimations of the overlapping neighborhoods. The proposed method obtained 0.85, 0.93, and 0.76 of average DSC for Brainstem, Mandible, and Parotid glangs respectively. Download and review this publication at: http://hdl.handle.net/10380/3539 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Feb 22 09:42:03 2016 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 22 Feb 2016 09:42:03 -0500 (EST) Subject: [ITK] [ITK-users] New Submission: Head and Neck Auto Segmentation Challenge based on Non-Local Generative Models Message-ID: <20160222144203.1494F3D62102@insight-journal.org> Hello, A new submission has been added to the MIDAS Journal. Title: Head and Neck Auto Segmentation Challenge based on Non-Local Generative Models Authors: Orbes Arteaga M., C??rdenas Pe??a D., Castellanos Dominguez G. Abstract: We have presented a novel patch label fusion method based on generative probabilistic approach for weighting the label votes of the neighborhood patches, additionally a 3D sliding Gaussian window is used to combine the multiples estimations of the overlapping neighborhoods. The proposed method obtained 0.85, 0.93, and 0.76 of average DSC for Brainstem, Mandible, and Parotid glangs respectively. Download and review this publication at: http://hdl.handle.net/10380/3538 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Feb 22 09:42:51 2016 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 22 Feb 2016 09:42:51 -0500 (EST) Subject: [ITK] [ITK-users] New Submission: Fully Automatic Segmentation of Head and Neck Organs using Active Appearance Models Message-ID: <20160222144251.C20E63D62177@insight-journal.org> Hello, A new submission has been added to the MIDAS Journal. Title: Fully Automatic Segmentation of Head and Neck Organs using Active Appearance Models Authors: Mannion-Haworth R., Bowes M., Ashman A., Guillard G., Brett A., Vincent G. Abstract: We present a fully automatic model based system for segmenting the mandible, parotid and submandibular glands, brainstem, optic nerves and the optic chiasm in CT images, which won the MICCAI 2015 Head and Neck Auto Segmentation Grand Challenge. The method is based on Active Appearance Models (AAM) built from manually segmented examples via a cancer imaging archive provided by the challenge organisers. High quality anatomical correspondences for the models are generated using a Minimum Description Length (MDL) Groupwise Image Registration method. A multi start optimisation scheme is used to robustly match the model to new images. The model has been cross validated on the training data to a good degree of accuracy, and successfully segmented all the test data. Download and review this publication at: http://hdl.handle.net/10380/3537 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Feb 22 09:43:41 2016 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 22 Feb 2016 09:43:41 -0500 (EST) Subject: [ITK] [ITK-users] New Submission: Multi Atlas Segmentation with Active Shape Model Refinement for Multi-Organ Segmentation in Head and Neck Cancer Radiotherapy Planning Message-ID: <20160222144341.7D7DA3D622EB@insight-journal.org> Hello, A new submission has been added to the MIDAS Journal. Title: Multi Atlas Segmentation with Active Shape Model Refinement for Multi-Organ Segmentation in Head and Neck Cancer Radiotherapy Planning Authors: Albrecht T., Gass T., Langguth C., L??thi M. Abstract: We describe a segmentation method that was used in the Head and Neck Auto Segmentation Challenge held at the MICCAI 2015 conference. The algorithm consists of two building blocks. First, we employ a multi-atlas segmentation to obtain an initial segmentation for the considered organs at risk. Secondly, we use an Active Shape Model (ASM) segmentation to refine the initial segmentation of some of the organs. Leave-one-out experiments with the training data were used to determine suitable parameters for the individual steps of the segmentation. The ASM refinement resulted in improved segmentation for the optic nerves and submandibular glands, while for the brain stem, parotid glands, chiasm, and mandibular bone, the multi-atlas segmentation was preferable. Our submission achieved the second rank in the challenge. Download and review this publication at: http://hdl.handle.net/10380/3531 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From kayarre at gmail.com Mon Feb 22 12:50:11 2016 From: kayarre at gmail.com (Kurt Sansom) Date: Mon, 22 Feb 2016 09:50:11 -0800 Subject: [ITK] ITK Ctest errors reply Message-ID: yes it does see below. Thanks for replying. ~Kurt ~/build/VTK/build/lib]$ pwd /Users/sansomk/build/VTK/build/lib ~/build/VTK/build/lib]$ ll libvtkRenderingAnnotation-7* -rwxr-xr-x 1 sansomk staff 733K Feb 18 11:42 libvtkRenderingAnnotation-7.0.1.dylib -rw-r--r-- 1 sansomk staff 1.4M Feb 17 23:02 libvtkRenderingAnnotation-7.0.a lrwxr-xr-x 1 sansomk staff 37B Feb 18 11:42 libvtkRenderingAnnotation-7.0.dylib -> libvtkRenderingAnnotation-7.0.1.dylib On Mon, Feb 22, 2016 at 6:24 AM, Matt McCormick wrote: > Hi Kurt, > > Does > > libvtkRenderingAnnotation-7.0.1.dylib > > exist in /VTK/build/lib/ ? > > Thanks, > Matt > > On Mon, Feb 22, 2016 at 3:01 AM, Kurt Sansom wrote: > >> I have ITK and VTK built with shared libraries on OSX 10.11, and have >> DYLD_LIBRARY_PATH set to >> >> /VTK/build/lib:/ITK/build/lib >> >> But several tests fail with same kind of error.