From M.Staring at lumc.nl Wed Jun 1 03:45:08 2016 From: M.Staring at lumc.nl (M.Staring at lumc.nl) Date: Wed, 1 Jun 2016 07:45:08 +0000 Subject: [ITK] [ITK-dev] linear interpolator leaks? Message-ID: <24D8AA23EC0DCB4498C35EC60401E76144003202@MAIL-MB02.lumcnet.prod.intern> Hi all, I noticed that our valgrind build of elastix has reports like this: UMR ==5253== Invalid read of size 2 ==5253== at 0x552241: itk::LinearInterpolateImageFunction, double>::EvaluateOptimized(itk::LinearInterpolateImageFunction, double>::Dispatch<2u> const&, itk::ContinuousIndex const&) const (itkLinearInterpolateImageFunction.h:173) ==5253== by 0x54976C: itk::LinearInterpolateImageFunction, double>::EvaluateAtContinuousIndex(itk::ContinuousIndex const&) const (itkLinearInterpolateImageFunction.h:99) ==5253== by 0x54397B: bool TestInterpolators<2u>() (itkAdvancedLinearInterpolatorTest.cxx:171) ==5253== by 0x53E232: main (itkAdvancedLinearInterpolatorTest.cxx:279) ==5253== Address 0x6822b94 is 52 bytes inside a block of size 83 free'd ==5253== at 0x4C2C2BC: operator delete(void*) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) ==5253== by 0x5ED884: itk::ObjectFactoryBase::CreateObject(char const*) (in /home/marius/nightly-builds/elastix/bin_debug/bin/itkAdvancedLinearInterpolatorTest) ==5253== by 0x5EF91B: itk::ObjectFactoryBase::CreateInstance(char const*) (in /home/marius/nightly-builds/elastix/bin_debug/bin/itkAdvancedLinearInterpolatorTest) ==5253== by 0x550335: itk::ObjectFactory, double> >::Create() (itkObjectFactory.h:60) ==5253== by 0x548A90: itk::LinearInterpolateImageFunction, double>::New() (in /home/marius/nightly-builds/elastix/bin_debug/bin/itkAdvancedLinearInterpolatorTest) ==5253== by 0x543540: bool TestInterpolators<2u>() (itkAdvancedLinearInterpolatorTest.cxx:114) ==5253== by 0x53E232: main (itkAdvancedLinearInterpolatorTest.cxx:279) ==5253== On inspection these lines in itk LinearInterpolateImageFunction.h seem troublesome: const RealType & val000 = inputImagePtr->GetPixel(basei); Note that a real type is obtained by reference from a function that often does not return a real type. Is this allowed? Best, Marius Marius Staring, PhD Division of Image Processing (LKEB) Department of Radiology Leiden University Medical Center PO Box 9600, 2300 RC Leiden, The Netherlands phone: +31 (0)71 52 62137, fax: +31 (0)71 524 8256 m.staring at lumc.nl -------------- 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 Christian.K.Gustafsson at skane.se Wed Jun 1 05:05:13 2016 From: Christian.K.Gustafsson at skane.se (Gustafsson Christian K) Date: Wed, 1 Jun 2016 09:05:13 +0000 Subject: [ITK] InvertDisplacementFieldImageFilter in SimpleITK In-Reply-To: <7A08CC76-99D0-4FC1-BF0E-767252A58FDD@mail.nih.gov> References: <31BA9FED7BDD6A429EDBA37671C8C47026C3054D@RSMAIL112.REG.SKANE.SE> <7A08CC76-99D0-4FC1-BF0E-767252A58FDD@mail.nih.gov> Message-ID: <31BA9FED7BDD6A429EDBA37671C8C47026C30645@RSMAIL112.REG.SKANE.SE> Hi! Thanks for your reply. I can not find out any more from the code. If it is physical space, what unit is used? Default seems to be m_MaxErrorToleranceThreshold(0.1), m_MeanErrorToleranceThreshold(0.001), so I guess this is not meters, but rather mm (?). Fr?n: Lowekamp, Bradley (NIH/NLM/LHC) [C] [mailto:blowekamp at mail.nih.gov] Skickat: den 31 maj 2016 16:03 Till: Gustafsson Christian K Kopia: community at itk.org ?mne: Re: [ITK] InvertDisplacementFieldImageFilter in SimpleITK Hello, My assumption would be that the error is in physical space and not pixels as this is standard ITK practice. While the documentation is rather sparse you can look at the source code to gain insight into these types of questions [1]. Also note that there is the InverseDisplacementFieldImageFilter. I don?t recall the difference and if one is generally preferred of the other. HTH, Brad [1] https://github.com/InsightSoftwareConsortium/ITK/blob/1257b0468c147ba2b1a65bae67169bdf35f4fa50/Modules/Filtering/DisplacementField/include/itkInvertDisplacementFieldImageFilter.hxx#L215-L248 On May 31, 2016, at 8:40 AM, Gustafsson Christian K > wrote: Hello! What is the unit of measurement that is used in the criterias MeanErrorToleranceThreshold and MaxErrorToleranceThreshold /* Set/Get the mean stopping criterion */ itkSetMacro( MeanErrorToleranceThreshold, RealType ); itkGetConstMacro( MeanErrorToleranceThreshold, RealType ); /* Set/Get the max stopping criterion */ itkSetMacro( MaxErrorToleranceThreshold, RealType ); itkGetConstMacro( MaxErrorToleranceThreshold, RealType ); in InvertDisplacementFieldImageFilter in SimpleITK? Is it amount of pixels? Best regards ________________________________________ Christian Gustafsson Medical Physicist, MRI, PhD candidate Department of Radiation Physics Klinikgatan 5 Sk?ne University Hospital SE 221 85 Lund +46 46 177647 Christian.K.Gustafsson at skane.se _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From luc.hermitte at c-s.fr Wed Jun 1 05:02:07 2016 From: luc.hermitte at c-s.fr (Luc Hermitte) Date: Wed, 1 Jun 2016 11:02:07 +0200 Subject: [ITK] [ITK-dev] linear interpolator leaks? In-Reply-To: <24D8AA23EC0DCB4498C35EC60401E76144003202@MAIL-MB02.lumcnet.prod.intern> References: <24D8AA23EC0DCB4498C35EC60401E76144003202@MAIL-MB02.lumcnet.prod.intern> Message-ID: Hi, Le 01/06/2016 ? 09:45, M.Staring at lumc.nl a ?crit : > I noticed that our valgrind build of elastix has reports like this: > > *UMR*==5253== Invalid read of size 2 > > ==5253== at 0x552241: > itk::LinearInterpolateImageFunction, > double>::EvaluateOptimized(itk::LinearInterpolateImageFunction 2u>, double>::Dispatch<2u> const&, itk::ContinuousIndex > const&) const (itkLinearInterpolateImageFunction.h:173) > > ==5253== by 0x54976C: > itk::LinearInterpolateImageFunction, > double>::EvaluateAtContinuousIndex(itk::ContinuousIndex > const&) const (itkLinearInterpolateImageFunction.h:99) > > ==5253== by 0x54397B: bool TestInterpolators<2u>() > (itkAdvancedLinearInterpolatorTest.cxx:171) > > ==5253== by 0x53E232: main (itkAdvancedLinearInterpolatorTest.cxx:279) > > ==5253== Address 0x6822b94 is 52 bytes inside a block of size 83 free'd > > ==5253== at 0x4C2C2BC: operator delete(void*) (in > /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) > > ==5253== by 0x5ED884: itk::ObjectFactoryBase::CreateObject(char > const*) (in > /home/marius/nightly-builds/elastix/bin_debug/bin/itkAdvancedLinearInterpolatorTest) > > ==5253== by 0x5EF91B: itk::ObjectFactoryBase::CreateInstance(char > const*) (in > /home/marius/nightly-builds/elastix/bin_debug/bin/itkAdvancedLinearInterpolatorTest) > > ==5253== by 0x550335: > itk::ObjectFactory 2u>, double> >::Create() (itkObjectFactory.h:60) > > ==5253== by 0x548A90: > itk::LinearInterpolateImageFunction, > double>::New() (in > /home/marius/nightly-builds/elastix/bin_debug/bin/itkAdvancedLinearInterpolatorTest) > > ==5253== by 0x543540: bool TestInterpolators<2u>() > (itkAdvancedLinearInterpolatorTest.cxx:114) > > ==5253== by 0x53E232: main (itkAdvancedLinearInterpolatorTest.cxx:279) > > ==5253== > > > > On inspection these lines in itk LinearInterpolateImageFunction.h seem > troublesome: > > > > const RealType & val000 = inputImagePtr->GetPixel(basei); > > > Note that a real type is obtained by reference from a function that > often does not return a real type. Is this allowed? It should be fine. We are authorized to get a const reference to the result of a function that returns by value. Most of the time, it's never done because this is quite odd. As long as the function doesn't return a reference/address to a local variable, there is no problem. Have you checked without the "const&" ? Any way, this won't cause a leak. We could have suspected a dangling reference, but there should be none IIRC this part of the code. See https://herbsutter.com/2008/01/01/gotw-88-a-candidate-for-the-most-important-const/ I'd check whether the index produced in within the boundaries on the internal buffer with a `assert(offset < m_Buffer->Size());` in itk::Image::GetPixel. I'd be curious to see what clang address sanatizer says (it may give more information than valgrind -- like where the free'd address was allocated then free'd) Regards -- Luc Hermitte _______________________________________________ Powered by www.kitware.com 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 tevain at telecom-paristech.fr Wed Jun 1 05:21:19 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Wed, 1 Jun 2016 11:21:19 +0200 (CEST) Subject: [ITK] InvertDisplacementFieldImageFilter in SimpleITK In-Reply-To: <31BA9FED7BDD6A429EDBA37671C8C47026C30645@RSMAIL112.REG.SKANE.SE> References: <31BA9FED7BDD6A429EDBA37671C8C47026C3054D@RSMAIL112.REG.SKANE.SE> <7A08CC76-99D0-4FC1-BF0E-767252A58FDD@mail.nih.gov> <31BA9FED7BDD6A429EDBA37671C8C47026C30645@RSMAIL112.REG.SKANE.SE> Message-ID: <603767000.72858770.1464772879056.JavaMail.zimbra@enst.fr> Hi Christian, Physical space only depend of your data. The unit will be the one in the header or meta-data. I don't know what data you're using, but mms are rather common indeed. HTH, Tim ----- Mail original ----- De: "Gustafsson Christian K" ?: "Bradley Lowekamp (NIH/NLM/LHC) [C]" Cc: community at itk.org, "Fredrik Nordstr?m" Envoy?: Mercredi 1 Juin 2016 11:05:13 Objet: Re: [ITK] InvertDisplacementFieldImageFilter in SimpleITK Hi! Thanks for your reply. I can not find out any more from the code. If it is physical space, what unit is used? Default seems to be m_MaxErrorToleranceThreshold(0.1), m_MeanErrorToleranceThreshold(0.001), so I guess this is not meters, but rather mm (?). Fr?n: Lowekamp, Bradley (NIH/NLM/LHC) [C] [mailto:blowekamp at mail.nih.gov] Skickat: den 31 maj 2016 16:03 Till: Gustafsson Christian K Kopia: community at itk.org ?mne: Re: [ITK] InvertDisplacementFieldImageFilter in SimpleITK Hello, My assumption would be that the error is in physical space and not pixels as this is standard ITK practice. While the documentation is rather sparse you can look at the source code to gain insight into these types of questions [1]. Also note that there is the InverseDisplacementFieldImageFilter. I don?t recall the difference and if one is generally preferred of the other. HTH, Brad [1] https://github.com/InsightSoftwareConsortium/ITK/blob/1257b0468c147ba2b1a65bae67169bdf35f4fa50/Modules/Filtering/DisplacementField/include/itkInvertDisplacementFieldImageFilter.hxx#L215-L248 On May 31, 2016, at 8:40 AM, Gustafsson Christian K < Christian.K.Gustafsson at skane.se > wrote: Hello! What is the unit of measurement that is used in the criterias MeanErrorToleranceThreshold and MaxErrorToleranceThreshold /* Set/Get the mean stopping criterion */ itkSetMacro( MeanErrorToleranceThreshold, RealType ); itkGetConstMacro( MeanErrorToleranceThreshold, RealType ); /* Set/Get the max stopping criterion */ itkSetMacro( MaxErrorToleranceThreshold, RealType ); itkGetConstMacro( MaxErrorToleranceThreshold, RealType ); in InvertDisplacementFieldImageFilter in SimpleITK? Is it amount of pixels? Best regards ________________________________________ Christian Gustafsson Medical Physicist, MRI, PhD candidate Department of Radiation Physics Klinikgatan 5 Sk?ne University Hospital SE 221 85 Lund +46 46 177647 Christian.K.Gustafsson at skane.se _______________________________________________ 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 vrnova at gmail.com Wed Jun 1 08:27:31 2016 From: vrnova at gmail.com (Yanling Liu) Date: Wed, 1 Jun 2016 08:27:31 -0400 Subject: [ITK] [ITK-users] MutualInformationAffine example broken Message-ID: Hello, I downloaded the MutualInformationAffine example from https://itk.org/Wiki/ITK/Examples/Registration/MutualInformationAffine, compiled it using ITK 4.9.1 and it reported follow error message: ExceptionObject caught ! itk::ExceptionObject (0x2030010) Location: "void itk::MutualInformationImageToImageMetric::SampleFixedImageDomain(itk::MutualInformationImageToImageMetric::SpatialSampleContainer&) const [with TFixedImage = itk::Image; TMovingImage = itk::Image; itk::MutualInformationImageToImageMetric::SpatialSampleContainer = std::vector, itk::Image >::SpatialSample, std::allocator, itk::Image >::SpatialSample> >]" File: /home/yliu/Imaging/Libraries/ITK/InsightToolkit-4.9.1/install/include/ITK-4.9/itkMutualInformationImageToImageMetric.hxx Line: 196 Description: itk::ERROR: MutualInformationImageToImageMetric(0x202fd10): All the sampled point mapped to outside of the moving image Anyone may help to fix this example? I did not change the source code of the example at all. Thanks, Yanling -------------- 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 javij1 at gmail.com Thu Jun 2 11:39:08 2016 From: javij1 at gmail.com (=?UTF-8?Q?Javier_Juan_Albarrac=c3=adn?=) Date: Thu, 2 Jun 2016 17:39:08 +0200 Subject: [ITK] [ITK-users] Set image pixel type and dimension through IOBase methods Message-ID: <1f455784-df74-d36c-9df9-4fa0787091cb@gmail.com> Hello, I have to read a NIfTI file and I don't know which pixel type has (int, double, char, etc). Thus, I am using an ImageIOBase object to retrieve the image information before loading it. I have followed the code of the ITK examples, which is something similar to // NIfTI IO Factory itk::NiftiImageIOFactory::RegisterOneFactory(); // Typedefs typedef itk::ImageIOBase::IOComponentType PixelType; itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(filename, itk::ImageIOFactory::ReadMode); imageIO->SetFileName(argv[1]); imageIO->ReadImageInformation(); Here I know the pixel type and the image dimensio through "imageIO->GetComponentType()" and "imageIO->GetDimensions()". Hence, I wan to declare an image type with this parameters to work with it on my methods. I would know if there is some way to declare the image without performing a long "switch - case double, case int, case ..." code to declare the image type, i.e. something similar to this: // I know this do not compile and it is wrong but something similar typedef itk::ImageGetComponentType(), imageIO->GetDimensions()> ImageType; Thank you. Regards. Javier. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 Thu Jun 2 11:59:36 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 2 Jun 2016 15:59:36 +0000 Subject: [ITK] [ITK-users] Set image pixel type and dimension through IOBase methods In-Reply-To: <1f455784-df74-d36c-9df9-4fa0787091cb@gmail.com> References: <1f455784-df74-d36c-9df9-4fa0787091cb@gmail.com> Message-ID: <55CC9F1B-BD53-4EBC-A675-663FAAB8DB1E@mail.nih.gov> Hello, To accomplish this in C++ you need to use this long switch statement in combination with template functions. It?s really not too bad. You only write the switch statement once and then just work in the template method [1]. Alternatively, SimpleITK has created a typeless layer on top of ITK so that the types can easily be dealt with at run-time. This interface can easily be used in Python. Similarly, there are the ITK?s python bindings too, which use Pythons weak typing in combination with dictionaries to types all put together with a convent interface. HTH, Brad [1] https://itk.org/ITKExamples/src/IO/ImageBase/ReadUnknownImageType/Documentation.html > On Jun 2, 2016, at 11:39 AM, Javier Juan Albarrac?n wrote: > > > Hello, > > I have to read a NIfTI file and I don't know which pixel type has (int, double, char, etc). Thus, I am using an ImageIOBase object to retrieve the image information before loading it. I have followed the code of the ITK examples, which is something similar to > > // NIfTI IO Factory > itk::NiftiImageIOFactory::RegisterOneFactory(); > > // Typedefs > typedef itk::ImageIOBase::IOComponentType PixelType; > itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(filename, itk::ImageIOFactory::ReadMode); > > imageIO->SetFileName(argv[1]); > imageIO->ReadImageInformation(); > > Here I know the pixel type and the image dimensio through "imageIO->GetComponentType()" and "imageIO->GetDimensions()". Hence, I wan to declare an image type with this parameters to work with it on my methods. > I would know if there is some way to declare the image without performing a long "switch - case double, case int, case ..." code to declare the image type, i.e. something similar to this: > > // I know this do not compile and it is wrong but something similar > typedef itk::ImageGetComponentType(), imageIO->GetDimensions()> ImageType; > > Thank you. > Regards. > Javier. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 javij1 at gmail.com Thu Jun 2 13:02:38 2016 From: javij1 at gmail.com (=?UTF-8?Q?Javier_Juan_Albarrac=c3=adn?=) Date: Thu, 2 Jun 2016 19:02:38 +0200 Subject: [ITK] [ITK-users] Set image pixel type and dimension through IOBase methods In-Reply-To: <55CC9F1B-BD53-4EBC-A675-663FAAB8DB1E@mail.nih.gov> References: <1f455784-df74-d36c-9df9-4fa0787091cb@gmail.com> <55CC9F1B-BD53-4EBC-A675-663FAAB8DB1E@mail.nih.gov> Message-ID: Thank you for the quick anwser. I am sorry but I do not clearly see how can I later work with the image and with the filters that need the ImageType to declare the object. In the [1] example, the "ReadScalarImage" function implements the long switch statement code to load the image with the corresponding type. However, I cannot return a pointer to the image because depending on the case statement, it has one type or another. Inside each case statement the corresponding image type is known, so templated functions can be called and the image type can be inferred for each one. This means that I have to embed all my code, my function and methods calls inside each case statement to know the ImageType? Surely I am not understanding something because I don't believe this approach is correct. Thank you very much. Regards. Javier. El 02/06/2016 a las 17:59, Lowekamp, Bradley (NIH/NLM/LHC) [C] escribi?: > Hello, > > To accomplish this in C++ you need to use this long switch statement in combination with template functions. It?s really not too bad. You only write the switch statement once and then just work in the template method [1]. > > Alternatively, SimpleITK has created a typeless layer on top of ITK so that the types can easily be dealt with at run-time. This interface can easily be used in Python. > > Similarly, there are the ITK?s python bindings too, which use Pythons weak typing in combination with dictionaries to types all put together with a convent interface. > > > HTH, > Brad > > [1] https://itk.org/ITKExamples/src/IO/ImageBase/ReadUnknownImageType/Documentation.html > >> On Jun 2, 2016, at 11:39 AM, Javier Juan Albarrac?n wrote: >> >> >> Hello, >> >> I have to read a NIfTI file and I don't know which pixel type has (int, double, char, etc). Thus, I am using an ImageIOBase object to retrieve the image information before loading it. I have followed the code of the ITK examples, which is something similar to >> >> // NIfTI IO Factory >> itk::NiftiImageIOFactory::RegisterOneFactory(); >> >> // Typedefs >> typedef itk::ImageIOBase::IOComponentType PixelType; >> itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(filename, itk::ImageIOFactory::ReadMode); >> >> imageIO->SetFileName(argv[1]); >> imageIO->ReadImageInformation(); >> >> Here I know the pixel type and the image dimensio through "imageIO->GetComponentType()" and "imageIO->GetDimensions()". Hence, I wan to declare an image type with this parameters to work with it on my methods. >> I would know if there is some way to declare the image without performing a long "switch - case double, case int, case ..." code to declare the image type, i.e. something similar to this: >> >> // I know this do not compile and it is wrong but something similar >> typedef itk::ImageGetComponentType(), imageIO->GetDimensions()> ImageType; >> >> Thank you. >> Regards. >> Javier. >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 blowekamp at mail.nih.gov Thu Jun 2 13:15:15 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 2 Jun 2016 17:15:15 +0000 Subject: [ITK] [ITK-users] Set image pixel type and dimension through IOBase methods In-Reply-To: References: <1f455784-df74-d36c-9df9-4fa0787091cb@gmail.com> <55CC9F1B-BD53-4EBC-A675-663FAAB8DB1E@mail.nih.gov> Message-ID: Hi, You are correct that you can?t return a typed pointer from the template functions. But not that you should implement your code inside the case statement. You can implement your code in the templates functions, then call other functions with templates of the type or classes which the type as templates. HTH, Brad > On Jun 2, 2016, at 1:02 PM, Javier Juan Albarrac?n wrote: > > > Thank you for the quick anwser. > > I am sorry but I do not clearly see how can I later work with the image and with the filters that need the ImageType to declare the object. In the [1] example, the "ReadScalarImage" function implements the long switch statement code to load the image with the corresponding type. However, I cannot return a pointer to the image because depending on the case statement, it has one type or another. > > Inside each case statement the corresponding image type is known, so templated functions can be called and the image type can be inferred for each one. This means that I have to embed all my code, my function and methods calls inside each case statement to know the ImageType? Surely I am not understanding something because I don't believe this approach is correct. > > Thank you very much. > > Regards. > > Javier. > > > El 02/06/2016 a las 17:59, Lowekamp, Bradley (NIH/NLM/LHC) [C] escribi?: >> Hello, >> >> To accomplish this in C++ you need to use this long switch statement in combination with template functions. It?s really not too bad. You only write the switch statement once and then just work in the template method [1]. >> >> Alternatively, SimpleITK has created a typeless layer on top of ITK so that the types can easily be dealt with at run-time. This interface can easily be used in Python. >> >> Similarly, there are the ITK?s python bindings too, which use Pythons weak typing in combination with dictionaries to types all put together with a convent interface. >> >> >> HTH, >> Brad >> >> [1] https://itk.org/ITKExamples/src/IO/ImageBase/ReadUnknownImageType/Documentation.html >> >>> On Jun 2, 2016, at 11:39 AM, Javier Juan Albarrac?n wrote: >>> >>> >>> Hello, >>> >>> I have to read a NIfTI file and I don't know which pixel type has (int, double, char, etc). Thus, I am using an ImageIOBase object to retrieve the image information before loading it. I have followed the code of the ITK examples, which is something similar to >>> >>> // NIfTI IO Factory >>> itk::NiftiImageIOFactory::RegisterOneFactory(); >>> >>> // Typedefs >>> typedef itk::ImageIOBase::IOComponentType PixelType; >>> itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(filename, itk::ImageIOFactory::ReadMode); >>> >>> imageIO->SetFileName(argv[1]); >>> imageIO->ReadImageInformation(); >>> >>> Here I know the pixel type and the image dimensio through "imageIO->GetComponentType()" and "imageIO->GetDimensions()". Hence, I wan to declare an image type with this parameters to work with it on my methods. >>> I would know if there is some way to declare the image without performing a long "switch - case double, case int, case ..." code to declare the image type, i.e. something similar to this: >>> >>> // I know this do not compile and it is wrong but something similar >>> typedef itk::ImageGetComponentType(), imageIO->GetDimensions()> ImageType; >>> >>> Thank you. >>> Regards. >>> Javier. >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the 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 javij1 at gmail.com Thu Jun 2 13:18:37 2016 From: javij1 at gmail.com (=?UTF-8?Q?Javier_Juan_Albarrac=c3=adn?=) Date: Thu, 2 Jun 2016 19:18:37 +0200 Subject: [ITK] [ITK-users] Set image pixel type and dimension through IOBase methods In-Reply-To: <55CC9F1B-BD53-4EBC-A675-663FAAB8DB1E@mail.nih.gov> References: <1f455784-df74-d36c-9df9-4fa0787091cb@gmail.com> <55CC9F1B-BD53-4EBC-A675-663FAAB8DB1E@mail.nih.gov> Message-ID: Well, sorry. I just now understand what you are referring. You are refering to start to work inside the function "ReadImage" of the [1] example (maybe changing his name to some more informative) as if it was the "main" function because inside this templated function we have the ImageType as the template arg. Yes, it solves my problem. Anyway, it is a little bit anoying for me. Maybe I can load the image in double format to avoid truncation problems and perform a final casting to the original type, but surely, in some point I should pass through the long switch statement. Thank you Brad Javier. El 02/06/2016 a las 17:59, Lowekamp, Bradley (NIH/NLM/LHC) [C] escribi?: > Hello, > > To accomplish this in C++ you need to use this long switch statement in combination with template functions. It?s really not too bad. You only write the switch statement once and then just work in the template method [1]. > > Alternatively, SimpleITK has created a typeless layer on top of ITK so that the types can easily be dealt with at run-time. This interface can easily be used in Python. > > Similarly, there are the ITK?s python bindings too, which use Pythons weak typing in combination with dictionaries to types all put together with a convent interface. > > > HTH, > Brad > > [1] https://itk.org/ITKExamples/src/IO/ImageBase/ReadUnknownImageType/Documentation.html > >> On Jun 2, 2016, at 11:39 AM, Javier Juan Albarrac?n wrote: >> >> >> Hello, >> >> I have to read a NIfTI file and I don't know which pixel type has (int, double, char, etc). Thus, I am using an ImageIOBase object to retrieve the image information before loading it. I have followed the code of the ITK examples, which is something similar to >> >> // NIfTI IO Factory >> itk::NiftiImageIOFactory::RegisterOneFactory(); >> >> // Typedefs >> typedef itk::ImageIOBase::IOComponentType PixelType; >> itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(filename, itk::ImageIOFactory::ReadMode); >> >> imageIO->SetFileName(argv[1]); >> imageIO->ReadImageInformation(); >> >> Here I know the pixel type and the image dimensio through "imageIO->GetComponentType()" and "imageIO->GetDimensions()". Hence, I wan to declare an image type with this parameters to work with it on my methods. >> I would know if there is some way to declare the image without performing a long "switch - case double, case int, case ..." code to declare the image type, i.e. something similar to this: >> >> // I know this do not compile and it is wrong but something similar >> typedef itk::ImageGetComponentType(), imageIO->GetDimensions()> ImageType; >> >> Thank you. >> Regards. >> Javier. >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 jchris.fillionr at kitware.com Fri Jun 3 09:52:10 2016 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Fri, 3 Jun 2016 09:52:10 -0400 Subject: [ITK] [ITK-dev] [ANN] ITK 4.10.0 has been released! 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 4.10.0 has been released! Links to the Sourceforge.net tarballs can be found on the download page: http://www.itk.org/ITK/resources/software.html [image: TwoProjectionRegistrationDiagram.png] Insight Journal article included as a Remote Module: TwoProjectionRegistration . Digitally reconstructed radiographs (DRR) generated as part of the registration are shown above. 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 offersis a platform for commercial product development. A few selected highlights for the 4.10 release include the following: - New Remote module: TwoProjectionRegistration performs simultaneous registration of two projection images to a 3D image volume, which is useful for external beam radiotherapy and other applications. It uses Powell?s method for optimization and the Siddon-Jacobs fast ray-tracing algorithm. - First update to internal VNL in five years. Many improvements were made to upstream VNL. We now push patches upstream and stay in sync via a Git subtree workflow. - Windows builds now support processing 4GB+ images by default - GDCM updated for better DICOM support Congratulations to the 26 contributors to this release. We would especially like to recognize the new contributors: Andrey Fedorov, Sujin Philip, Francois Budin, and b'Alvaro Sanchez. Improved documentation in this release includes new examples on how to convert between ITK and VTK image data structures . Additionally, a new example demonstrates how to perform vector image registration with a mean-squares matching metric . The ITK Software Guide added documentation on how to add third party dependencies when creating an ITK module. This release also brings exciting rapid prototyping improvements to the ITK Python wrapping. Type specification is no longer necessary during the creation of most filters. The required type is inferred from a primary input passed on filter creation. For example, instead of the explicit type specification: median = itk.MedianImageFilter[ImageType, ImageType].New() median.SetInput(reader.GetOutput()) It is now possible to call: median = itk.MedianImageFilter.New(Input=reader.GetOutput()) Or, the shortened: median = itk.MedianImageFilter.New(reader.GetOutput()) Or: median = itk.MedianImageFliter.New(reader) An itk.ImageFileReader can be created by specifying the FileName during instantiation: reader = itk.ImageFileReader.New(FileName=?inputFile.mha?) Enjoy ITK! New Features --------------------- * Wrapping improvements - ITK_USE_64BITS_IDS supported on Windows - Faster builds (CastXML calls and build targets reduced by half) - Faster runtime loading and smaller binary size due to hidden symbol visibility - Wrapping with BUILD_SHARED_LIBS disabled is supported - Do not link to libpython when possible - Filter types do not need to be specified when ?Input=inputImage? is specified in the constructor - Improved wrapping class coverage - Visual Studio 2015 Update 2 Supported - GCC 6.1 supported * New Remote Module - TwoProjectionRegistration - 2D-3D registration designed for radiotherapy - http://hdl.handle.net/10380/3245 * Core Improvements - Data and build tool downloads now over HTTPS - Extended constexpr usage with ITK_CONSTEXPR and ITKCONSTEXPR_FUNC macros - ITK_USE_64BITS_IDS, required to process 4GB+ images on Windows, now enabled by default - VNL updated and modernized - CMake configuration major modernization - vcl has been removed in favor of the standard libraries - vnl_math_ function avoided in favor of std:: and itk::Math - VNL had suppressed integer data conversion warnings on Visual Studio (C4257); this suppression has been removed and all warnings addressed - Various improvements for building a module externally against an ITK build tree - CMAKE_POSITION_INDEPENDENT_CODE is enabled by default - Improved EXERCISE_BASIC_OBJECT_METHODS testing macro * Filtering Improvements - RGB pixel support added to itk::ImageToVTKImageFilter - itk::Box* filters moved out of the Review module - itk::GaussianDerivativeOperator moved out of the Review module - MaskLabel is deprecated in N4BiasFieldCorrectionFilter in favor any non-zero pixel * Registration Improvements - Fixed and moving masks added to the v4 registration methods * Documentation Improvements - Updates to the Software Guide, Doxygen, Wiki and Sphinx Examples - New examples on to convert between ITK and VTK - New example on how to perform vector image registration - The ITK Software Guide describes how to add a third-party dependency to a module * Third Party Library Updates - pygccxml updated to v1.7.3 - GDCM updated to the release branch latest - VNL updated to latest upstream - MINC updated to the latest upstream - SWIG updated to v3.0.8 - PCRE update to v8.38 * Improved code coverage -- we are at 85.0%! * *Lots* of important bug fixes * And much more! See details in the log below. Changes from v4.10rc02..v4.10.0 ------------------------------------------------ Bradley Lowekamp (3): COMP: Address uninitialized warning of size COMP: Devirtualize private methods to prevent instantiation COMP: Use well defined ZeroValue for unused initial value. Hans Johnson (1): BUG: try_compile needs to have CMAKE_CXX_STANDARD passed Hyun Jae Kang (1): COMP: Fix unexpected data-cast results of itkCastImageFilter Jon Haitz Legarreta (1): BUG: Fix OpenCV-2.4.9 camera empty image issue. Matthew McCormick (13): COMP: Bump CastXML for GCC 6.1 support. STYLE: Improvements to HardConnectedComponentsImageFilter. ENH: Add baseline for itkHardConnectedComponentImageFilterTest. STYLE: Improvements for itkHardConnectedComponentImageFilterTest COMP: HardConnectedComponentImageFilter autological constant out of range DOC: Sphinx examples update to 2016-05-22. DOC: Wiki examples update to 2016-05-22. COMP: MSVC result of 32-bit shift implicitly converted to 64 bits BUG: Disable building the netlib example. ENH: Add FloatAddULP BUG: Decrement index in BSplineTransform by ULPs. BUG: Adjust index decrement in BSplineTransform BUG: Remove VNL README left over from subtree merge. Sumedha Singla (1): ENH: WhatModulesITK was not finding modules on Windows Changes from v4.10rc01..v4.10rc02 ------------------------------------------------ Davis Vigneault (1): BUG: Improve error checking and testing for ConnectedRegionsMesh Hyun Jae Kang (2): BUG: Address the issue of "Missing Delete" within SwapZeroCornerToIRP. COMP: Fixed Mac OSX wrapping configuration warning Matthew McCormick (6): BUG: The ImageFileReader internal pipeline methods should be protected. BUG: Use new VNL include directory variables. COMP: Add missing NeighborhoodAccessor methods to PhasedArray3D image. BUG: Adjust itk.org ExternalData URL. COMP: Do not use target_include_directories with CMake 2.8.11.2. BUG: Address missing shared_ptr for VS9 Changes from v4.9.0..v4.10rc01 ------------------------------------------------ Alvaro Sanchez (1): STYLE: moved itkKappaSigmaThresholdImageFilter/Calculator from Nonunit/Review Andrey Fedorov (2): BUG: Add missing itk_expat_mangle.h install target BUG: fix typo in file name Bill Hoffman (2): COMP: fix shared build on Windows when Review is on. COMP: work around for VS 2015 optimizer bug causing test failures. Bill Lorensen (6): ENH: Bump version for style fixups. ENH: Bump wiki examples version, new remote module process ENH: Bump wiki examples version, new remote module process STYLE: SuperClass should be Superclass COMP: Resolve clang linkage issue BUG: Valgrind detected an invalid read Bradley Lowekamp (21): BUG: Compilation problem with GCC 4.1 and explicit instantiation ENH: Update Insight Journal handle links to https ENH: Adding const qualifier to results BUG: Adding missing const qualifier for GetConfusionMatrix method BUG: Use Set/GetMacros, fix const correctness and PrintSelf. ENH: added inlined Zero and one values for integer NumericTraits ENH: Use constexpr for floating point NumericTraits ENH: Make NumericTraits functions constexpr for intrinsic BUG: Add definition of static constexpr NumericTrait members BUG: Declared static constexpr members need to be defined as constexpr ENH: ITK_CONSTEXPR_FUNC implies inline BUG: Addressing VS10 and VS11 NumericTraits linkage issue BUG: Use LargestPossible region for BSpline domain BUG: Remove errant file COMP: Address warning about this usage in initializer list ENH: Prefer ZeroValue function over variable STYLE: Use consistent path for try_compiles binary directory BUG: Don't use "=" in cmake variable name ENH: Test address of NumericTraits One and Zero constexpr ENH: Use ITK_USE_64BITS_IDS for windows 64 by default ENH: Enable run-time dependency on Python library Davis Vigneault (4): ENH: Update itkFileTools to allow std::string arguments. ENH: Add Floored and Truncated Modulus to VNL ENH: Add Ternary Operator Image Filter STYLE: Prefer static cast D?enan Zuki? (1): ENH: CovariantVector's Normalize returns the norm. Francois Budin (6): PERF: Simplify itkTemplate New() input type identification. ENH: Avoid template type specification for image reader in Python wrapping BUG: Missing IOPixelType strings in ImageIOBase BUG: Wrapping intermediate files were not automatically updated ENH: Reduce number of dependencies for XML files generated for wrapping BUG: GCC is limited when calling overloaded base class functions GCC-XML Upstream (1): ENH: pygccxml v1.7.3 (reduced) GDCM Upstream (1): GDCM 2015-09-02 (1efe9e28) Hans Johnson (27): COMP: Static analysis warning COMP: Incorrect delete found by static analysis PERF: Avoid temporary std:vector copying. COMP: Provide VXL backward compatible includes COMP: ITK requires legacy methods ENH: Need propagate ITK_LIBRARY_PROPERTIES ENH: Added UpdateFromUpstream.sh for VNL ENH: Manual copy from vxl/master STYLE: vnl_math_[min|max] -> std::[min|max] STYLE: Text files should end with a newline COMP: Prefer C++11 constexpr when possible COMP: Prefer C++11 constexpr when possible ENH: Simplify std:: math function definitions COMP: Error in constexpr usage COMP: Add const to previous const variables COMP: SizeValueType can has different definition for itkArray ENH: Added utility for modernizing vcl_ to std:: ENH: Reference vnl_math.h constants directly ENH: Avoid using vnl_math_ functions COMP: Missing symbol for itkStaticConstMacro COMP: Function override missing in BioCell ENH: Convert vcl_ to std:: BUG: Windows vcl_snprintf failures addressed COMP: Disabmiguate function calls to SetData ENH: Provided static code API for external applications COMP: Remove possible type conversion warnings ENH: Merge GDCM release branch Hyun Jae Kang (25): COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6 BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6 BUG: Fixed the runtime crash of itkTimeProbeTest2 BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's tests on OSX 10.6 BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6 COMP: Fixed the data conversion warning messages of itkResourceProbe BUG: Fixed the runtime crash of itkLabelOverlapMeasuresImageFilterTest BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6 BUG: Fixed the runtime crash of itkMRIBiasFieldCorrectionFilterTest BUG: Fixed the runtime crash of itkBinaryShapeOpeningImageFilterTest1 BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6 BUG: Fixed the runtime crash of vnl_test_numeric_traits BUG: Fixed the runtime crash of test_pow_log on OSX 10.6 BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6 BUG: Fixed the failed test case of itkSTLThreadTest on OS X 10.8 COMP: Update KWStyle to utilize the latest boost library COMP: Fixed the compiler error of ITK on Mingw-w64 COMP: Temporarily suppress the warning messages of data-conversion on VS14 COMP: Put back the disappeared option of "BUILD EXAMPLES". BUG: Fix segmentation faults on mingw-W64 x86_64. BUG: Fix the failed test of itkCastImageFilterTest on mingw-w64 compiler. COMP: Fixed the cmake configuration for ITK_WRAP_DOC COMP: Fixed the warning messages on VS14. COMP: Add a missing head file at itkNumericTraitsStdVector.h COMP: Fix the wraning message of data-conversion Jean-Christophe Fillion-Robin (4): COMP: ITKExternalModule: Support building module without test directory. STYLE: Facilitate maintenance of CastXML generator refactoring CMakeLists COMP: Allow use of multiple "ITK external modules" in the same project. STYLE: UseITK: Document static registration of ITK IO factories. See #3393 Jon Haitz Legarreta (7): COMP: Delete unused variable compiler warning. ENH: Refactored itkBioCellTest ENH: Exercise non-tested itk::Math methods. ENH: Improve MersenneTwister class and test. ENH: Improve itkFEMLoadPoint coverage. ENH: Improve itkVersion class code coverage. ENH: Perform class name checks in test macro KWSys Robot (1): KWSys 2016-03-09 (36d8666f) Lucas Gandel (9): ENH: Implement GetNumberOfParameter() in ImageToSpatialObjectMetric COMP: Enable wrapping of multiple "ITK external modules" in the same project COMP: Fix CASTXML_EXECUTABLE value for multiple external module COMP: Fix external module testing COMP: Fix git protocol setup ENH: Conditionally add testing for External Modules BUG: Fix call to std::max() with different variable types Manuel Grizonnet (1): COMP: add ITKCommon_EXPORT to fix link issues with external applications Matthew McCormick (73): ENH: Add TwoProjectionRegistration Remote Module. ENH: Allow ITKVideoBridgeOpenCV to be built externally. COMP: Add export specification for itk::ResourceProbe. ENH: Do not force shared libraries when wrapping. BUG: BUILD_TESTING should be not advanced. ENH: Bump ITK version to 4.10.0. DOC: Correct ITKImageNoise description spelling. ENH: Wrap FFTNormalizedCorrelationImageFilter. BUG: Remove Azure ExternalData resource. BUG: ExternalData downloads from midas3.kitware.com only supports https. BUG: Update ExternalData resource. BUG: slicer.kitware.com/midas3/ ExternalData will not support http. ENH: Add ITK_CUSTOM_LIBRARY_SUFFIX variable. ENH: Wrap PipelineMonitorImageFilter. BUG: Update MIDAS url for https in archive testing data script. ENH: Wrap std::vector< itk::ImageRegion >. BUG: Fix wrapping build with DEFAULT_MODULES OFF. ENH: Add RGB pixel support to ImageToVTKImageFilter. ENH: Add RGB and vector pixel type wrapping for ImageToVTKImageFilter. STYLE: Use PixelType and ImageType in Python tests. ENH: Avoid template type specification in Python wrapping. COMP: Do not use has_key in itkTemplate New. DOC: Emphasize that push access is not required to contribute patches. ENH: Download SWIG and PCRE from midas3.kitware.com. COMP: Ignore build warning from KWStyle's boost. BUG: Remove Azure ExternalData resource. BUG: ExternalData downloads from midas3.kitware.com only supports https. BUG: slicer.kitware.com/midas3/ ExternalData will not support http. ENH: Update the VNL README-ITK.txt subtree commit revision. BUG: Mark VXL internal CMake variables as advanced. BUG: Run itk_module_target on itknetlib. DOC: Direct patches for VXL upstream to the GitHub repository. BUG: Run itk_module_target on itknetlib. COMP: Account for removal of vcl_* from upstream VXL. COMP: Remove itkTypeMacro from BioCellHelper. COMP: Convert itkBioCellTest arguments from double to int. COMP: Turn off BUILD_DOCUMENTATION for VNL. BUG: Install VXL config files to backwards-compatible locations. ENH: Remove vcl_complex from the wrapping. BUG: Install vnl_export.h and vnl_algo_export.h to previous locations. BUG: midas3.kitware.com only supports the https protocol. BUG: ImageIOBase SetDimensions should take SizeValueType. ENH: Add wrapping for ImagePCAShapeModelEstimator. COMP: Do not specify COMPONENTS with find_package(VTK. DOC: Fix FFTW warning grammar. COMP: Build against system HDF5 1.8.16. ENH: Set a default CMAKE_BUILD_TYPE when building a module externally COMP: Make initial HDF5 discovery of 1.8.16 quiet. ENH: Use hidden symbol visibility for the CPython extension modules. ENH: Turn on CMAKE_POSITION_INDEPENDENT_CODE by default. BUG: FEMLoadPoint uninitialized value in the constructor. BUG: Fix wrapping of complex types in VNL. ENH: Bump CMakeLists.txt version 4.9.1. COMP: Address ITKCommon Python submodule order. BUG: Extend ExternalData_TIMEOUT_ABSOLUTE to 900 seconds. BUG: Do not run KWStyle Git config on a release tarball. COMP: Ambiguous RGBPixel access in CustomColormapFunction. BUG: Prevent division by zero in PhasedArray3DSpecialCoordinatesImage. BUG: Initialize azimuth and elevation to pi/2 in PhasedArray3D. BUG: Increase MaskLabel backwards compatibility in N4 bias correction. ENH: Deprecate MaskLabel in N4BiasFieldCorrectionImageFilter. COMP: Update CastXML to support Visual Studio 2015 Update 2. COMP: Do not set wrapping library visibility with static builds. COMP: Update CastXML to support Visual Studio 2015 Update 2. COMP: Broaden the KWStyle warning exception. COMP: Update KWStyle version. BUG: Do not use the same output file in N4BiasField Test 2,3. COMP: Expand EXERCISE_BASIC_OBJECT_METHODS for other GCC versions. ENH: Update Cuberille Remote to 2015-05-01. ENH: Enable registration of the IOOpenSlide module through CMake. ENH: Update itk.org URL's for HTTPS support. BUG: Use CastXML built against LLVM with LLVM_ENABLE_TERMINFO OFF. BUG: Fix Python wrapping on Windows when ITK_USE_64BIT_IDS is ON. Michka Popoff (12): ENH: Use importlib for python 3.4 instead of imp ENH: Update to Swig 3.0.8 ENH: Update PCRE to version 8.38 ENH: Wrap RayCastInterpolateImageFunction ENH: Wrap RayCastInterpolateImageFunction COMP: Remove debug output after vcl_complex removal from wrapping ENH: Consolidate .idx file generation with swig .i generation. ENH: Update UpdatepygccxmlFromUpstream.sh script COMP: Set CastXML path and name for pygccxml 1.7.3 COMP: Fix RayCastInterpolateImageFunction wrapping for image dim 2 ENH: Use argparse instead of optparse in igenerator.py ENH: Use https URL for OS X castxml binary (for consistency) Nick Tustison (2): ENH: Add fixed/moving masking in reg. methods. ENH: Making the mask usage consistent with ITK. Pablo Hernandez-Cerdan (1): COMP: Fix warn in FFTW about delete []. Sean McBride (18): COMP: Made script OS X compatible COMP: mark GDCM GetSeriesHelper() method as deprecated BUG: update script to fetch GDCM from its release-2-4 branch instead of master DOC: Updated comment to reflect new GDCM version COMP: Fixed recently introduced build error with deprecated GDCM method BUG: Fixed invalid memory access found by ASan COMP: Fixed clang warning about macro expansion giving defined COMP: Fixed minor dashboards warnings and typos. COMP: Fixed a bunch of clang -Wunreachable-code-break warnings COMP: fixed some dashboard warnings (dead code, false positive) BUG: Fixed off-by-1 error found by ASan COMP: Fixed clang -Wcomma warning COMP: Introduce ITK_FALLTHROUGH, to suppress switch fall through warnings COMP: Fixed -Wwritable-strings warnings COMP: Fixed remaining -Wcomma warnings ENH: switch gdcm to release branch, not release-2-4 COMP: Hack HDF5 to build under ASan & UBSan COMP: fixed clang -Wdeprecated-writable-strings warning Shawn Waldon (1): STYLE: move itkGaussianDerivativeOperator Sujin Philip (1): STYLE: Move itkBox* Filters Sumedha Singla (3): ENH: Issue: ITK#3363 Replaced assignment in SetParameters function. ENH: Remove unnecessary const_cast BUG: Fixed the test itkHDF5ImageIOTest VXL Maintainers (9): VNL 2015-11-22 (ea1d60fb) VNL 2016-03-02 (cb31149e) VNL 2016-03-13 (ae34f0fc) VNL 2016-03-15 (751698ab) VNL 2016-03-19 (df10fefa) VNL 2016-03-25 (f0040231) VNL 2016-03-30 (88f50849) VNL 2016-04-22 (0ed18124) VNL 2016-04-26 (6b168535) Vladimir S. FONOV (3): MINC 2015-12-17 (dcb93a5f) MINC 2016-01-30 (783bca38) MINC 2016-02-24 (8632513e) Ziv Yaniv (1): BUG: Interpretation of the Euler angles ZYX or ZXY was not exported. ITK Sphinx Examples Changelog --------------------------------------------- D?enan Zuki? (1): ENH: Default is current directory. Avoid usage of the class SeriesHelper. Matt McCormick (19): BUG: Do not depend on the VTK/OpenCV build when system provided. ENH: Add ConvertAnitkImageTovtkImageData example. ENH: Bump VTK's superbuild version to 7.0.0. STYLE: CMake style updates to AddOffsetToIndex/CMakeLists.txt ENH: Updates to CreateNewExample.py.in ENH: Add ConvertvtkImageDataToAnitkImage example. ENH: Update sphinx-bootstrap-theme to v0.4.8 ENH: Add Python version of StreamAPipeline. ENH: Add ConvertAnRGBitkImageTovtkImageData ENH: Add a PACE progress bar. ENH: Add more Python content to CreateNewExample.py. ENH: Add ConvertRGBvtkImageDataToAnitkImage BUG: Disable Create3DVolume Python baseline test. ENH: Add PerformRegistrationOnVectorImages. ENH: Update itk.org URL's for HTTPS support. COMP: Use itk::IndexValueType for subdomain index. COMP: Bump OpenCV to 3.1.0. BUG: Fix superbuild dependencies. ENH: Bump ITK to v4.10.0. ITK Software Guide Changelog --------------------------------------------- Matt McCormick (6): DOC: Correct spelling in the wrapping description. BUG: ExternalData servers now use https. ENH: Update itk.org URL's for HTTPS support. DOC: Adding wrapper .dll's to PATH on Windows is no longer necessary. DOC: Document how to add a third-party dependency to a module. ENH: Bump ITK ExternalProject to v4.10.0 -------------- 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 jchris.fillionr at kitware.com Fri Jun 3 09:52:10 2016 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Fri, 3 Jun 2016 09:52:10 -0400 Subject: [ITK] [ITK-users] [ANN] ITK 4.10.0 has been released! 