(see below) does anyone >> have any insight into what is causing this. I looked at using otool -L to >> look at what the library is trying to ling to but I didn't see anything >> weird or don't know enough to properly interpret. >> >> Thank you. >> >> ~Kurt >> >> >> 2783: Test command: /Users/sansomk/build/ITK/build/bin/itkTestDriver >> "--add-before-env" "PYTHONPATH" >> "/Users/sansomk/build/ITK/build/Wrapping/Generators/Python/Release" >> "--add-before-env" "PYTHONPATH" >> "/Users/sansomk/build/ITK/build/Wrapping/Generators/Python" >> "--add-before-env" "PYTHONPATH" >> "/Users/sansomk/build/ITK/build/lib/Release" "--add-before-env" >> "PYTHONPATH" "/Users/sansomk/build/ITK/build/lib" "--add-before-libpath" >> "/Users/sansomk/build/ITK/build/lib/Release" "--add-before-libpath" >> "/Users/sansomk/build/ITK/build/lib" "--add-before-libpath" >> "/Users/sansomk/build/ITK/build/bin/Release" "--add-before-libpath" >> "/Users/sansomk/build/ITK/build/bin" "--add-before-libpath" >> "/Users/sansomk/build/ITK/build" "arch" "-x86_64" >> "/Users/sansomk/anaconda/bin/python2.7" >> "/Users/sansomk/build/ITK/ITKLatestRelease/Examples/IO/test/../DicomSliceRead.py" >> "/Users/sansomk/build/ITK/build/ExternalData/Testing/Data/Input/dicom-sc_cs-1.dcm" >> "/Users/sansomk/build/ITK/build/Testing/Temporary/DicomSliceReadPythonOutput.png" >> "--compare" >> "/Users/sansomk/build/ITK/build/Testing/Temporary/DicomSliceReadPythonOutput.png" >> "/Users/sansomk/build/ITK/build/ExternalData/Examples/IO/test/Baseline/DicomSliceReadPythonOutputBaseline.png" >> >> 2783: Test timeout computed to be: 1500 >> >> 2783: Traceback (most recent call last): >> >> 2783: File >> "/Users/sansomk/build/ITK/ITKLatestRelease/Examples/IO/test/../DicomSliceRead.py", >> line 36, in >> >> 2783: InputImageType = itk.Image.SS2 >> >> 2783: File >> "/Users/sansomk/build/ITK/build/Wrapping/Generators/Python/itkLazy.py", >> line 42, in __getattribute__ >> >> 2783: itkBase.LoadModule(module, namespace) >> >> 2783: File >> "/Users/sansomk/build/ITK/build/Wrapping/Generators/Python/itkBase.py", >> line 128, in LoadModule >> >> 2783: module = loader.load(swigModuleName) >> >> 2783: File >> "/Users/sansomk/build/ITK/build/Wrapping/Generators/Python/itkBase.py", >> line 245, in load >> >> 2783: return imp.load_module(name, fp, pathname, description) >> >> 2783: File "/Users/sansomk/build/ITK/build/lib/ITKCommonPython.py", >> line 32, in >> >> 2783: _ITKCommonPython = swig_import_helper() >> >> 2783: File "/Users/sansomk/build/ITK/build/lib/ITKCommonPython.py", >> line 28, in swig_import_helper >> >> 2783: _mod = imp.load_module('_ITKCommonPython', fp, pathname, >> description) >> >> 2783: ImportError: >> dlopen(/Users/sansomk/build/ITK/build/lib/_ITKCommonPython.so, 2): Library >> not loaded: libvtkRenderingAnnotation-7.0.1.dylib >> >> 2783: Referenced from: >> /Users/sansomk/build/ITK/build/lib/_ITKCommonPython.so >> >> 2783: Reason: image not found >> >> 2783: itkTestDriver: Process exited with return value: 1 >> >> 74/74 Test #2783: DicomSliceReadPythonTest >> ..................................***Failed 0.60 sec >> >> Does >> -- >> Kurt Sansom >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> >> > -- Kurt Sansom -------------- next part -------------- An HTML attachment was scrubbed... URL: From kolin9105 at gmail.com Mon Feb 22 13:34:30 2016 From: kolin9105 at gmail.com (meikolin saimara) Date: Tue, 23 Feb 2016 01:34:30 +0700 Subject: [ITK] [ITK-users] (no subject) Message-ID: hello guys I need your help. I have a image of head with brain tumor and I want to analyze the area of the brain tumor now my problem is how I can find it without visualization. I just use ITK library can you give sourcecode for this?? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: IM-0001-0009.dcm Type: application/octet-stream Size: 169478 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From dzenanz at gmail.com Mon Feb 22 13:51:15 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 22 Feb 2016 13:51:15 -0500 Subject: [ITK] [ITK-users] (no subject) In-Reply-To: References: Message-ID: Hi Saimara, what you want to do is called image segmentation . How to do it is an open question in science. Open means there is no universally accepted solution, there are only partial solutions which work well for some case or which partially work for most cases. ITK has many algorithms which do basic image processing operations, and it is your task to assemble them into a program which solves your problem (brain tumor segmentation). One way to get going is to pick an introduction , read it and then try writing source code which implements one method. ITK has many basic operations (like Gaussian blurring, watershed calculation etc) already implemented. Regards, D?enan On Mon, Feb 22, 2016 at 1:34 PM, meikolin saimara wrote: > hello guys I need your help. > I have a image of head with brain tumor and I want to analyze the area of > the brain tumor > now my problem is how I can find it without visualization. > I just use ITK library > can you give sourcecode for this?? > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From LCHEN41 at mgh.harvard.edu Tue Feb 23 17:48:47 2016 From: LCHEN41 at mgh.harvard.edu (Chen, Lifan) Date: Tue, 23 Feb 2016 22:48:47 +0000 Subject: [ITK] ITK try to read 4D dicom time series(3d, t), but get 3d*t Message-ID: Hi all, These days, I am trying to use ITK to handle 4D dicom series (3d+t). I use GDCMSeriesFileNames to generate seriesUIDs and ImageSeriesReader to read these images. The following is part of my code: typedef double PixelType; typedef itk::Image< PixelType, 4> Image4DType; //4D image type typedef itk::Image< PixelType, 3> Image3DType; //3D image type typedef itk::ImageSeriesReader< Image4DType > ReaderType; typedef itk::GDCMImageIO ImageIOType; reader = ReaderType::New(); dicomIO = ImageIOType::New(); typedef itk::GDCMSeriesFileNames NamesGeneratorType; NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New(); nameGenerator->AddSeriesRestriction("0008|0021"); nameGenerator->SetUseSeriesDetails(true); nameGenerator->SetDirectory(_filename); typedef std::vector< std::string > SeriesIdContainer; const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs(); _isFileLoaded = !(seriesUID.empty()); if (true == _isFileLoaded){ SeriesIdContainer::const_iterator seriesItr = seriesUID.begin(); SeriesIdContainer::const_iterator seriesEnd = seriesUID.end(); std::string seriesIdentifier = seriesUID.begin()->c_str(); typedef std::vector< std::string > FileNamesContainer; FileNamesContainer fileNames; fileNames = nameGenerator->GetFileNames(seriesIdentifier); reader->SetFileNames(fileNames); reader->SetImageIO(dicomIO); reader->Update(); } I have tried this code and the reader worked well. However I got a [x,y,z*t, 1] data, but not [x, y, z, t] data. I understand the problem may caused by nameGenerator, but I use SetUseSeriesDetails and AddSeriesRestriction("0008|0021")(aquisition time)which are implied by documents to handle 4d images.I have also tried several methods but all not work. I wonder whether ITK have an original method to handle 4d images. Have anyone ever met this problem before? Any help or recommendations would be appreciated. Thanks, Lifan The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From gunjan_naik at persistent.com Wed Feb 24 00:34:38 2016 From: gunjan_naik at persistent.com (Gunjan Naik) Date: Wed, 24 Feb 2016 05:34:38 +0000 Subject: [ITK] [ITK-users] Issue with Seed points in Geodesic Active contour In-Reply-To: References: Message-ID: Thanks D?enan. It worked after I set origin to (0,0). Regards, Gunjan Naik Gunjan G. Naik | Persistent LABS | PhD Student ? University of Pune gunjan_naik at persistent.com | Cell: +91-8087996979 | Tel: +91-20-670 34878 Persistent Systems Ltd. | Partners in Innovation | www.persistent.com From: D?enan Zuki? [mailto:dzenanz at gmail.com] Sent: Tuesday, February 16, 2016 8:46 PM To: Gunjan Naik Cc: insight-users at itk.org Subject: Re: [ITK-users] Issue with Seed points in Geodesic Active contour Hi Naik, with directions being identity matrix and Size: [240, 240, 155] Spacing: [1, 1, 1] Origin: [0, -239, 0] the physical extent of your image is x: -0.5 to 239.5, y: -239.5 to 0.5 and z: -0.5 to 154.5 (all millimeters). In other words, x and z are positive, while y is negative. HTH, D?enan On Tue, Feb 16, 2016 at 7:40 AM, Gunjan Naik > wrote: Hi D?enan I am using T1 weighted brain tumor image from BRATS challenge. The meta information is as follows: Image (00000000193D62F0) RTTI typeinfo: class itk::Image Reference Count: 1 Modified Time: 1194 Debug: Off Object Name: Observers: none Source: (none) Source output name: (none) Release Data: Off Data Released: False Global Release Data: Off PipelineMTime: 1034 UpdateMTime: 1193 RealTimeStamp: 0 seconds LargestPossibleRegion: Dimension: 3 Index: [0, 0, 0] Size: [240, 240, 155] BufferedRegion: Dimension: 3 Index: [0, 0, 0] Size: [240, 240, 155] RequestedRegion: Dimension: 3 Index: [0, 0, 0] Size: [240, 240, 155] Spacing: [1, 1, 1] Origin: [0, -239, 0] Direction: 1 0 0 0 1 0 0 0 1 IndexToPointMatrix: 1 0 0 0 1 0 0 0 1 PointToIndexMatrix: 1 0 0 0 1 0 0 0 1 Inverse Direction: 1 0 0 0 1 0 0 0 1 PixelContainer: ImportImageContainer (000000001917BD50) RTTI typeinfo: class itk::ImportImageContainer Reference Count: 1 Modified Time: 1190 Debug: Off Object Name: Observers: none Pointer: 000000001B8E0040 Container manages memory: true Size: 8928000 Capacity: 8928000 I am passing co-ordinate to tumor region using Opencv. Thanks and Regards, Gunjan Naik Gunjan G. Naik | Persistent LABS | PhD Student ? University of Pune gunjan_naik at persistent.com | Cell: +91-8087996979 | Tel: +91-20-670 34878 Persistent Systems Ltd. | Partners in Innovation | www.persistent.com From: D?enan Zuki? [mailto:dzenanz at gmail.com] Sent: Tuesday, February 09, 2016 8:53 PM To: Gunjan Naik > Cc: insight-users at itk.org Subject: Re: [ITK-users] Issue with Seed points in Geodesic Active contour Hi Naik, you should provide your image's meta-information e.g. by: std::cout<> wrote: Hi All, I am using geodesic active contour for brain tumor segmentation. In that, I have to give seed points for creating level set. I have calculated seed points using opencv, but when I input these points using ?TransformPhysicalPointToIndex? it throws error stating that index out of bounds. It works for only points [(0,0)]. Please provide me directions. Thanks and Regards, Gunjan Naik Gunjan G. Naik | Persistent LABS | PhD Student ? University of Pune gunjan_naik at persistent.com | Cell: +91-8087996979 | Tel: +91-20-670 34878 Persistent Systems Ltd. | Partners in Innovation | www.persistent.com DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From artem.ogre at gmail.com Wed Feb 24 04:59:01 2016 From: artem.ogre at gmail.com (Artem Amirkhanov) Date: Wed, 24 Feb 2016 10:59:01 +0100 Subject: [ITK] 3D Sobel implementation Message-ID: Hello, In the documentation of SobelOperator ( http://www.itk.org/Doxygen/html/classitk_1_1SobelOperator.html) the original technical report by Irwin Sobel is mentioned: "Irwin Sobel. An Isotropic 3x3x3 Volume Gradient Operator. Technical report, Hewlett-Packard Laboratories, April 1995." This paper is nowhere to be found online and ITK is basically the only place that refers to it. Could anyone please provide this paper to me? I would really like to clarify some moments in the derivation of the operator. Thank you, Artem -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Wed Feb 24 10:10:25 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 24 Feb 2016 10:10:25 -0500 Subject: [ITK] 3D Sobel implementation In-Reply-To: References: Message-ID: Hi Artem, looking at the Wikipedia article , the first reference is this: https://www.researchgate.net/publication/239398674_An_Isotropic_3_3_Image_Gradient_Operator HTH, D?enan On Wed, Feb 24, 2016 at 4:59 AM, Artem Amirkhanov wrote: > Hello, > > In the documentation of SobelOperator ( > http://www.itk.org/Doxygen/html/classitk_1_1SobelOperator.html) the > original technical report by Irwin Sobel is mentioned: "Irwin Sobel. An > Isotropic 3x3x3 Volume Gradient Operator. Technical report, Hewlett-Packard > Laboratories, April 1995." > > This paper is nowhere to be found online and ITK is basically the only > place that refers to it. Could anyone please provide this paper to me? I > would really like to clarify some moments in the derivation of the operator. > > Thank you, > Artem > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From LCHEN41 at mgh.harvard.edu Wed Feb 24 11:22:34 2016 From: LCHEN41 at mgh.harvard.edu (Chen, Lifan) Date: Wed, 24 Feb 2016 16:22:34 +0000 Subject: [ITK] =?gb2312?b?16q3ojogSVRLIHRyeSB0byByZWFkIDREIGRpY29tIHRpbWUg?= =?gb2312?b?c2VyaWVzKDNkLCB0KSwgYnV0IGdldCAzZCp0?= In-Reply-To: References: Message-ID: Hey all, Any help would be appreciated. This problem really gets me in for couple of days. Thanks, Lifan ________________________________ ???: Chen, Lifan ????: 2016?2?23? 