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 4.10.0 has been released! Links to the Sourceforge.net tarballs can be found on the download page: http://www.itk.org/ITK/resources/software.html [image: TwoProjectionRegistrationDiagram.png] Insight Journal article included as a Remote Module: TwoProjectionRegistration . Digitally reconstructed radiographs (DRR) generated as part of the registration are shown above. 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 offersis a platform for commercial product development. A few selected highlights for the 4.10 release include the following: - New Remote module: TwoProjectionRegistration performs simultaneous registration of two projection images to a 3D image volume, which is useful for external beam radiotherapy and other applications. It uses Powell?s method for optimization and the Siddon-Jacobs fast ray-tracing algorithm. - First update to internal VNL in five years. Many improvements were made to upstream VNL. We now push patches upstream and stay in sync via a Git subtree workflow. - Windows builds now support processing 4GB+ images by default - GDCM updated for better DICOM support Congratulations to the 26 contributors to this release. We would especially like to recognize the new contributors: Andrey Fedorov, Sujin Philip, Francois Budin, and b'Alvaro Sanchez. Improved documentation in this release includes new examples on how to convert between ITK and VTK image data structures . Additionally, a new example demonstrates how to perform vector image registration with a mean-squares matching metric . The ITK Software Guide added documentation on how to add third party dependencies when creating an ITK module. This release also brings exciting rapid prototyping improvements to the ITK Python wrapping. Type specification is no longer necessary during the creation of most filters. The required type is inferred from a primary input passed on filter creation. For example, instead of the explicit type specification: median = itk.MedianImageFilter[ImageType, ImageType].New() median.SetInput(reader.GetOutput()) It is now possible to call: median = itk.MedianImageFilter.New(Input=reader.GetOutput()) Or, the shortened: median = itk.MedianImageFilter.New(reader.GetOutput()) Or: median = itk.MedianImageFliter.New(reader) An itk.ImageFileReader can be created by specifying the FileName during instantiation: reader = itk.ImageFileReader.New(FileName=?inputFile.mha?) Enjoy ITK! New Features --------------------- * Wrapping improvements - ITK_USE_64BITS_IDS supported on Windows - Faster builds (CastXML calls and build targets reduced by half) - Faster runtime loading and smaller binary size due to hidden symbol visibility - Wrapping with BUILD_SHARED_LIBS disabled is supported - Do not link to libpython when possible - Filter types do not need to be specified when ?Input=inputImage? is specified in the constructor - Improved wrapping class coverage - Visual Studio 2015 Update 2 Supported - GCC 6.1 supported * New Remote Module - TwoProjectionRegistration - 2D-3D registration designed for radiotherapy - http://hdl.handle.net/10380/3245 * Core Improvements - Data and build tool downloads now over HTTPS - Extended constexpr usage with ITK_CONSTEXPR and ITKCONSTEXPR_FUNC macros - ITK_USE_64BITS_IDS, required to process 4GB+ images on Windows, now enabled by default - VNL updated and modernized - CMake configuration major modernization - vcl has been removed in favor of the standard libraries - vnl_math_ function avoided in favor of std:: and itk::Math - VNL had suppressed integer data conversion warnings on Visual Studio (C4257); this suppression has been removed and all warnings addressed - Various improvements for building a module externally against an ITK build tree - CMAKE_POSITION_INDEPENDENT_CODE is enabled by default - Improved EXERCISE_BASIC_OBJECT_METHODS testing macro * Filtering Improvements - RGB pixel support added to itk::ImageToVTKImageFilter - itk::Box* filters moved out of the Review module - itk::GaussianDerivativeOperator moved out of the Review module - MaskLabel is deprecated in N4BiasFieldCorrectionFilter in favor any non-zero pixel * Registration Improvements - Fixed and moving masks added to the v4 registration methods * Documentation Improvements - Updates to the Software Guide, Doxygen, Wiki and Sphinx Examples - New examples on to convert between ITK and VTK - New example on how to perform vector image registration - The ITK Software Guide describes how to add a third-party dependency to a module * Third Party Library Updates - pygccxml updated to v1.7.3 - GDCM updated to the release branch latest - VNL updated to latest upstream - MINC updated to the latest upstream - SWIG updated to v3.0.8 - PCRE update to v8.38 * Improved code coverage -- we are at 85.0%! * *Lots* of important bug fixes * And much more! See details in the log below. Changes from v4.10rc02..v4.10.0 ------------------------------------------------ Bradley Lowekamp (3): COMP: Address uninitialized warning of size COMP: Devirtualize private methods to prevent instantiation COMP: Use well defined ZeroValue for unused initial value. Hans Johnson (1): BUG: try_compile needs to have CMAKE_CXX_STANDARD passed Hyun Jae Kang (1): COMP: Fix unexpected data-cast results of itkCastImageFilter Jon Haitz Legarreta (1): BUG: Fix OpenCV-2.4.9 camera empty image issue. Matthew McCormick (13): COMP: Bump CastXML for GCC 6.1 support. STYLE: Improvements to HardConnectedComponentsImageFilter. ENH: Add baseline for itkHardConnectedComponentImageFilterTest. STYLE: Improvements for itkHardConnectedComponentImageFilterTest COMP: HardConnectedComponentImageFilter autological constant out of range DOC: Sphinx examples update to 2016-05-22. DOC: Wiki examples update to 2016-05-22. COMP: MSVC result of 32-bit shift implicitly converted to 64 bits BUG: Disable building the netlib example. ENH: Add FloatAddULP BUG: Decrement index in BSplineTransform by ULPs. BUG: Adjust index decrement in BSplineTransform BUG: Remove VNL README left over from subtree merge. Sumedha Singla (1): ENH: WhatModulesITK was not finding modules on Windows Changes from v4.10rc01..v4.10rc02 ------------------------------------------------ Davis Vigneault (1): BUG: Improve error checking and testing for ConnectedRegionsMesh Hyun Jae Kang (2): BUG: Address the issue of "Missing Delete" within SwapZeroCornerToIRP. COMP: Fixed Mac OSX wrapping configuration warning Matthew McCormick (6): BUG: The ImageFileReader internal pipeline methods should be protected. BUG: Use new VNL include directory variables. COMP: Add missing NeighborhoodAccessor methods to PhasedArray3D image. BUG: Adjust itk.org ExternalData URL. COMP: Do not use target_include_directories with CMake 2.8.11.2. BUG: Address missing shared_ptr for VS9 Changes from v4.9.0..v4.10rc01 ------------------------------------------------ Alvaro Sanchez (1): STYLE: moved itkKappaSigmaThresholdImageFilter/Calculator from Nonunit/Review Andrey Fedorov (2): BUG: Add missing itk_expat_mangle.h install target BUG: fix typo in file name Bill Hoffman (2): COMP: fix shared build on Windows when Review is on. COMP: work around for VS 2015 optimizer bug causing test failures. Bill Lorensen (6): ENH: Bump version for style fixups. ENH: Bump wiki examples version, new remote module process ENH: Bump wiki examples version, new remote module process STYLE: SuperClass should be Superclass COMP: Resolve clang linkage issue BUG: Valgrind detected an invalid read Bradley Lowekamp (21): BUG: Compilation problem with GCC 4.1 and explicit instantiation ENH: Update Insight Journal handle links to https ENH: Adding const qualifier to results BUG: Adding missing const qualifier for GetConfusionMatrix method BUG: Use Set/GetMacros, fix const correctness and PrintSelf. ENH: added inlined Zero and one values for integer NumericTraits ENH: Use constexpr for floating point NumericTraits ENH: Make NumericTraits functions constexpr for intrinsic BUG: Add definition of static constexpr NumericTrait members BUG: Declared static constexpr members need to be defined as constexpr ENH: ITK_CONSTEXPR_FUNC implies inline BUG: Addressing VS10 and VS11 NumericTraits linkage issue BUG: Use LargestPossible region for BSpline domain BUG: Remove errant file COMP: Address warning about this usage in initializer list ENH: Prefer ZeroValue function over variable STYLE: Use consistent path for try_compiles binary directory BUG: Don't use "=" in cmake variable name ENH: Test address of NumericTraits One and Zero constexpr ENH: Use ITK_USE_64BITS_IDS for windows 64 by default ENH: Enable run-time dependency on Python library Davis Vigneault (4): ENH: Update itkFileTools to allow std::string arguments. ENH: Add Floored and Truncated Modulus to VNL ENH: Add Ternary Operator Image Filter STYLE: Prefer static cast D?enan Zuki? (1): ENH: CovariantVector's Normalize returns the norm. Francois Budin (6): PERF: Simplify itkTemplate New() input type identification. ENH: Avoid template type specification for image reader in Python wrapping BUG: Missing IOPixelType strings in ImageIOBase BUG: Wrapping intermediate files were not automatically updated ENH: Reduce number of dependencies for XML files generated for wrapping BUG: GCC is limited when calling overloaded base class functions GCC-XML Upstream (1): ENH: pygccxml v1.7.3 (reduced) GDCM Upstream (1): GDCM 2015-09-02 (1efe9e28) Hans Johnson (27): COMP: Static analysis warning COMP: Incorrect delete found by static analysis PERF: Avoid temporary std:vector copying. COMP: Provide VXL backward compatible includes COMP: ITK requires legacy methods ENH: Need propagate ITK_LIBRARY_PROPERTIES ENH: Added UpdateFromUpstream.sh for VNL ENH: Manual copy from vxl/master STYLE: vnl_math_[min|max] -> std::[min|max] STYLE: Text files should end with a newline COMP: Prefer C++11 constexpr when possible COMP: Prefer C++11 constexpr when possible ENH: Simplify std:: math function definitions COMP: Error in constexpr usage COMP: Add const to previous const variables COMP: SizeValueType can has different definition for itkArray ENH: Added utility for modernizing vcl_ to std:: ENH: Reference vnl_math.h constants directly ENH: Avoid using vnl_math_ functions COMP: Missing symbol for itkStaticConstMacro COMP: Function override missing in BioCell ENH: Convert vcl_ to std:: BUG: Windows vcl_snprintf failures addressed COMP: Disabmiguate function calls to SetData ENH: Provided static code API for external applications COMP: Remove possible type conversion warnings ENH: Merge GDCM release branch Hyun Jae Kang (25): COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6 BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6 BUG: Fixed the runtime crash of itkTimeProbeTest2 BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's tests on OSX 10.6 BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6 COMP: Fixed the data conversion warning messages of itkResourceProbe BUG: Fixed the runtime crash of itkLabelOverlapMeasuresImageFilterTest BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6 BUG: Fixed the runtime crash of itkMRIBiasFieldCorrectionFilterTest BUG: Fixed the runtime crash of itkBinaryShapeOpeningImageFilterTest1 BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6 BUG: Fixed the runtime crash of vnl_test_numeric_traits BUG: Fixed the runtime crash of test_pow_log on OSX 10.6 BUG: Exclude a test code of ITKLabelMapTestDriver on OSX 10.6 BUG: Fixed the failed test case of itkSTLThreadTest on OS X 10.8 COMP: Update KWStyle to utilize the latest boost library COMP: Fixed the compiler error of ITK on Mingw-w64 COMP: Temporarily suppress the warning messages of data-conversion on VS14 COMP: Put back the disappeared option of "BUILD EXAMPLES". BUG: Fix segmentation faults on mingw-W64 x86_64. BUG: Fix the failed test of itkCastImageFilterTest on mingw-w64 compiler. COMP: Fixed the cmake configuration for ITK_WRAP_DOC COMP: Fixed the warning messages on VS14. COMP: Add a missing head file at itkNumericTraitsStdVector.h COMP: Fix the wraning message of data-conversion Jean-Christophe Fillion-Robin (4): COMP: ITKExternalModule: Support building module without test directory. STYLE: Facilitate maintenance of CastXML generator refactoring CMakeLists COMP: Allow use of multiple "ITK external modules" in the same project. STYLE: UseITK: Document static registration of ITK IO factories. See #3393 Jon Haitz Legarreta (7): COMP: Delete unused variable compiler warning. ENH: Refactored itkBioCellTest ENH: Exercise non-tested itk::Math methods. ENH: Improve MersenneTwister class and test. ENH: Improve itkFEMLoadPoint coverage. ENH: Improve itkVersion class code coverage. ENH: Perform class name checks in test macro KWSys Robot (1): KWSys 2016-03-09 (36d8666f) Lucas Gandel (9): ENH: Implement GetNumberOfParameter() in ImageToSpatialObjectMetric COMP: Enable wrapping of multiple "ITK external modules" in the same project COMP: Fix CASTXML_EXECUTABLE value for multiple external module COMP: Fix external module testing COMP: Fix git protocol setup ENH: Conditionally add testing for External Modules BUG: Fix call to std::max() with different variable types Manuel Grizonnet (1): COMP: add ITKCommon_EXPORT to fix link issues with external applications Matthew McCormick (73): ENH: Add TwoProjectionRegistration Remote Module. ENH: Allow ITKVideoBridgeOpenCV to be built externally. COMP: Add export specification for itk::ResourceProbe. ENH: Do not force shared libraries when wrapping. BUG: BUILD_TESTING should be not advanced. ENH: Bump ITK version to 4.10.0. DOC: Correct ITKImageNoise description spelling. ENH: Wrap FFTNormalizedCorrelationImageFilter. BUG: Remove Azure ExternalData resource. BUG: ExternalData downloads from midas3.kitware.com only supports https. BUG: Update ExternalData resource. BUG: slicer.kitware.com/midas3/ ExternalData will not support http. ENH: Add ITK_CUSTOM_LIBRARY_SUFFIX variable. ENH: Wrap PipelineMonitorImageFilter. BUG: Update MIDAS url for https in archive testing data script. ENH: Wrap std::vector< itk::ImageRegion >. BUG: Fix wrapping build with DEFAULT_MODULES OFF. ENH: Add RGB pixel support to ImageToVTKImageFilter. ENH: Add RGB and vector pixel type wrapping for ImageToVTKImageFilter. STYLE: Use PixelType and ImageType in Python tests. ENH: Avoid template type specification in Python wrapping. COMP: Do not use has_key in itkTemplate New. DOC: Emphasize that push access is not required to contribute patches. ENH: Download SWIG and PCRE from midas3.kitware.com. COMP: Ignore build warning from KWStyle's boost. BUG: Remove Azure ExternalData resource. BUG: ExternalData downloads from midas3.kitware.com only supports https. BUG: slicer.kitware.com/midas3/ ExternalData will not support http. ENH: Update the VNL README-ITK.txt subtree commit revision. BUG: Mark VXL internal CMake variables as advanced. BUG: Run itk_module_target on itknetlib. DOC: Direct patches for VXL upstream to the GitHub repository. BUG: Run itk_module_target on itknetlib. COMP: Account for removal of vcl_* from upstream VXL. COMP: Remove itkTypeMacro from BioCellHelper. COMP: Convert itkBioCellTest arguments from double to int. COMP: Turn off BUILD_DOCUMENTATION for VNL. BUG: Install VXL config files to backwards-compatible locations. ENH: Remove vcl_complex from the wrapping. BUG: Install vnl_export.h and vnl_algo_export.h to previous locations. BUG: midas3.kitware.com only supports the https protocol. BUG: ImageIOBase SetDimensions should take SizeValueType. ENH: Add wrapping for ImagePCAShapeModelEstimator. COMP: Do not specify COMPONENTS with find_package(VTK. DOC: Fix FFTW warning grammar. COMP: Build against system HDF5 1.8.16. ENH: Set a default CMAKE_BUILD_TYPE when building a module externally COMP: Make initial HDF5 discovery of 1.8.16 quiet. ENH: Use hidden symbol visibility for the CPython extension modules. ENH: Turn on CMAKE_POSITION_INDEPENDENT_CODE by default. BUG: FEMLoadPoint uninitialized value in the constructor. BUG: Fix wrapping of complex types in VNL. ENH: Bump CMakeLists.txt version 4.9.1. COMP: Address ITKCommon Python submodule order. BUG: Extend ExternalData_TIMEOUT_ABSOLUTE to 900 seconds. BUG: Do not run KWStyle Git config on a release tarball. COMP: Ambiguous RGBPixel access in CustomColormapFunction. BUG: Prevent division by zero in PhasedArray3DSpecialCoordinatesImage. BUG: Initialize azimuth and elevation to pi/2 in PhasedArray3D. BUG: Increase MaskLabel backwards compatibility in N4 bias correction. ENH: Deprecate MaskLabel in N4BiasFieldCorrectionImageFilter. COMP: Update CastXML to support Visual Studio 2015 Update 2. COMP: Do not set wrapping library visibility with static builds. COMP: Update CastXML to support Visual Studio 2015 Update 2. COMP: Broaden the KWStyle warning exception. COMP: Update KWStyle version. BUG: Do not use the same output file in N4BiasField Test 2,3. COMP: Expand EXERCISE_BASIC_OBJECT_METHODS for other GCC versions. ENH: Update Cuberille Remote to 2015-05-01. ENH: Enable registration of the IOOpenSlide module through CMake. ENH: Update itk.org URL's for HTTPS support. BUG: Use CastXML built against LLVM with LLVM_ENABLE_TERMINFO OFF. BUG: Fix Python wrapping on Windows when ITK_USE_64BIT_IDS is ON. Michka Popoff (12): ENH: Use importlib for python 3.4 instead of imp ENH: Update to Swig 3.0.8 ENH: Update PCRE to version 8.38 ENH: Wrap RayCastInterpolateImageFunction ENH: Wrap RayCastInterpolateImageFunction COMP: Remove debug output after vcl_complex removal from wrapping ENH: Consolidate .idx file generation with swig .i generation. ENH: Update UpdatepygccxmlFromUpstream.sh script COMP: Set CastXML path and name for pygccxml 1.7.3 COMP: Fix RayCastInterpolateImageFunction wrapping for image dim 2 ENH: Use argparse instead of optparse in igenerator.py ENH: Use https URL for OS X castxml binary (for consistency) Nick Tustison (2): ENH: Add fixed/moving masking in reg. methods. ENH: Making the mask usage consistent with ITK. Pablo Hernandez-Cerdan (1): COMP: Fix warn in FFTW about delete []. Sean McBride (18): COMP: Made script OS X compatible COMP: mark GDCM GetSeriesHelper() method as deprecated BUG: update script to fetch GDCM from its release-2-4 branch instead of master DOC: Updated comment to reflect new GDCM version COMP: Fixed recently introduced build error with deprecated GDCM method BUG: Fixed invalid memory access found by ASan COMP: Fixed clang warning about macro expansion giving defined COMP: Fixed minor dashboards warnings and typos. COMP: Fixed a bunch of clang -Wunreachable-code-break warnings COMP: fixed some dashboard warnings (dead code, false positive) BUG: Fixed off-by-1 error found by ASan COMP: Fixed clang -Wcomma warning COMP: Introduce ITK_FALLTHROUGH, to suppress switch fall through warnings COMP: Fixed -Wwritable-strings warnings COMP: Fixed remaining -Wcomma warnings ENH: switch gdcm to release branch, not release-2-4 COMP: Hack HDF5 to build under ASan & UBSan COMP: fixed clang -Wdeprecated-writable-strings warning Shawn Waldon (1): STYLE: move itkGaussianDerivativeOperator Sujin Philip (1): STYLE: Move itkBox* Filters Sumedha Singla (3): ENH: Issue: ITK#3363 Replaced assignment in SetParameters function. ENH: Remove unnecessary const_cast BUG: Fixed the test itkHDF5ImageIOTest VXL Maintainers (9): VNL 2015-11-22 (ea1d60fb) VNL 2016-03-02 (cb31149e) VNL 2016-03-13 (ae34f0fc) VNL 2016-03-15 (751698ab) VNL 2016-03-19 (df10fefa) VNL 2016-03-25 (f0040231) VNL 2016-03-30 (88f50849) VNL 2016-04-22 (0ed18124) VNL 2016-04-26 (6b168535) Vladimir S. FONOV (3): MINC 2015-12-17 (dcb93a5f) MINC 2016-01-30 (783bca38) MINC 2016-02-24 (8632513e) Ziv Yaniv (1): BUG: Interpretation of the Euler angles ZYX or ZXY was not exported. ITK Sphinx Examples Changelog --------------------------------------------- D?enan Zuki? (1): ENH: Default is current directory. Avoid usage of the class SeriesHelper. Matt McCormick (19): BUG: Do not depend on the VTK/OpenCV build when system provided. ENH: Add ConvertAnitkImageTovtkImageData example. ENH: Bump VTK's superbuild version to 7.0.0. STYLE: CMake style updates to AddOffsetToIndex/CMakeLists.txt ENH: Updates to CreateNewExample.py.in ENH: Add ConvertvtkImageDataToAnitkImage example. ENH: Update sphinx-bootstrap-theme to v0.4.8 ENH: Add Python version of StreamAPipeline. ENH: Add ConvertAnRGBitkImageTovtkImageData ENH: Add a PACE progress bar. ENH: Add more Python content to CreateNewExample.py. ENH: Add ConvertRGBvtkImageDataToAnitkImage BUG: Disable Create3DVolume Python baseline test. ENH: Add PerformRegistrationOnVectorImages. ENH: Update itk.org URL's for HTTPS support. COMP: Use itk::IndexValueType for subdomain index. COMP: Bump OpenCV to 3.1.0. BUG: Fix superbuild dependencies. ENH: Bump ITK to v4.10.0. ITK Software Guide Changelog --------------------------------------------- Matt McCormick (6): DOC: Correct spelling in the wrapping description. BUG: ExternalData servers now use https. ENH: Update itk.org URL's for HTTPS support. DOC: Adding wrapper .dll's to PATH on Windows is no longer necessary. DOC: Document how to add a third-party dependency to a module. ENH: Bump ITK ExternalProject to v4.10.0 -------------- 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 ssult003 at odu.edu Fri Jun 3 18:01:31 2016 From: ssult003 at odu.edu (Sharmin Sultana) Date: Fri, 3 Jun 2016 18:01:31 -0400 Subject: [ITK] [ITK-users] Estimation of initial rotation for Euler3DTransform Message-ID: Dear all, I am trying to register two pointsets where each pointset represents a curve. I have tried using the IterativeClosestPointRegistration2.cxx example. But the problem with the results here is that while the translation seems to be OK, the rotation is not when I do not set an initial rotation. According to the user guide, the Euler3DTranform cannot handle for large rotations, and the user has to provide an initial rotation that is correct to within 10 or 20 degrees. When I have provided the initial rotations, and the resulting registered curve seems to be correct. I got the initial rotations by manually rotating and translating the moving pointset in Paraview against the fixed pointset using the Transform filter. Is there a way to automatically estimate the initial rotation required? Below are the pointsets that I was using. Fixed PointSet 70.3771 16.9556 -77.8874 69.2143 17.2079 -77.253 68.1514 17.8068 -76.7957 66.9762 18.1519 -76.4658 65.8135 18.6132 -76.2163 64.67 19.0656 -75.7242 63.5119 19.2921 -75.3272 62.3751 19.597 -75.0951 61.2921 19.8394 -74.793 60.2845 20.1405 -74.4514 59.3191 20.3305 -74.1283 58.408 20.3767 -73.9007 57.5404 20.4277 -73.9293 56.8618 20.7408 -73.5224 55.4173 20.853 -72.9256 54.7285 20.8667 -72.693 53.6634 20.0938 -72.5906 Moving PointSet: -1.158 -9.962 -7.944 -1.026 -9.224 -7.430 -0.883 -8.423 -6.872 -0.757 -7.646 -6.300 -0.640 -6.883 -5.727 -0.518 -6.120 -5.179 -0.406 -5.366 -4.622 -0.352 -4.661 -4.000 -0.291 -3.939 -3.394 -0.185 -3.181 -2.817 -0.042 -2.460 -2.183 0.074 -1.710 -1.531 0.174 -0.927 -0.853 0.296 -0.109 -0.120 0.459 0.737 0.693 0.640 1.647 1.657 0.861 2.763 2.808 Thanks and regards, -- Sharmin Sultana Old Dominion University -------------- 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 egolkar at siswa.ukm.edu.my Fri Jun 3 22:20:49 2016 From: egolkar at siswa.ukm.edu.my (Favour) Date: Fri, 3 Jun 2016 19:20:49 -0700 (MST) Subject: [ITK] [ITK-users] fatal error: 'itkScalarChanAndVeseDenseLevelSetImageFilter.h' file not found In-Reply-To: <1464707791419-37233.post@n7.nabble.com> References: <1464707791419-37233.post@n7.nabble.com> Message-ID: <1465006849394-37245.post@n7.nabble.com> I found the mistake During compiling ITK, the module_itkReview = ON should be done, in the help it is just mentioned about vtkGlu module -- View this message in context: http://itk-users.7.n7.nabble.com/fatal-error-itkScalarChanAndVeseDenseLevelSetImageFilter-h-file-not-found-tp37233p37245.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 tevain at telecom-paristech.fr Mon Jun 6 05:23:07 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Mon, 6 Jun 2016 11:23:07 +0200 (CEST) Subject: [ITK] [ITK-users] Estimation of initial rotation for Euler3DTransform In-Reply-To: References: Message-ID: <2117231066.78015108.1465204987982.JavaMail.zimbra@enst.fr> Hi Sharmin, If your are able to know which point of dataset 1 correspond to each point of dataset 2 (e.g. the point [-1.158 -9.962 -7.944] should match the point [70.3771 16.9556 -77.8874] after registration), then your problem is the one of Absolute Orientation. You could find the exact rotation solving this problem. You could refer to the Horn method (http://people.csail.mit.edu/bkph/papers/Absolute_Orientation.pdf) or the paper of Besl and McKay which introduce the ICP (http://graphics.stanford.edu/courses/cs164-09-spring/Handouts/paper_icp.pdf) to know how to do it. They are using quaternion for the rotation, but you could retrieve the rotation matrix from it, hence the euler angles (if you know the sequence of rotation, ITK's one is Z->Y->X if I remember correctly). Or you could go with the itkVersorRigid3DTransform. If you're unable to know the correspondence, you could maybe do a PCA to find principal directions (at least 2) of each curve, take a point in each direction plus the centroid, and resolve the Absolute Orientation with them (you need at least 3 points). But I've never tried it. HTH, Tim ----- Mail original ----- De: "Sharmin Sultana" ?: insight-users at itk.org Envoy?: Samedi 4 Juin 2016 00:01:31 Objet: [ITK] [ITK-users] Estimation of initial rotation for Euler3DTransform Dear all, I am trying to register two pointsets where each pointset represents a curve. I have tried using the IterativeClosestPointRegistration2.cxx example. But the problem with the results here is that while the translation seems to be OK, the rotation is not when I do not set an initial rotation. According to the user guide, the Euler3DTranform cannot handle for large rotations, and the user has to provide an initial rotation that is correct to within 10 or 20 degrees. When I have provided the initial rotations, and the resulting registered curve seems to be correct. I got the initial rotations by manually rotating and translating the moving pointset in Paraview against the fixed pointset using the Transform filter. Is there a way to automatically estimate the initial rotation required? Below are the pointsets that I was using. Fixed PointSet 70.3771 16.9556 -77.8874 69.2143 17.2079 -77.253 68.1514 17.8068 -76.7957 66.9762 18.1519 -76.4658 65.8135 18.6132 -76.2163 64.67 19.0656 -75.7242 63.5119 19.2921 -75.3272 62.3751 19.597 -75.0951 61.2921 19.8394 -74.793 60.2845 20.1405 -74.4514 59.3191 20.3305 -74.1283 58.408 20.3767 -73.9007 57.5404 20.4277 -73.9293 56.8618 20.7408 -73.5224 55.4173 20.853 -72.9256 54.7285 20.8667 -72.693 53.6634 20.0938 -72.5906 Moving PointSet: -1.158 -9.962 -7.944 -1.026 -9.224 -7.430 -0.883 -8.423 -6.872 -0.757 -7.646 -6.300 -0.640 -6.883 -5.727 -0.518 -6.120 -5.179 -0.406 -5.366 -4.622 -0.352 -4.661 -4.000 -0.291 -3.939 -3.394 -0.185 -3.181 -2.817 -0.042 -2.460 -2.183 0.074 -1.710 -1.531 0.174 -0.927 -0.853 0.296 -0.109 -0.120 0.459 0.737 0.693 0.640 1.647 1.657 0.861 2.763 2.808 Thanks and regards, -- Sharmin Sultana Old Dominion University _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 brad at lowekamp.net Mon Jun 6 11:10:27 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Mon, 6 Jun 2016 11:10:27 -0400 Subject: [ITK] [ITK-dev] Gerrit robots down? Message-ID: <9344A230-B8A3-4464-8960-37E87D6C2185@mail.nih.gov> I am not seeing any of robots working on gerrit. Can we get these working again? Thanks Brad _______________________________________________ Powered by www.kitware.com 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 scorpiuni at gmail.com Mon Jun 6 11:34:51 2016 From: scorpiuni at gmail.com (Robert) Date: Mon, 6 Jun 2016 08:34:51 -0700 (MST) Subject: [ITK] [ITK-users] Levelset not segmenting the shape Message-ID: <1465227291962-7588954.post@n2.nabble.com> Hello, I am working on a semi automatic 3D segmentation using the Geodesic active contour with shape guidance. No crashes occur anymore, but something is not right yet, and I can't get behind the error. Help would be much appreciated. The following is my code: https://www.dropbox.com/s/ot8gn0i38mh83ql/GeodesicActiveContourShapePriorLevelSetImageFilter.cxx?dl=0 I preprocess the input image etc, this all seems to work fine judging from the output images from those filters. (line 194 - 201) In line 203, I take the output from the underlying levelset (here, fastmarching), and change the metadata (direction, origin, spacing) to the one I get from my input image (line 206-209) in order to be even able to set my levelset as input to the geodesic filter, and I set my feature image as feature parameter(l 265&266). I now set some smoothing and geodesic-filter parameters, those are mostly taken from the example in 2D. The user gives 3 seedpoints, which should be located inside the shape. Line 465 is the beginning of the "shape guidance" part. Here I set my number of PCA images, my mean image, read them, change their metadata as well, so that in the end, all involved images have the same origin etc. (l 468 - 543). I now set those images as parameters to my PCAShapeSignedDistanceFunction. I now initialize a 3D Euler transform (l 554), a cost function (l 565) and an optimizer (l.610). Finally, I give my shape as parameter to the geodesic filter ( l.669). This should all be correct, right? all the changes in the metadata make sense as soon as you see the datasets in 3D, they now all occupy exactely the same space(see imgur pictures). However, the result I get is the following: http://imgur.com/a/aKRuV Middle picture is the "out" file alone, first and last pic is a 3d render from the output, and showing the mean image of the structure I want to find as well as the preprocessed, actual input image. It seems like my program does not take into account any shape guidance at all, and it just creates 3 "blobs" originating from my seeds... Please take the time to have a look at my stuff, I really can't get behind the mistake I made.... If you'd like to test it for your own, here are some sample pictures (the ones I used) as well as the command I used to execute the program: https://www.dropbox.com/sh/j2ognv5y5zv61wu/AABOAn-w4PIlYAq-WSW_lPOMa?dl=0 with ./GeodesicActiveContourShapePriorLevelSetImageFilter CochleaCropped.nrrd out.nrrd 33 26 14 32 29 13 25 32 12 3 0.6 0.5 0.02 meanImage.nrrd 3 pcImage*.nrrd 10 10 10 Thanks, Robert -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Levelset-not-segmenting-the-shape-tp7588954.