17:48 ???: community at itk.org ??: ITK try to read 4D dicom time series(3d, t), but get 3d*t Hi all, These days, I am trying to use ITK to handle 4D dicom series (3d+t). I use GDCMSeriesFileNames to generate seriesUIDs and ImageSeriesReader to read these images. The following is part of my code: typedef double PixelType; typedef itk::Image< PixelType, 4> Image4DType; //4D image type typedef itk::Image< PixelType, 3> Image3DType; //3D image type typedef itk::ImageSeriesReader< Image4DType > ReaderType; typedef itk::GDCMImageIO ImageIOType; reader = ReaderType::New(); dicomIO = ImageIOType::New(); typedef itk::GDCMSeriesFileNames NamesGeneratorType; NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New(); nameGenerator->AddSeriesRestriction("0008|0021"); nameGenerator->SetUseSeriesDetails(true); nameGenerator->SetDirectory(_filename); typedef std::vector< std::string > SeriesIdContainer; const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs(); _isFileLoaded = !(seriesUID.empty()); if (true == _isFileLoaded){ SeriesIdContainer::const_iterator seriesItr = seriesUID.begin(); SeriesIdContainer::const_iterator seriesEnd = seriesUID.end(); std::string seriesIdentifier = seriesUID.begin()->c_str(); typedef std::vector< std::string > FileNamesContainer; FileNamesContainer fileNames; fileNames = nameGenerator->GetFileNames(seriesIdentifier); reader->SetFileNames(fileNames); reader->SetImageIO(dicomIO); reader->Update(); } I have tried this code and the reader worked well. However I got a [x,y,z*t, 1] data, but not [x, y, z, t] data. I understand the problem may caused by nameGenerator, but I use SetUseSeriesDetails and AddSeriesRestriction("0008|0021")(aquisition time)which are implied by documents to handle 4d images.I have also tried several methods but all not work. I wonder whether ITK have an original method to handle 4d images. Have anyone ever met this problem before? Any help or recommendations would be appreciated. Thanks, Lifan The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Wed Feb 24 12:46:57 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 24 Feb 2016 12:46:57 -0500 Subject: [ITK] =?utf-8?b?6L2s5Y+ROiBJVEsgdHJ5IHRvIHJlYWQgNEQgZGljb20gdGlt?= =?utf-8?q?e_series=283d=2C_t=29=2C_but_get_3d*t?= In-Reply-To: References: Message-ID: Hi Lifan, did you examine the DICOM headers? Do different timepoints have different acquisition times? Regards, D?enan On Wed, Feb 24, 2016 at 11:22 AM, Chen, Lifan wrote: > Hey all, > > Any help would be appreciated. This problem really gets me in for couple > of days. > > Thanks, > Lifan > ------------------------------ > *???:* Chen, Lifan > *????:* 2016?2?23? 17:48 > *???:* community at itk.org > *??:* ITK try to read 4D dicom time series(3d, t), but get 3d*t > > Hi all, > > These days, I am trying to use ITK to handle 4D dicom series (3d+t). I > use GDCMSeriesFileNames to generate seriesUIDs and ImageSeriesReader to > read these images. > > The following is part of my code: > typedef double PixelType; > typedef itk::Image< PixelType, 4> Image4DType; > //4D image type > typedef itk::Image< PixelType, 3> Image3DType; > //3D image type > typedef itk::ImageSeriesReader< Image4DType > ReaderType; > typedef itk::GDCMImageIO ImageIOType; > reader = ReaderType::New(); > dicomIO = ImageIOType::New(); > typedef itk::GDCMSeriesFileNames NamesGeneratorType; > NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New(); > nameGenerator->AddSeriesRestriction("0008|0021"); > nameGenerator->SetUseSeriesDetails(true); > nameGenerator->SetDirectory(_filename); > typedef std::vector< std::string > SeriesIdContainer; > const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs(); > _isFileLoaded = !(seriesUID.empty()); > if (true == _isFileLoaded){ > SeriesIdContainer::const_iterator seriesItr = seriesUID.begin(); > SeriesIdContainer::const_iterator seriesEnd = seriesUID.end(); > std::string seriesIdentifier = seriesUID.begin()->c_str(); > typedef std::vector< std::string > FileNamesContainer; > FileNamesContainer fileNames; > fileNames = nameGenerator->GetFileNames(seriesIdentifier); > reader->SetFileNames(fileNames); > reader->SetImageIO(dicomIO); > reader->Update(); > } > > I have tried this code and the reader worked well. However I got a > [x,y,z*t, 1] data, but not [x, y, z, t] data. I understand the problem may > caused by nameGenerator, but I use SetUseSeriesDetails > and AddSeriesRestriction("0008|0021")(aquisition time)which are implied by > documents to handle 4d images.I have also tried several methods but all not > work. I wonder whether ITK have an original method to handle 4d images. > > Have anyone ever met this problem before? Any help or recommendations > would be appreciated. > > Thanks, > Lifan > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andinet.enqu at kitware.com Thu Feb 25 07:50:19 2016 From: andinet.enqu at kitware.com (Andinet Enquobahrie) Date: Thu, 25 Feb 2016 07:50:19 -0500 Subject: [ITK] [ITK-users] ANN: Medical Computing Group at Kitware is hiring R&D engineers and technical leads in image analysis and visualization Message-ID: Apologies for duplicate postings. =================== Hi folks, We are looking to hire talented individuals for image guided intervention and image analysis and visualization application development in our Medical Computing group. We have four job opportunities Technical Lead in Biomedical Image Analysis and Visualization http://tinyurl.com/jx3cgnc Image-Guided Intervention Applications Research and Development Engineer http://tinyurl.com/zxlpyyj Biomechanical Modeling and Surgical Simulation Research and Development Engineer http://tinyurl.com/jtsnf2y Research and Development Involving Machine Learning and Medical Image Analysis http://tinyurl.com/hy58kq8 For other job openings at Kitware, please check http://jobs.kitware.com/opportunities.html -- Andinet Enquobahrie, Ph.D., MBA Assistant Director of Medical Computing Kitware, Inc. http://www.kitware.com (919) 969-6990 x311 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From andinet.enqu at kitware.com Thu Feb 25 07:50:19 2016 From: andinet.enqu at kitware.com (Andinet Enquobahrie) Date: Thu, 25 Feb 2016 07:50:19 -0500 Subject: [ITK] [ITK-dev] ANN: Medical Computing Group at Kitware is hiring R&D engineers and technical leads in image analysis and visualization Message-ID: Apologies for duplicate postings. =================== Hi folks, We are looking to hire talented individuals for image guided intervention and image analysis and visualization application development in our Medical Computing group. We have four job opportunities Technical Lead in Biomedical Image Analysis and Visualization http://tinyurl.com/jx3cgnc Image-Guided Intervention Applications Research and Development Engineer http://tinyurl.com/zxlpyyj Biomechanical Modeling and Surgical Simulation Research and Development Engineer http://tinyurl.com/jtsnf2y Research and Development Involving Machine Learning and Medical Image Analysis http://tinyurl.com/hy58kq8 For other job openings at Kitware, please check http://jobs.kitware.com/opportunities.html -- Andinet Enquobahrie, Ph.D., MBA Assistant Director of Medical Computing Kitware, Inc. http://www.kitware.com (919) 969-6990 x311 _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From dzenanz at gmail.com Fri Feb 26 09:47:14 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 26 Feb 2016 09:47:14 -0500 Subject: [ITK] =?utf-8?b?6L2s5Y+ROiBJVEsgdHJ5IHRvIHJlYWQgNEQgZGljb20gdGlt?= =?utf-8?q?e_series=283d=2C_t=29=2C_but_get_3d*t?= In-Reply-To: References: Message-ID: I only now see that you sent this only to me Cyril! I CC'd Lifan and the list. On Thu, Feb 25, 2016 at 11:34 AM, Cyril Jaudet wrote: > Hi Lifan, > here some code that i past in the python interpreter of 3dslicer based on > vtk. > > _First download slicer and load multi image module. > _Import your serie with the dicom importer. > _Go into the multivolume support/multivolume explorer > _Enable frame copying or something similar. > Now you have two serie (module data to see/rename them) > 1 multiframe serie > 1 image that will be used as reference to extract the 3d + t image > _Copy/paste the following line in the python interpreter of 3dslicer. > > > from __main__ import vtk, qt, ctk, slicer > from math import * > import numpy as np > from vtk.util import numpy_support > import SimpleITK as sitk > import sitkUtils as su > import math > > def convert4Dto3D(multi,reference): > multiNode=slicer.util.getNode(multi) > refNode=slicer.util.getNode(reference) > multiImage=multiNode.GetImageData() > N=multiNode.GetNumberOfFrames() > for i in range (N): #extract image > im=vtk.vtkImageExtractComponents() > im.SetInputData(multiImage) > im.SetComponents(i) > im.Update() > > frame=slicer.modules.volumes.logic().CloneVolume(slicer.mrmlScene,refNode,'frame_'+str(i)) > frame.SetAndObserveImageData(im.GetOutput()) > > > _then type: > convert4Dto3D(multi,reference) > changing the name of multi and reference by the corresponding name of your > data > _it will extract the image under the name frame0, frame1... > _save them > > Hope that help, > > Cyril Jaudet > UZBrussel > > 2016-02-24 18:46 GMT+01:00 D?enan Zuki? : > >> Hi Lifan, >> >> did you examine the DICOM headers? Do different timepoints have different >> acquisition times? >> >> Regards, >> D?enan >> >> On Wed, Feb 24, 2016 at 11:22 AM, Chen, Lifan >> wrote: >> >>> Hey all, >>> >>> Any help would be appreciated. This problem really gets me in for couple >>> of days. >>> >>> Thanks, >>> Lifan >>> ------------------------------ >>> *???:* Chen, Lifan >>> *????:* 2016?2?23? 17:48 >>> *???:* community at itk.org >>> *??:* ITK try to read 4D dicom time series(3d, t), but get 3d*t >>> >>> Hi all, >>> >>> These days, I am trying to use ITK to handle 4D dicom series (3d+t). I >>> use GDCMSeriesFileNames to generate seriesUIDs and ImageSeriesReader to >>> read these images. >>> >>> The following is part of my code: >>> typedef double PixelType; >>> typedef itk::Image< PixelType, 4> Image4DType; >>> //4D image type >>> typedef itk::Image< PixelType, 3> Image3DType; >>> //3D image type >>> typedef itk::ImageSeriesReader< Image4DType > ReaderType; >>> typedef itk::GDCMImageIO ImageIOType; >>> reader = ReaderType::New(); >>> dicomIO = ImageIOType::New(); >>> typedef itk::GDCMSeriesFileNames NamesGeneratorType; >>> NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New(); >>> nameGenerator->AddSeriesRestriction("0008|0021"); >>> nameGenerator->SetUseSeriesDetails(true); >>> nameGenerator->SetDirectory(_filename); >>> typedef std::vector< std::string > SeriesIdContainer; >>> const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs(); >>> _isFileLoaded = !(seriesUID.empty()); >>> if (true == _isFileLoaded){ >>> SeriesIdContainer::const_iterator seriesItr = seriesUID.begin(); >>> SeriesIdContainer::const_iterator seriesEnd = seriesUID.end(); >>> std::string seriesIdentifier = seriesUID.begin()->c_str(); >>> typedef std::vector< std::string > FileNamesContainer; >>> FileNamesContainer fileNames; >>> fileNames = nameGenerator->GetFileNames(seriesIdentifier); >>> reader->SetFileNames(fileNames); >>> reader->SetImageIO(dicomIO); >>> reader->Update(); >>> } >>> >>> I have tried this code and the reader worked well. However I got a >>> [x,y,z*t, 1] data, but not [x, y, z, t] data. I understand the problem may >>> caused by nameGenerator, but I use SetUseSeriesDetails >>> and AddSeriesRestriction("0008|0021")(aquisition time)which are implied by >>> documents to handle 4d images.I have also tried several methods but all not >>> work. I wonder whether ITK have an original method to handle 4d images. >>> >>> Have anyone ever met this problem before? Any help or recommendations >>> would be appreciated. >>> >>> Thanks, >>> Lifan >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> >>> >> >> _______________________________________________ >> Community mailing list >> Community at itk.org >> http://public.kitware.com/mailman/listinfo/community >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From LCHEN41 at mgh.harvard.edu Fri Feb 26 14:02:43 2016 From: LCHEN41 at mgh.harvard.edu (Chen, Lifan) Date: Fri, 26 Feb 2016 19:02:43 +0000 Subject: [ITK] =?utf-8?b?562U5aSNOiAg6L2s5Y+ROiBJVEsgdHJ5IHRvIHJlYWQgNEQg?= =?utf-8?q?dicom_time_series=283d=2C_t=29=2C_but_get_3d*t?