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 scorpiuni at gmail.com Mon Jun 6 12:30:41 2016 From: scorpiuni at gmail.com (Robert) Date: Mon, 6 Jun 2016 09:30:41 -0700 (MST) Subject: [ITK] [ITK-users] Levelset not segmenting the shape In-Reply-To: <1465227291962-7588954.post@n2.nabble.com> References: <1465227291962-7588954.post@n2.nabble.com> Message-ID: <1465230641527-7588955.post@n2.nabble.com> What I forgot to mention is: I played around a while with different sigma values, as well as setting both propagationScaling and shapePriorScaling terms to 1.0, as well as adjusting the RMS. You now can kind of see that the result looks shaped like the cochlea (the object I want to find), but it is rotated in a weird way, if I use the actual CT data as backdrop, it does not match. (Rotation-wise). Also, it still looks kind of "clumpy", I know that the preprocessed images are low quality, but that's a constraint to deal with, as there is no micro-CT available. Any tips to enhance this code errors I can remove/change? -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Levelset-not-segmenting-the-shape-tp7588954p7588955.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 jchris.fillionr at kitware.com Mon Jun 6 15:17:06 2016 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Mon, 6 Jun 2016 15:17:06 -0400 Subject: [ITK] [ITK-dev] Gerrit robots down? In-Reply-To: <9344A230-B8A3-4464-8960-37E87D6C2185@mail.nih.gov> References: <9344A230-B8A3-4464-8960-37E87D6C2185@mail.nih.gov> Message-ID: Hi Brad, The missing robots are most likely due to the power failure caused by the remodeling/construction in our North Carolina office. I anticipate they will be back online tomorrow or the day after. Thanks for your patience, Jc On Mon, Jun 6, 2016 at 11:10 AM, Bradley Lowekamp wrote: > I am not seeing any of robots working on gerrit. Can we get these working > again? > > Thanks > Brad > _______________________________________________ > Powered by www.kitware.com > > 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 > -- +1 919 869 8849 -------------- 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 Wed Jun 8 02:50:08 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 8 Jun 2016 08:50:08 +0200 Subject: [ITK] [ITK-users] MutualInformationAffine example broken In-Reply-To: References: Message-ID: Hi Yanling, The usual reason for this is that the images do not overlap in image space, either with the initial transformation or due to divergence of the registration. If you run it in debug mode, you will have more information. Regards, D?enan On Jun 1, 2016 14:27, "Yanling Liu" wrote: > Hello, > > I downloaded the MutualInformationAffine example from > https://itk.org/Wiki/ITK/Examples/Registration/MutualInformationAffine, > compiled it using ITK 4.9.1 and it reported follow error message: > > ExceptionObject caught ! > > itk::ExceptionObject (0x2030010) > Location: "void itk::MutualInformationImageToImageMetric TMovingImage>::SampleFixedImageDomain(itk::MutualInformationImageToImageMetric TMovingImage>::SpatialSampleContainer&) const [with TFixedImage = > itk::Image; TMovingImage = itk::Image; > itk::MutualInformationImageToImageMetric TMovingImage>::SpatialSampleContainer = > std::vector, > itk::Image >::SpatialSample, > std::allocator 2u>, itk::Image >::SpatialSample> >]" > File: > /home/yliu/Imaging/Libraries/ITK/InsightToolkit-4.9.1/install/include/ITK-4.9/itkMutualInformationImageToImageMetric.hxx > Line: 196 > Description: itk::ERROR: MutualInformationImageToImageMetric(0x202fd10): > All the sampled point mapped to outside of the moving image > > Anyone may help to fix this example? I did not change the source code of > the example at all. > > Thanks, > > Yanling > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 panovr at gmail.com Wed Jun 8 03:36:36 2016 From: panovr at gmail.com (Yili Zhao) Date: Wed, 8 Jun 2016 15:36:36 +0800 Subject: [ITK] How to upgrade ITK from 4.09 to 4.10? Message-ID: Hi, I installed ITK 4.09 on Ubuntu 14.04 from source code built with CMake. It seems that there is no command "make uninstall" generated, so I want to ask that how to upgrade ITK from 4.09 to 4.10? Thanks! -- Yili Zhao -------------- next part -------------- An HTML attachment was scrubbed... URL: From jhlegarreta at vicomtech.org Wed Jun 8 07:17:57 2016 From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta) Date: Wed, 8 Jun 2016 13:17:57 +0200 Subject: [ITK] How to upgrade ITK from 4.09 to 4.10? In-Reply-To: References: Message-ID: Dear Yili, if you just built from source, you can safely delete both your sources and your binaries, then download ITK 4.10.0, and repeat the process for configuration/generation through CMake and compilation. Then you can link your own code against the libraries built. HTH, JON HAITZ On 8 June 2016 at 09:36, Yili Zhao wrote: > Hi, > I installed ITK 4.09 on Ubuntu 14.04 from source code built with CMake. > It seems that there is no command "make uninstall" generated, so I want > to ask that how to upgrade ITK from 4.09 to 4.10? > Thanks! > > -- > Yili Zhao > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ssult003 at odu.edu Wed Jun 8 13:57:51 2016 From: ssult003 at odu.edu (Sharmin Sultana) Date: Wed, 8 Jun 2016 13:57:51 -0400 Subject: [ITK] [ITK-users] Estimation of initial rotation for Euler3DTransform In-Reply-To: <2117231066.78015108.1465204987982.JavaMail.zimbra@enst.fr> References: <2117231066.78015108.1465204987982.JavaMail.zimbra@enst.fr> Message-ID: Hi Tim Thanks for your reply. I have somewhat solve the pointset registration problem using itkVersorRigid3DTransform. Now the rotation is working fine after applying itk::TransformMeshFilter to the initial mesh. But I'm still unable to register those pointset using itk::AffineTransform. I need to scale the initial mesh. Isn't it possible to apply affine transform to a pointset or mesh ? Thanks and Regards. Sharmin On Mon, Jun 6, 2016 at 5:23 AM, Timothee Evain wrote: > Hi Sharmin, > > If your are able to know which point of dataset 1 correspond to each point > of dataset 2 (e.g. the point [-1.158 -9.962 -7.944] should match the point > [70.3771 16.9556 -77.8874] after registration), then your problem is the > one of Absolute Orientation. You could find the exact rotation solving this > problem. > You could refer to the Horn method ( > http://people.csail.mit.edu/bkph/papers/Absolute_Orientation.pdf) or the > paper of Besl and McKay which introduce the ICP ( > http://graphics.stanford.edu/courses/cs164-09-spring/Handouts/paper_icp.pdf) > to know how to do it. They are using quaternion for the rotation, but you > could retrieve the rotation matrix from it, hence the euler angles (if you > know the sequence of rotation, ITK's one is Z->Y->X if I remember > correctly). Or you could go with the itkVersorRigid3DTransform. > > If you're unable to know the correspondence, you could maybe do a PCA to > find principal directions (at least 2) of each curve, take a point in each > direction plus the centroid, and resolve the Absolute Orientation with them > (you need at least 3 points). But I've never tried it. > > HTH, > > Tim > > > > ----- Mail original ----- > De: "Sharmin Sultana" > ?: insight-users at itk.org > Envoy?: Samedi 4 Juin 2016 00:01:31 > Objet: [ITK] [ITK-users] Estimation of initial rotation for > Euler3DTransform > > Dear all, > > I am trying to register two pointsets where each pointset represents a > curve. I have tried using the IterativeClosestPointRegistration2.cxx > example. But the problem with the results here is that while the > translation seems to be OK, the rotation is not when I do not set an > initial rotation. > > According to the user guide, the Euler3DTranform cannot handle for large > rotations, and the user has to provide an initial rotation that is correct > to within 10 or 20 degrees. When I have provided the initial rotations, and > the resulting registered curve seems to be correct. I got the initial > rotations by manually rotating and translating the moving pointset in > Paraview against the fixed pointset using the Transform filter. > > Is there a way to automatically estimate the initial rotation required? > Below are the pointsets that I was using. > > Fixed PointSet > 70.3771 16.9556 -77.8874 > 69.2143 17.2079 -77.253 > 68.1514 17.8068 -76.7957 > 66.9762 18.1519 -76.4658 > 65.8135 18.6132 -76.2163 > 64.67 19.0656 -75.7242 > 63.5119 19.2921 -75.3272 > 62.3751 19.597 -75.0951 > 61.2921 19.8394 -74.793 > 60.2845 20.1405 -74.4514 > 59.3191 20.3305 -74.1283 > 58.408 20.3767 -73.9007 > 57.5404 20.4277 -73.9293 > 56.8618 20.7408 -73.5224 > 55.4173 20.853 -72.9256 > 54.7285 20.8667 -72.693 > 53.6634 20.0938 -72.5906 > > Moving PointSet: > -1.158 -9.962 -7.944 > -1.026 -9.224 -7.430 > -0.883 -8.423 -6.872 > -0.757 -7.646 -6.300 > -0.640 -6.883 -5.727 > -0.518 -6.120 -5.179 > -0.406 -5.366 -4.622 > -0.352 -4.661 -4.000 > -0.291 -3.939 -3.394 > -0.185 -3.181 -2.817 > -0.042 -2.460 -2.183 > 0.074 -1.710 -1.531 > 0.174 -0.927 -0.853 > 0.296 -0.109 -0.120 > 0.459 0.737 0.693 > 0.640 1.647 1.657 > 0.861 2.763 2.808 > > Thanks and regards, > > > -- > Sharmin Sultana > Old Dominion University > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 dzenanz at gmail.com Thu Jun 9 03:29:55 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Thu, 9 Jun 2016 09:29:55 +0200 Subject: [ITK] [ITK-users] fatal error: 'itkScalarChanAndVeseDenseLevelSetImageFilter.h' file not found In-Reply-To: <1465006849394-37245.post@n7.nabble.com> References: <1464707791419-37233.post@n7.nabble.com> <1465006849394-37245.post@n7.nabble.com> Message-ID: Hi Favour, looking at the up-to-date documentation , it is clearly visible that this class belongs to Review module, and there is no mention of VTKGlue. Which documentation were you looking at? Regards, D?enan On Sat, Jun 4, 2016 at 4:20 AM, Favour wrote: > I found the mistake > > During compiling ITK, the module_itkReview = ON should be done, in the help > it is just mentioned about vtkGlu module > > > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/fatal-error-itkScalarChanAndVeseDenseLevelSetImageFilter-h-file-not-found-tp37233p37245.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 tevain at telecom-paristech.fr Thu Jun 9 03:36:48 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Thu, 9 Jun 2016 09:36:48 +0200 (CEST) Subject: [ITK] [ITK-users] Estimation of initial rotation for Euler3DTransform In-Reply-To: References: <2117231066.78015108.1465204987982.JavaMail.zimbra@enst.fr> Message-ID: <30125847.81064973.1465457808716.JavaMail.zimbra@enst.fr> If you're able to register with the itkVersorRigid3DTransform and you need scale, just use the itkSimilarity3DTransform, which is an isotropic scaling followed by the VersorRigid3Transform. HTH, Tim ----- Mail original ----- De: "Sharmin Sultana" ?: "Timothee Evain" Cc: insight-users at itk.org Envoy?: Mercredi 8 Juin 2016 19:57:51 Objet: Re: [ITK] [ITK-users] Estimation of initial rotation for Euler3DTransform Hi Tim Thanks for your reply. I have somewhat solve the pointset registration problem using itkVersorRigid3DTransform. Now the rotation is working fine after applying itk::TransformMeshFilter to the initial mesh. But I'm still unable to register those pointset using itk::AffineTransform. I need to scale the initial mesh. Isn't it possible to apply affine transform to a pointset or mesh ? Thanks and Regards. Sharmin On Mon, Jun 6, 2016 at 5:23 AM, Timothee Evain wrote: > Hi Sharmin, > > If your are able to know which point of dataset 1 correspond to each point > of dataset 2 (e.g. the point [-1.158 -9.962 -7.944] should match the point > [70.3771 16.9556 -77.8874] after registration), then your problem is the > one of Absolute Orientation. You could find the exact rotation solving this > problem. > You could refer to the Horn method ( > http://people.csail.mit.edu/bkph/papers/Absolute_Orientation.pdf) or the > paper of Besl and McKay which introduce the ICP ( > http://graphics.stanford.edu/courses/cs164-09-spring/Handouts/paper_icp.pdf) > to know how to do it. They are using quaternion for the rotation, but you > could retrieve the rotation matrix from it, hence the euler angles (if you > know the sequence of rotation, ITK's one is Z->Y->X if I remember > correctly). Or you could go with the itkVersorRigid3DTransform. > > If you're unable to know the correspondence, you could maybe do a PCA to > find principal directions (at least 2) of each curve, take a point in each > direction plus the centroid, and resolve the Absolute Orientation with them > (you need at least 3 points). But I've never tried it. > > HTH, > > Tim > > > > ----- Mail original ----- > De: "Sharmin Sultana" > ?: insight-users at itk.org > Envoy?: Samedi 4 Juin 2016 00:01:31 > Objet: [ITK] [ITK-users] Estimation of initial rotation for > Euler3DTransform > > Dear all, > > I am trying to register two pointsets where each pointset represents a > curve. I have tried using the IterativeClosestPointRegistration2.cxx > example. But the problem with the results here is that while the > translation seems to be OK, the rotation is not when I do not set an > initial rotation. > > According to the user guide, the Euler3DTranform cannot handle for large > rotations, and the user has to provide an initial rotation that is correct > to within 10 or 20 degrees. When I have provided the initial rotations, and > the resulting registered curve seems to be correct. I got the initial > rotations by manually rotating and translating the moving pointset in > Paraview against the fixed pointset using the Transform filter. > > Is there a way to automatically estimate the initial rotation required? > Below are the pointsets that I was using. > > Fixed PointSet > 70.3771 16.9556 -77.8874 > 69.2143 17.2079 -77.253 > 68.1514 17.8068 -76.7957 > 66.9762 18.1519 -76.4658 > 65.8135 18.6132 -76.2163 > 64.67 19.0656 -75.7242 > 63.5119 19.2921 -75.3272 > 62.3751 19.597 -75.0951 > 61.2921 19.8394 -74.793 > 60.2845 20.1405 -74.4514 > 59.3191 20.3305 -74.1283 > 58.408 20.3767 -73.9007 > 57.5404 20.4277 -73.9293 > 56.8618 20.7408 -73.5224 > 55.4173 20.853 -72.9256 > 54.7285 20.8667 -72.693 > 53.6634 20.0938 -72.5906 > > Moving PointSet: > -1.158 -9.962 -7.944 > -1.026 -9.224 -7.430 > -0.883 -8.423 -6.872 > -0.757 -7.646 -6.300 > -0.640 -6.883 -5.727 > -0.518 -6.120 -5.179 > -0.406 -5.366 -4.622 > -0.352 -4.661 -4.000 > -0.291 -3.939 -3.394 > -0.185 -3.181 -2.817 > -0.042 -2.460 -2.183 > 0.074 -1.710 -1.531 > 0.174 -0.927 -0.853 > 0.296 -0.109 -0.120 > 0.459 0.737 0.693 > 0.640 1.647 1.657 > 0.861 2.763 2.808 > > Thanks and regards, > > > -- > Sharmin Sultana > Old Dominion University > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 tevain at telecom-paristech.fr Thu Jun 9 03:44:48 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Thu, 9 Jun 2016 09:44:48 +0200 (CEST) Subject: [ITK] [ITK-users] Estimation of initial rotation for Euler3DTransform In-Reply-To: References: <2117231066.78015108.1465204987982.JavaMail.zimbra@enst.fr> Message-ID: <1772589326.81073485.1465458288560.JavaMail.zimbra@enst.fr> By the way, I don't know how you're doing your registration, but rather than using meshes, you could go with the itkPointSetToPointSetRegistrationMethod, which seems to be the best fit for your data. Tim ----- Mail original ----- De: "Sharmin Sultana" ?: "Timothee Evain" Cc: insight-users at itk.org Envoy?: Mercredi 8 Juin 2016 19:57:51 Objet: Re: [ITK] [ITK-users] Estimation of initial rotation for Euler3DTransform Hi Tim Thanks for your reply. I have somewhat solve the pointset registration problem using itkVersorRigid3DTransform. Now the rotation is working fine after applying itk::TransformMeshFilter to the initial mesh. But I'm still unable to register those pointset using itk::AffineTransform. I need to scale the initial mesh. Isn't it possible to apply affine transform to a pointset or mesh ? Thanks and Regards. Sharmin On Mon, Jun 6, 2016 at 5:23 AM, Timothee Evain wrote: > Hi Sharmin, > > If your are able to know which point of dataset 1 correspond to each point > of dataset 2 (e.g. the point [-1.158 -9.962 -7.944] should match the point > [70.3771 16.9556 -77.8874] after registration), then your problem is the > one of Absolute Orientation. You could find the exact rotation solving this > problem. > You could refer to the Horn method ( > http://people.csail.mit.edu/bkph/papers/Absolute_Orientation.pdf) or the > paper of Besl and McKay which introduce the ICP ( > http://graphics.stanford.edu/courses/cs164-09-spring/Handouts/paper_icp.pdf) > to know how to do it. They are using quaternion for the rotation, but you > could retrieve the rotation matrix from it, hence the euler angles (if you > know the sequence of rotation, ITK's one is Z->Y->X if I remember > correctly). Or you could go with the itkVersorRigid3DTransform. > > If you're unable to know the correspondence, you could maybe do a PCA to > find principal directions (at least 2) of each curve, take a point in each > direction plus the centroid, and resolve the Absolute Orientation with them > (you need at least 3 points). But I've never tried it. > > HTH, > > Tim > > > > ----- Mail original ----- > De: "Sharmin Sultana" > ?: insight-users at itk.org > Envoy?: Samedi 4 Juin 2016 00:01:31 > Objet: [ITK] [ITK-users] Estimation of initial rotation for > Euler3DTransform > > Dear all, > > I am trying to register two pointsets where each pointset represents a > curve. I have tried using the IterativeClosestPointRegistration2.cxx > example. But the problem with the results here is that while the > translation seems to be OK, the rotation is not when I do not set an > initial rotation. > > According to the user guide, the Euler3DTranform cannot handle for large > rotations, and the user has to provide an initial rotation that is correct > to within 10 or 20 degrees. When I have provided the initial rotations, and > the resulting registered curve seems to be correct. I got the initial > rotations by manually rotating and translating the moving pointset in > Paraview against the fixed pointset using the Transform filter. > > Is there a way to automatically estimate the initial rotation required? > Below are the pointsets that I was using. > > Fixed PointSet > 70.3771 16.9556 -77.8874 > 69.2143 17.2079 -77.253 > 68.1514 17.8068 -76.7957 > 66.9762 18.1519 -76.4658 > 65.8135 18.6132 -76.2163 > 64.67 19.0656 -75.7242 > 63.5119 19.2921 -75.3272 > 62.3751 19.597 -75.0951 > 61.2921 19.8394 -74.793 > 60.2845 20.1405 -74.4514 > 59.3191 20.3305 -74.1283 > 58.408 20.3767 -73.9007 > 57.5404 20.4277 -73.9293 > 56.8618 20.7408 -73.5224 > 55.4173 20.853 -72.9256 > 54.7285 20.8667 -72.693 > 53.6634 20.0938 -72.5906 > > Moving PointSet: > -1.158 -9.962 -7.944 > -1.026 -9.224 -7.430 > -0.883 -8.423 -6.872 > -0.757 -7.646 -6.300 > -0.640 -6.883 -5.727 > -0.518 -6.120 -5.179 > -0.406 -5.366 -4.622 > -0.352 -4.661 -4.000 > -0.291 -3.939 -3.394 > -0.185 -3.181 -2.817 > -0.042 -2.460 -2.183 > 0.074 -1.710 -1.531 > 0.174 -0.927 -0.853 > 0.296 -0.109 -0.120 > 0.459 0.737 0.693 > 0.640 1.647 1.657 > 0.861 2.763 2.808 > > Thanks and regards, > > > -- > Sharmin Sultana > Old Dominion University > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 christopherrmullins at gmail.com Thu Jun 9 10:14:42 2016 From: christopherrmullins at gmail.com (Christopher Mullins) Date: Thu, 9 Jun 2016 10:14:42 -0400 Subject: [ITK] [ITK-users] Build errors in python wrapping of 4.10.0 Message-ID: Hi all, Apparently my subscription to this list has lapsed and my first email was rejected (despite receiving the list in my inbox every day). Sorry if there's a double post. I'm getting the following build errors when building ITK 4.10.0 with the WRAP_PYTHON option ON[1], [3]. Is this a known issue, or is there a configuration setting I've set improperly? Platform is Arch linux, GCC v6.1.1, Python v3.5.1, CMake v3.5.2. There are no warnings. See all output details for this machine here [2], and please let me know if I can provide any others. The faster I fix this the faster I'll feel comfortable updating the Arch linux AUR PKGBUILD for ITK, so I appreciate any help you can offer. Thanks, Chris [1] https://open.cdash.org/viewBuildError.php?buildid=4403379 [2] https://open.cdash.org/buildSummary.php?buildid=4403379 [3] To save you a click, and for the sake of archiving, the error is: /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp: In function 'PyObject* _wrap_new_itkTriangleHelperPD2(PyObject*, PyObject*)': /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5854:65: error: no matching function for call to 'itk::TriangleHelper >::TriangleHelper()' result = (itkTriangleHelperPD2 *)new itkTriangleHelperPD2(); -------------- 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 marco.giord at gmail.com Thu Jun 9 10:45:30 2016 From: marco.giord at gmail.com (marco giordano) Date: Thu, 9 Jun 2016 16:45:30 +0200 Subject: [ITK] [ITK-users] Read 4D CT cardiac dicom series and save it as a single 4D nifti file Message-ID: Hi there, I need to import a 4D Siemens cardiac CT dataset (3D+ t) from Dicom into nifti format (or any other format). The dicom comes as a collection of 2D slices. The 2D slices belonging to the same volume have the same acquisition time. I can read the volumes by using the Content Time ("0008|0033") as a restriction (similarly as in DicomSeriesReadImageWrite2.cxx) but then I do not understand how I can write the volumes in a single 4D nifti file. I tried with the VectorImage but it needs the dimension to be specified in advance which I do not know. Any help is appreciated. Regards, -- Marco -------------- 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 varasteh at to.infn.it Thu Jun 9 11:06:26 2016 From: varasteh at to.infn.it (Mohammad Varasteh) Date: Thu, 9 Jun 2016 08:06:26 -0700 (MST) Subject: [ITK] [ITK-users] Read 4D CT cardiac dicom series and save it as a single 4D nifti file In-Reply-To: References: Message-ID: <1465484786789-7588963.post@n2.nabble.com> Dear Marco, Actually I do not know how to do it in the ITK but for such cases (if it is few cases) I normally use "VV: the 4D slicer". You can find it in the following link: http://www.creatis.insa-lyon.fr/rio/vv I hope this will be of some use. Varasteh -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Read-4D-CT-cardiac-dicom-series-and-save-it-as-a-single-4D-nifti-file-tp7588962p7588963.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 scapegoat.sarthak at gmail.com Thu Jun 9 11:21:18 2016 From: scapegoat.sarthak at gmail.com (Scapegoat Sarthak) Date: Thu, 9 Jun 2016 11:21:18 -0400 Subject: [ITK] [ITK-users] Read 4D CT cardiac dicom series and save it as a single 4D nifti file In-Reply-To: <1465484786789-7588963.post@n2.nabble.com> References: <1465484786789-7588963.post@n2.nabble.com> Message-ID: You can do it pretty easily: Read DICOM using SeriesFileReader and then connect output to a FileWriter with the file name of your choice (in this case, it would be "output.nii.gz"). On 9 June 2016 at 11:06, Mohammad Varasteh wrote: > Dear Marco, > > Actually I do not know how to do it in the ITK but for such cases (if it is > few cases) I normally use "VV: the 4D slicer". You can find it in the > following link: > > http://www.creatis.insa-lyon.fr/rio/vv > > I hope this will be of some use. > > Varasteh > > > > -- > View this message in context: > http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Read-4D-CT-cardiac-dicom-series-and-save-it-as-a-single-4D-nifti-file-tp7588962p7588963.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 brad at lowekamp.net Thu Jun 9 14:38:02 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Thu, 9 Jun 2016 14:38:02 -0400 Subject: [ITK] [ITK-dev] Gerrit robots down? In-Reply-To: References: <9344A230-B8A3-4464-8960-37E87D6C2185@mail.nih.gov> Message-ID: <409259DD-F91B-4278-ADF7-148D788097A2@lowekamp.net> Hello, I am still not seeing any robot build in gerrit. Thanks, Brad > On Jun 6, 2016, at 3:17 PM, Jean-Christophe Fillion-Robin wrote: > > Hi Brad, > > The missing robots are most likely due to the power failure caused by the remodeling/construction in our North Carolina office. > > I anticipate they will be back online tomorrow or the day after. > > Thanks for your patience, > Jc > > > On Mon, Jun 6, 2016 at 11:10 AM, Bradley Lowekamp > wrote: > I am not seeing any of robots working on gerrit. Can we get these working again? > > Thanks > Brad > _______________________________________________ > Powered by www.kitware.com > > 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 > > > > -- > +1 919 869 8849 -------------- 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 jchris.fillionr at kitware.com Thu Jun 9 15:10:56 2016 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Thu, 9 Jun 2016 15:10:56 -0400 Subject: [ITK] [ITK-dev] Gerrit robots down? In-Reply-To: <409259DD-F91B-4278-ADF7-148D788097A2@lowekamp.net> References: <9344A230-B8A3-4464-8960-37E87D6C2185@mail.nih.gov> <409259DD-F91B-4278-ADF7-148D788097A2@lowekamp.net> Message-ID: Hi Brad, Considering our office floor is undergoing some construction/remodelling, the power in the room physically hosting the server was out. This most likely explained the downtime. Now the power is back, I just restarted the machine, it is currently running a "disk check". I will let you know how it goes. Thanks Jc On Thu, Jun 9, 2016 at 2:38 PM, Bradley Lowekamp wrote: > Hello, > > I am still not seeing any robot build in gerrit. > > Thanks, > Brad > > On Jun 6, 2016, at 3:17 PM, Jean-Christophe Fillion-Robin < > jchris.fillionr at kitware.com> wrote: > > Hi Brad, > > The missing robots are most likely due to the power failure caused by the > remodeling/construction in our North Carolina office. > > I anticipate they will be back online tomorrow or the day after. > > Thanks for your patience, > Jc > > > On Mon, Jun 6, 2016 at 11:10 AM, Bradley Lowekamp > wrote: > >> I am not seeing any of robots working on gerrit. Can we get these working >> again? >> >> Thanks >> Brad >> _______________________________________________ >> Powered by www.kitware.com >> >> 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 >> > > > > -- > +1 919 869 8849 > > > -- +1 919 869 8849 -------------- 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 marco.giord at gmail.com Fri Jun 10 17:31:36 2016 From: marco.giord at gmail.com (marco giordano) Date: Fri, 10 Jun 2016 23:31:36 +0200 Subject: [ITK] [ITK-users] Read 4D CT cardiac dicom series and save it as a single 4D nifti file In-Reply-To: References: <1465484786789-7588963.post@n2.nabble.com> Message-ID: Hi there, Thanks for the suggestions. VV is not really an option since I have to analyze many cases. I even tried to use VV but it gives me the wrong order of the slices. I am trying the "itk::ImageSeriesReader" (right?) but it is complaining that "Position is not unique". I think it refers to the fact that the slices in my "series" have the "same location". Not sure this is meant to transform 2D into 4D if it expects different locations, maybe it is for 2D into 3D. Any idea? Regards 2016-06-09 17:21 GMT+02:00 Scapegoat Sarthak : > You can do it pretty easily: > > Read DICOM using SeriesFileReader and then connect output to a FileWriter > with the file name of your choice (in this case, it would be > "output.nii.gz"). > > > On 9 June 2016 at 11:06, Mohammad Varasteh wrote: > >> Dear Marco, >> >> Actually I do not know how to do it in the ITK but for such cases (if it >> is >> few cases) I normally use "VV: the 4D slicer". You can find it in the >> following link: >> >> http://www.creatis.insa-lyon.fr/rio/vv >> >> I hope this will be of some use. >> >> Varasteh >> >> >> >> -- >> View this message in context: >> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Read-4D-CT-cardiac-dicom-series-and-save-it-as-a-single-4D-nifti-file-tp7588962p7588963.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 > > -- Marco Giordano SKYPE:marcogiord81 -------------- 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 david.paik at elucidbio.com Fri Jun 10 19:24:03 2016 From: david.paik at elucidbio.com (David S. Paik (Elucid Bioimaging)) Date: Fri, 10 Jun 2016 23:24:03 +0000 Subject: [ITK] Redudancy in LevelSetBase hierarchy Message-ID: <7B2A0371-4D8A-473C-B201-54267261DA68@elucidbio.com> I am going through the level set v4 classes in 4.9.1 and I noticed a few things. In itk::LevelSetBase - EvaluateMeanCurvature( const InputType& iP ) is declared pure virtual (.h line 75) but a definition is provided (.hxx line 88). While syntactically permissible, this seems more likely an oversight rather than an intentional design. (see below) - Both versions of EvaluateLaplacian are pure virtual even though they could be computed at this point in the hierarchy as the trace of the Hessian matrix. This is analogous to how EvaluateGradientNorm is calculated even though EvaluateGradient is still pure virtual in this class. (see below) In itk::DiscreteLevelSetImage - EvaluateLaplacian (both versions) do their own redundant calculation of second derivatives even though they may have already been calculated in the Hessian matrix. There?s probably a design tradeoff between redundantly computing the Laplacian (as it is now) vs. Laplacian triggering a full Hessian computation even if the off diagonal elements of the Hessian are not used. One possibility is to check to see if Hessian has been computed and if so use it but not trigger a full Hessian computation. - EvaluateMeanCurvature (both versions) override itk::LevelSetBase?s version but they appear to be exactly the same. The virtual function calls should work from the base class. Not a bug but this seems to be an unnecessary redundancy. Am I missing something? David From lasso at queensu.ca Sat Jun 11 00:25:23 2016 From: lasso at queensu.ca (Andras Lasso) Date: Sat, 11 Jun 2016 04:25:23 +0000 Subject: [ITK] [ITK-users] Read 4D CT cardiac dicom series and save it as a single 4D nifti file In-Reply-To: References: <1465484786789-7588963.post@n2.nabble.com> , Message-ID: 3D Slicer can load some 4D CTs a 3D+t sequence and you cab save it as a 4D nrrd. You may give it a try. If it doesn't work for your sequence then report the problem on the slicer-users mailing list. If you can provide a sample data set then slicer developers most likely will be able to make it work. Andras From: marco giordano Sent: June 10, 2016 17:32 To: Scapegoat Sarthak Cc: insight-users at itk.org Subject: Re: [ITK] [ITK-users] Read 4D CT cardiac dicom series and save it as a single 4D nifti file Hi there, Thanks for the suggestions. VV is not really an option since I have to analyze many cases. I even tried to use VV but it gives me the wrong order of the slices. I am trying the "itk::ImageSeriesReader" (right?) but it is complaining that "Position is not unique". I think it refers to the fact that the slices in my "series" have the "same location". Not sure this is meant to transform 2D into 4D if it expects different locations, maybe it is for 2D into 3D. Any idea? Regards 2016-06-09 17:21 GMT+02:00 Scapegoat Sarthak >: You can do it pretty easily: Read DICOM using SeriesFileReader and then connect output to a FileWriter with the file name of your choice (in this case, it would be "output.nii.gz"). On 9 June 2016 at 11:06, Mohammad Varasteh > wrote: Dear Marco, Actually I do not know how to do it in the ITK but for such cases (if it is few cases) I normally use "VV: the 4D slicer". You can find it in the following link: http://www.creatis.insa-lyon.fr/rio/vv I hope this will be of some use. Varasteh -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Read-4D-CT-cardiac-dicom-series-and-save-it-as-a-single-4D-nifti-file-tp7588962p7588963.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 -- Marco Giordano SKYPE:marcogiord81 -------------- 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 zhuangming.shen at sphic.org.cn Sun Jun 12 01:33:13 2016 From: zhuangming.shen at sphic.org.cn (=?utf-8?B?5rKI5bqE5piO?=) Date: Sun, 12 Jun 2016 05:33:13 +0000 Subject: [ITK] [ITK-users] Issue on itk.QuadEdgeMeshCellTraitsInfo Message-ID: <1465709590989.57546@sphic.org.cn> ?Hi all, When I used python-supported ITK 4.10.0 to get the types of itk.QuadEdgeMeshCellTraitsInfo for the first time, I got two warnings Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 2,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,2,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,2,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface' Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 3,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface' Options: If I run itk.QuadEdgeMeshCellTraitsInfo.GetTypes() again or use ITK 4.9.1 instead, it just displays Options: So what's the problem? What is the unknown parameter? Has someone met this issue? Thanks. Regards, Zhuangming Shen -------------- 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 brad at lowekamp.net Mon Jun 13 09:39:35 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Mon, 13 Jun 2016 09:39:35 -0400 Subject: [ITK] [ITK-dev] Gerrit robots down? In-Reply-To: References: <9344A230-B8A3-4464-8960-37E87D6C2185@mail.nih.gov> <409259DD-F91B-4278-ADF7-148D788097A2@lowekamp.net> Message-ID: I am still not seeing any sign of the robots on the dashboard? Brad > On Jun 9, 2016, at 3:10 PM, Jean-Christophe Fillion-Robin wrote: > > Hi Brad, > > Considering our office floor is undergoing some construction/remodelling, the power in the room physically hosting the server was out. This most likely explained the downtime. > > Now the power is back, I just restarted the machine, it is currently running a "disk check". I will let you know how it goes. > > Thanks > Jc > > On Thu, Jun 9, 2016 at 2:38 PM, Bradley Lowekamp > wrote: > Hello, > > I am still not seeing any robot build in gerrit. > > Thanks, > Brad > >> On Jun 6, 2016, at 3:17 PM, Jean-Christophe Fillion-Robin > wrote: >> >> Hi Brad, >> >> The missing robots are most likely due to the power failure caused by the remodeling/construction in our North Carolina office. >> >> I anticipate they will be back online tomorrow or the day after. >> >> Thanks for your patience, >> Jc >> >> >> On Mon, Jun 6, 2016 at 11:10 AM, Bradley Lowekamp > wrote: >> I am not seeing any of robots working on gerrit. Can we get these working again? >> >> Thanks >> Brad >> _______________________________________________ >> Powered by www.kitware.com >> >> 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 >> >> >> >> -- >> +1 919 869 8849 > > > > > -- > +1 919 869 8849 -------------- 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 jchris.fillionr at kitware.com Tue Jun 14 09:30:14 2016 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Tue, 14 Jun 2016 09:30:14 -0400 Subject: [ITK] [ITK-dev] Gerrit robots down? In-Reply-To: References: <9344A230-B8A3-4464-8960-37E87D6C2185@mail.nih.gov> <409259DD-F91B-4278-ADF7-148D788097A2@lowekamp.net> Message-ID: Hi Hans, Brad, The issue has been identified. The machine used internally as "Jenkins" server (the one mentioned in my earlier email) does not finalize its bootup sequence. We are working on setting up a replacement server using the backed up configuration. Thanks for your patience, Jc On Mon, Jun 13, 2016 at 9:39 AM, Bradley Lowekamp wrote: > I am still not seeing any sign of the robots on the dashboard? > > Brad > > On Jun 9, 2016, at 3:10 PM, Jean-Christophe Fillion-Robin < > jchris.fillionr at kitware.com> wrote: > > Hi Brad, > > Considering our office floor is undergoing some construction/remodelling, > the power in the room physically hosting the server was out. This most > likely explained the downtime. > > Now the power is back, I just restarted the machine, it is currently > running a "disk check". I will let you know how it goes. > > Thanks > Jc > > On Thu, Jun 9, 2016 at 2:38 PM, Bradley Lowekamp > wrote: > >> Hello, >> >> I am still not seeing any robot build in gerrit. >> >> Thanks, >> Brad >> >> On Jun 6, 2016, at 3:17 PM, Jean-Christophe Fillion-Robin < >> jchris.fillionr at kitware.com> wrote: >> >> Hi Brad, >> >> The missing robots are most likely due to the power failure caused by the >> remodeling/construction in our North Carolina office. >> >> I anticipate they will be back online tomorrow or the day after. >> >> Thanks for your patience, >> Jc >> >> >> On Mon, Jun 6, 2016 at 11:10 AM, Bradley Lowekamp >> wrote: >> >>> I am not seeing any of robots working on gerrit. Can we get these >>> working again? >>> >>> Thanks >>> Brad >>> _______________________________________________ >>> Powered by www.kitware.com >>> >>> 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 >>> >> >> >> >> -- >> +1 919 869 8849 >> >> >> > > > -- > +1 919 869 8849 > > > -- +1 919 869 8849 -------------- 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 jchris.fillionr at kitware.com Tue Jun 14 14:39:13 2016 From: jchris.fillionr at kitware.com (Jean-Christophe Fillion-Robin) Date: Tue, 14 Jun 2016 14:39:13 -0400 Subject: [ITK] [ITK-dev] Gerrit robots down? In-Reply-To: References: <9344A230-B8A3-4464-8960-37E87D6C2185@mail.nih.gov> <409259DD-F91B-4278-ADF7-148D788097A2@lowekamp.net> Message-ID: Hi Brad, Hans, The Jenkins server is now back online (on our internal network). I will check the status of the build bots. We should then expect the queue of topic to be processed. Thanks for your patience, Jc On Jun 14, 2016 9:30 AM, "Jean-Christophe Fillion-Robin" < jchris.fillionr at kitware.com> wrote: Hi Hans, Brad, The issue has been identified. The machine used internally as "Jenkins" server (the one mentioned in my earlier email) does not finalize its bootup sequence. We are working on setting up a replacement server using the backed up configuration. Thanks for your patience, Jc On Mon, Jun 13, 2016 at 9:39 AM, Bradley Lowekamp wrote: > I am still not seeing any sign of the robots on the dashboard? > > Brad > > On Jun 9, 2016, at 3:10 PM, Jean-Christophe Fillion-Robin < > jchris.fillionr at kitware.com> wrote: > > Hi Brad, > > Considering our office floor is undergoing some construction/remodelling, > the power in the room physically hosting the server was out. This most > likely explained the downtime. > > Now the power is back, I just restarted the machine, it is currently > running a "disk check". I will let you know how it goes. > > Thanks > Jc > > On Thu, Jun 9, 2016 at 2:38 PM, Bradley Lowekamp > wrote: > >> Hello, >> >> I am still not seeing any robot build in gerrit. >> >> Thanks, >> Brad >> >> On Jun 6, 2016, at 3:17 PM, Jean-Christophe Fillion-Robin < >> jchris.fillionr at kitware.com> wrote: >> >> Hi Brad, >> >> The missing robots are most likely due to the power failure caused by the >> remodeling/construction in our North Carolina office. >> >> I anticipate they will be back online tomorrow or the day after. >> >> Thanks for your patience, >> Jc >> >> >> On Mon, Jun 6, 2016 at 11:10 AM, Bradley Lowekamp >> wrote: >> >>> I am not seeing any of robots working on gerrit. Can we get these >>> working again? >>> >>> Thanks >>> Brad >>> _______________________________________________ >>> Powered by www.kitware.com >>> >>> 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 >>> >> >> >> >> -- >> +1 919 869 8849 >> >> >> > > > -- > +1 919 869 8849 > > > -- +1 919 869 8849 -------------- 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 y.borokh at gmail.com Wed Jun 15 06:00:14 2016 From: y.borokh at gmail.com (Yurii Borokh) Date: Wed, 15 Jun 2016 03:00:14 -0700 (MST) Subject: [ITK] [ITK-users] Fast image creation from a signed distance function Message-ID: <1465984814443-7588969.post@n2.nabble.com> Hi all,I'm searching for a filter that could effectively create an image from a signed distance function.Of course, it can be done straightforwardly by calculation of distance in each pixel. But I would like to minimize the number of calls to distance function since it's implemented via RBF and calls are rather expensive. Does ITK has some kind of such functionality?Any hints would be appreciated.Regards,Yurii -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Fast-image-creation-from-a-signed-distance-function-tp7588969.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 pierre.barbierdereuille at gmail.com Wed Jun 15 09:36:37 2016 From: pierre.barbierdereuille at gmail.com (Pierre Barbier de Reuille) Date: Wed, 15 Jun 2016 13:36:37 +0000 Subject: [ITK] [ITK-dev] Error using fftwf_* functions when FFTW is compiled with double Message-ID: Hey, I just compiled the latest version of ITK (4.10.0) with MinGW under windows and I had a problem. I compiled it with FFTW compiled with double precision, but in the file Module/Filtering/FFT/src/itkFFTWGlobalConfiguration.cxx the function fftwf_import_wisdom_from_file is used twice when fftw_import_wisdom_from_file should be used: on lines 632 and 709. Otherwise, everything compiled just fine. Cheers, Pierre -- Dr. Barbier de Reuille, Pierre Institute of Plant Sciences University of Bern Altenbergrain 21, CH-3013 Bern, Switzerland -------------- 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 abou_zeid_wassim at hotmail.com Wed Jun 15 11:04:10 2016 From: abou_zeid_wassim at hotmail.com (wassim bouzeid) Date: Wed, 15 Jun 2016 15:04:10 +0000 Subject: [ITK] Cost Function Evaluations at MultiResolutions Message-ID: Hi Everyone, I want to determine the rotational transformations corresponding to the extrema of the cost function at the first level of resolution (both images are subsampled by a factor of 8 and interpolated). I am using an exhaustive optimizer (itk::ExhaustiveOptimizerv4) to explore the parametric space using VersorTranfrom (only 3D rotations). The parametric space is explored using large rotation angles (coarse grid) with large step size . For example, If I have three values per dimension, there is 125 possible configurations for my parameter settings ((-20,-20,-10),(-20,-20,-10)...(-20,-20,10)). //*******************************Here is my code********* typedef itk::ExhaustiveOptimizerv4< double > ExOptimizerType; ExOptimizerType::StepsType stepsLevel8( initialTransformCOM->GetParameters() ); stepsLevel8[0] = 3; stepsLevel8[1] = 3; stepsLevel8[2] = 3; optimizerLevel8->SetNumberOfSteps( stepsLevel8 ); optimizerLevel8->SetStepLength( 10 ); //*******************************Here is my code********* I am feeling that I am missing something such the range that the optimizer has to explore. Is this the correct way to do it? Any help would be appreciated. Thanks, Sam -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Wed Jun 15 11:47:58 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 15 Jun 2016 11:47:58 -0400 Subject: [ITK] Cost Function Evaluations at MultiResolutions In-Reply-To: References: Message-ID: This example may help: https://itk.org/Wiki/ITK/Examples/Registration/ExhaustiveOptimizer On Wed, Jun 15, 2016 at 11:04 AM, wassim bouzeid wrote: > Hi Everyone, > > I want to determine the rotational transformations corresponding to the > extrema of the cost function at the first level of resolution (both images > are subsampled by a factor of 8 and interpolated). > > I am using an exhaustive optimizer (itk::ExhaustiveOptimizerv4) to explore > the parametric space using VersorTranfrom (only 3D rotations). > > The parametric space is explored using large rotation angles (coarse grid) > with large step size . For example, If I have three values per dimension, > there is 125 possible configurations for my parameter settings > ((-20,-20,-10),(-20,-20,-10)...(-20,-20,10)). > > //*******************************Here is my code********* > typedef itk::ExhaustiveOptimizerv4< double > ExOptimizerType; > ExOptimizerType::StepsType stepsLevel8( initialTransformCOM->GetParameters() > ); > stepsLevel8[0] = 3; > stepsLevel8[1] = 3; > stepsLevel8[2] = 3; > optimizerLevel8->SetNumberOfSteps( stepsLevel8 ); > optimizerLevel8->SetStepLength( 10 ); > //*******************************Here is my code********* > > I am feeling that I am missing something such the range that the optimizer > has to explore. Is this the correct way to do it? > > Any help would be appreciated. > > Thanks, > Sam > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -- Unpaid intern in BillsBasement at noware dot com From blowekamp at mail.nih.gov Wed Jun 15 14:35:18 2016 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 15 Jun 2016 14:35:18 -0400 Subject: [ITK] [ITK-dev] Error using fftwf_* functions when FFTW is compiled with double In-Reply-To: References: Message-ID: Hello, Looks