= In-Reply-To: References: , Message-ID: Hey Cyril and D?enan, Thanks very much for your help. I now fix this problem by using itkJoinSeriesImageFilter. This class could elevate a series of 3D volumes (x,y,z)*t into 4D level (x,y,z, t). Though I am not sure this is the best way for ITK to do so, at least it is the best solution I could find for now and hope this could help if anyone would work on 4D series using ITK in future. Here is part of my code: typedef itk::JoinSeriesImageFilter JoinSeriesImageFilterType; typedef itk::GDCMSeriesFileNames NamesGeneratorType; joinFilter = JoinSeriesImageFilterType::New(); NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New(); nameGenerator->AddSeriesRestriction("0008|0032"); //Use diffrent restriction depend on the dicom header nameGenerator->SetUseSeriesDetails(true); nameGenerator->SetDirectory(_filename); typedef std::vector< std::string > FileNamesContainer; FileNamesContainer fileNames; if (true == _isFileLoaded){ SeriesIdContainer::const_iterator seriesItr = seriesUID.begin(); SeriesIdContainer::const_iterator seriesEnd = seriesUID.end(); for (seriesItr; seriesItr != seriesEnd; seriesItr++){ ReaderType::Pointer reader = ReaderType::New(); std::string seriesIdentifier = seriesItr->c_str(); fileNames = nameGenerator->GetFileNames(seriesIdentifier); reader->SetFileNames(fileNames); reader->Update(); joinFilter->SetInput(inputIndex, reader->GetOutput()); inputIndex++; } joinFilter->Update(); Best wishes, Lifan ________________________________ ???: D?enan Zuki? [dzenanz at gmail.com] ????: 2016?2?26? 9:47 ???: Cyril Jaudet ??: Chen, Lifan; community at itk.org ??: Re: [ITK] ??: ITK try to read 4D dicom time series(3d, t), but get 3d*t I only now see that you sent this only to me Cyril! I CC'd Lifan and the list. On Thu, Feb 25, 2016 at 11:34 AM, Cyril Jaudet > wrote: Hi Lifan, here some code that i past in the python interpreter of 3dslicer based on vtk. _First download slicer and load multi image module. _Import your serie with the dicom importer. _Go into the multivolume support/multivolume explorer _Enable frame copying or something similar. Now you have two serie (module data to see/rename them) 1 multiframe serie 1 image that will be used as reference to extract the 3d + t image _Copy/paste the following line in the python interpreter of 3dslicer. from __main__ import vtk, qt, ctk, slicer from math import * import numpy as np from vtk.util import numpy_support import SimpleITK as sitk import sitkUtils as su import math def convert4Dto3D(multi,reference): multiNode=slicer.util.getNode(multi) refNode=slicer.util.getNode(reference) multiImage=multiNode.GetImageData() N=multiNode.GetNumberOfFrames() for i in range (N): #extract image im=vtk.vtkImageExtractComponents() im.SetInputData(multiImage) im.SetComponents(i) im.Update() frame=slicer.modules.volumes.logic().CloneVolume(slicer.mrmlScene,refNode,'frame_'+str(i)) frame.SetAndObserveImageData(im.GetOutput()) _then type: convert4Dto3D(multi,reference) changing the name of multi and reference by the corresponding name of your data _it will extract the image under the name frame0, frame1... _save them Hope that help, Cyril Jaudet UZBrussel 2016-02-24 18:46 GMT+01:00 D?enan Zuki? >: Hi Lifan, did you examine the DICOM headers? Do different timepoints have different acquisition times? Regards, D?enan On Wed, Feb 24, 2016 at 11:22 AM, Chen, Lifan > wrote: Hey all, Any help would be appreciated. This problem really gets me in for couple of days. Thanks, Lifan ________________________________ ???: Chen, Lifan ????: 2016?2?23? 17:48 ???: community at itk.org ??: ITK try to read 4D dicom time series(3d, t), but get 3d*t Hi all, These days, I am trying to use ITK to handle 4D dicom series (3d+t). I use GDCMSeriesFileNames to generate seriesUIDs and ImageSeriesReader to read these images. The following is part of my code: typedef double PixelType; typedef itk::Image< PixelType, 4> Image4DType; //4D image type typedef itk::Image< PixelType, 3> Image3DType; //3D image type typedef itk::ImageSeriesReader< Image4DType > ReaderType; typedef itk::GDCMImageIO ImageIOType; reader = ReaderType::New(); dicomIO = ImageIOType::New(); typedef itk::GDCMSeriesFileNames NamesGeneratorType; NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New(); nameGenerator->AddSeriesRestriction("0008|0021"); nameGenerator->SetUseSeriesDetails(true); nameGenerator->SetDirectory(_filename); typedef std::vector< std::string > SeriesIdContainer; const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs(); _isFileLoaded = !(seriesUID.empty()); if (true == _isFileLoaded){ SeriesIdContainer::const_iterator seriesItr = seriesUID.begin(); SeriesIdContainer::const_iterator seriesEnd = seriesUID.end(); std::string seriesIdentifier = seriesUID.begin()->c_str(); typedef std::vector< std::string > FileNamesContainer; FileNamesContainer fileNames; fileNames = nameGenerator->GetFileNames(seriesIdentifier); reader->SetFileNames(fileNames); reader->SetImageIO(dicomIO); reader->Update(); } I have tried this code and the reader worked well. However I got a [x,y,z*t, 1] data, but not [x, y, z, t] data. I understand the problem may caused by nameGenerator, but I use SetUseSeriesDetails and AddSeriesRestriction("0008|0021")(aquisition time)which are implied by documents to handle 4d images.I have also tried several methods but all not work. I wonder whether ITK have an original method to handle 4d images. Have anyone ever met this problem before? Any help or recommendations would be appreciated. Thanks, Lifan The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From dzenanz at gmail.com Fri Feb 26 14:35:27 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Fri, 26 Feb 2016 14:35:27 -0500 Subject: [ITK] =?utf-8?b?562U5aSNOiAg6L2s5Y+ROiBJVEsgdHJ5IHRvIHJlYWQgNEQg?= =?utf-8?q?dicom_time_series=283d=2C_t=29=2C_but_get_3d*t?= In-Reply-To: References: Message-ID: Thanks for sharing the code Lifan, it might help somebody in the future. On Fri, Feb 26, 2016 at 2:02 PM, Chen, Lifan wrote: > Hey Cyril and D?enan, > > Thanks very much for your help. I now fix this problem by using > itkJoinSeriesImageFilter. This class could elevate a series of 3D volumes > (x,y,z)*t into 4D level (x,y,z, t). Though I am not sure this is the best > way for ITK to do so, at least it is the best solution I could find for now > and hope this could help if anyone would work on 4D series using ITK in > future. Here is part of my code: > > typedef itk::JoinSeriesImageFilter > JoinSeriesImageFilterType; > typedef itk::GDCMSeriesFileNames NamesGeneratorType; > joinFilter = JoinSeriesImageFilterType::New(); > NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New(); > nameGenerator->AddSeriesRestriction("0008|0032"); //Use diffrent > restriction depend on the dicom header > nameGenerator->SetUseSeriesDetails(true); > nameGenerator->SetDirectory(_filename); > typedef std::vector< std::string > FileNamesContainer; > FileNamesContainer fileNames; > if (true == _isFileLoaded){ > SeriesIdContainer::const_iterator seriesItr = seriesUID.begin(); > SeriesIdContainer::const_iterator seriesEnd = seriesUID.end(); > for (seriesItr; seriesItr != seriesEnd; seriesItr++){ > ReaderType::Pointer reader = ReaderType::New(); > std::string seriesIdentifier = seriesItr->c_str(); > fileNames = nameGenerator->GetFileNames(seriesIdentifier); > reader->SetFileNames(fileNames); > reader->Update(); > joinFilter->SetInput(inputIndex, reader->GetOutput()); > inputIndex++; > } > joinFilter->Update(); > > Best wishes, > Lifan > ------------------------------ > *???:* D?enan Zuki? [dzenanz at gmail.com] > *????:* 2016?2?26? 9:47 > *???:* Cyril Jaudet > *??:* Chen, Lifan; community at itk.org > *??:* Re: [ITK] ??: ITK try to read 4D dicom time series(3d, t), but get > 3d*t > > I only now see that you sent this only to me Cyril! I CC'd Lifan and the > list. > > On Thu, Feb 25, 2016 at 11:34 AM, Cyril Jaudet > wrote: > >> Hi Lifan, >> here some code that i past in the python interpreter of 3dslicer based on >> vtk. >> >> _First download slicer and load multi image module. >> _Import your serie with the dicom importer. >> _Go into the multivolume support/multivolume explorer >> _Enable frame copying or something similar. >> Now you have two serie (module data to see/rename them) >> 1 multiframe serie >> 1 image that will be used as reference to extract the 3d + t image >> _Copy/paste the following line in the python interpreter of 3dslicer. >> >> >> from __main__ import vtk, qt, ctk, slicer >> from math import * >> import numpy as np >> from vtk.util import numpy_support >> import SimpleITK as sitk >> import sitkUtils as su >> import math >> >> def convert4Dto3D(multi,reference): >> multiNode=slicer.util.getNode(multi) >> refNode=slicer.util.getNode(reference) >> multiImage=multiNode.GetImageData() >> N=multiNode.GetNumberOfFrames() >> for i in range (N): #extract image >> im=vtk.vtkImageExtractComponents() >> im.SetInputData(multiImage) >> im.SetComponents(i) >> im.Update() >> >> frame=slicer.modules.volumes.logic().CloneVolume(slicer.mrmlScene,refNode,'frame_'+str(i)) >> frame.SetAndObserveImageData(im.GetOutput()) >> >> >> _then type: >> convert4Dto3D(multi,reference) >> changing the name of multi and reference by the corresponding name of >> your data >> _it will extract the image under the name frame0, frame1... >> _save them >> >> Hope that help, >> >> Cyril Jaudet >> UZBrussel >> >> 2016-02-24 18:46 GMT+01:00 D?enan Zuki? : >> >>> Hi Lifan, >>> >>> did you examine the DICOM headers? Do different timepoints have >>> different acquisition times? >>> >>> Regards, >>> D?enan >>> >>> On Wed, Feb 24, 2016 at 11:22 AM, Chen, Lifan >>> wrote: >>> >>>> Hey all, >>>> >>>> Any help would be appreciated. This problem really gets me in for >>>> couple of days. >>>> >>>> Thanks, >>>> Lifan >>>> ------------------------------ >>>> *???:* Chen, Lifan >>>> *????:* 2016?2?23? 17:48 >>>> *???:* community at itk.org >>>> *??:* ITK try to read 4D dicom time series(3d, t), but get 3d*t >>>> >>>> Hi all, >>>> >>>> These days, I am trying to use ITK to handle 4D dicom series (3d+t). I >>>> use GDCMSeriesFileNames to generate seriesUIDs and ImageSeriesReader to >>>> read these images. >>>> >>>> The following is part of my code: >>>> typedef double PixelType; >>>> typedef itk::Image< PixelType, 4> Image4DType; >>>> //4D image type >>>> typedef itk::Image< PixelType, 3> Image3DType; >>>> //3D image type >>>> typedef itk::ImageSeriesReader< Image4DType > ReaderType; >>>> typedef itk::GDCMImageIO ImageIOType; >>>> reader = ReaderType::New(); >>>> dicomIO = ImageIOType::New(); >>>> typedef itk::GDCMSeriesFileNames NamesGeneratorType; >>>> NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New(); >>>> nameGenerator->AddSeriesRestriction("0008|0021"); >>>> nameGenerator->SetUseSeriesDetails(true); >>>> nameGenerator->SetDirectory(_filename); >>>> typedef std::vector< std::string > SeriesIdContainer; >>>> const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs(); >>>> _isFileLoaded = !(seriesUID.empty()); >>>> if (true == _isFileLoaded){ >>>> SeriesIdContainer::const_iterator seriesItr = seriesUID.begin(); >>>> SeriesIdContainer::const_iterator seriesEnd = seriesUID.end(); >>>> std::string seriesIdentifier = seriesUID.begin()->c_str(); >>>> typedef std::vector< std::string > FileNamesContainer; >>>> FileNamesContainer fileNames; >>>> fileNames = nameGenerator->GetFileNames(seriesIdentifier); >>>> reader->SetFileNames(fileNames); >>>> reader->SetImageIO(dicomIO); >>>> reader->Update(); >>>> } >>>> >>>> I have tried this code and the reader worked well. However I got a >>>> [x,y,z*t, 1] data, but not [x, y, z, t] data. I understand the problem may >>>> caused by nameGenerator, but I use SetUseSeriesDetails >>>> and AddSeriesRestriction("0008|0021")(aquisition time)which are implied by >>>> documents to handle 4d images.I have also tried several methods but all not >>>> work. I wonder whether ITK have an original method to handle 4d images. >>>> >>>> Have anyone ever met this problem before? Any help or recommendations >>>> would be appreciated. >>>> >>>> Thanks, >>>> Lifan >>>> >>>> The information in this e-mail is intended only for the person to whom >>>> it is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>> in error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>>> _______________________________________________ >>>> Community mailing list >>>> Community at itk.org >>>> http://public.kitware.com/mailman/listinfo/community >>>> >>>> >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community >>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at insightsoftwareconsortium.org Sat Feb 27 19:52:54 2016 From: noreply at insightsoftwareconsortium.org (Insight Journal) Date: Sat, 27 Feb 2016 19:52:54 -0500 (EST) Subject: [ITK] [ITK-users] New Submission: ITK in Biomedical Research and Commercial Applications Message-ID: <20160228005254.5A5E73D620A7@insight-journal.org> Hello, A new submission has been added to the Insight Journal. Title: ITK in Biomedical Research and Commercial Applications Authors: McCormick M., Aylward S., Johnson H., Lowekamp B. Abstract: The Insight Segmentation and Registration Toolkit (www.itk.org) has become a standard in academia and industry for medical image analysis. In recent years, the ITK developers' community has focused on providing programming interfaces to ITK from Python, Java, and Javascript and making ITK available via leading applications such as Slicer and ImageJ. In this course we present best practices for taking advantage of ITK in your imaging research and commercial products. We demonstrate how script writing and interactive GUIs can be used to access the algorithms in ITK and the multitude of ITK extensions that are freely available on the web. We also cover the opportunities and challenges with using open-source software in research and in commercial applications: from prototypes that can lead to venture capital funding to applications for first-in-human trials and ultimately for regulatory approval. Download and review this publication at: http://hdl.handle.net/10380/3542 Generated by the Insight Journal You are receiving this email because you asked to be informed by the Insight Journal for new submissions. To change your email preference visit http://insight-journal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From jothybasu at gmail.com Sun Feb 28 19:53:03 2016 From: jothybasu at gmail.com (Jothybasu Selvaraj) Date: Mon, 29 Feb 2016 11:53:03 +1100 Subject: [ITK] [ITK-users] Error downloading data from Midas Message-ID: Dear All I am trying to build ITK with fftw and fftd but I get the following error saying it could not connect to the server while building. I use mingw32-make. i tried even enabling the CMAKE_USE_OPENSSL. I use cmake 3.50rc3. Any hints? The errors message is: D:\Libs\ITK\Build>mingw32-make install [ 0%] Built target ITKData Scanning dependencies of target fftwd [ 0%] Creating directories for 'fftwd' [ 0%] Performing download step (download, verify and extract) for 'fftwd' -- downloading... src=' http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.downlo ad&checksum=2edab8c06b24feeb3b82bbb3ebf3e7b3&name=fftw-3.3.4.tar.gz' dst='D:/Libs/ITK/Build/fftwd/src/fftw-3.3.4.tar.gz' timeout='none' CMake Error at fftwd-stamp/download-fftwd.cmake:27 (message): error: downloading ' http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&chec ksum=2edab8c06b24feeb3b82bbb3ebf3e7b3&name=fftw-3.3.4.tar.gz' failed status_code: 7 status_string: "Couldn't connect to server" log: timeout on name lookup is not supported Trying 50.58.123.181... connect to 50.58.123.181 port 80 failed: Timed out Failed to connect to midas3.kitware.com port 80: Timed out Closing connection 0 Thanks Jothy -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From raghav.mehta at research.iiit.ac.in Mon Feb 29 04:39:24 2016 From: raghav.mehta at research.iiit.ac.in (Raghav Mehta) Date: Mon, 29 Feb 2016 15:09:24 +0530 (IST) Subject: [ITK] [Registration] Non-rigid registration for vector image Message-ID: <1038016696.2682434.1456738764927.JavaMail.zimbra@research.iiit.ac.in> Hi, Can anyone provide a good example of non-rigid registration on Vector images?? Regards, Raghav Mehta From dzenanz at gmail.com Mon Feb 29 11:43:06 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Mon, 29 Feb 2016 11:43:06 -0500 Subject: [ITK] [ITK-users] Error downloading data from Midas In-Reply-To: References: Message-ID: I can download it now. Maybe it was a temporary unavailability (power down, network down). Can you try again? On Sun, Feb 28, 2016 at 7:53 PM, Jothybasu Selvaraj wrote: > Dear All > > I am trying to build ITK with fftw and fftd but I get the following error > saying it could not connect to the server while building. > > I use mingw32-make. i tried even enabling the CMAKE_USE_OPENSSL. I use > cmake 3.50rc3. > > Any hints? > > The errors message is: > > D:\Libs\ITK\Build>mingw32-make install > [ 0%] Built target ITKData > Scanning dependencies of target fftwd > [ 0%] Creating directories for 'fftwd' > [ 0%] Performing download step (download, verify and extract) for 'fftwd' > -- downloading... > src=' > http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.downlo > ad&checksum=2edab8c06b24feeb3b82bbb3ebf3e7b3&name=fftw-3.3.4.tar.gz' > dst='D:/Libs/ITK/Build/fftwd/src/fftw-3.3.4.tar.gz' > timeout='none' > CMake Error at fftwd-stamp/download-fftwd.cmake:27 (message): > error: downloading > ' > http://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&chec > ksum=2edab8c06b24feeb3b82bbb3ebf3e7b3&name=fftw-3.3.4.tar.gz' > failed > > status_code: 7 > status_string: "Couldn't connect to server" > log: timeout on name lookup is not supported > Trying 50.58.123.181... > > connect to 50.58.123.181 port 80 failed: Timed out > > Failed to connect to midas3.kitware.com port 80: Timed out > > Closing connection 0 > > > Thanks > > Jothy > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From kyungmoo-lee at uiowa.edu Mon Feb 29 15:32:46 2016 From: kyungmoo-lee at uiowa.edu (Lee, Kyungmoo) Date: Mon, 29 Feb 2016 20:32:46 +0000 Subject: [ITK] Memory leaks with ITK and MFC Message-ID: Dear all, When I run InsightApplications-4.8.0/ItkMFC using ITK-4.8.2, MS Windows, and Visual Studio 2010/2012, I found memory leaks. Other persons in the following links have the same problem. I cannot find any solution on the web. Please help me. Thank you. https://cmake.org/pipermail/insight-users/2007-July/022885.html http://itk-insight-users.2283740.n2.nabble.com/No-one-knows-the-ITK-MFC-memory-leak-problem-td7583950.html Kit -------------- next part -------------- An HTML attachment was scrubbed... URL: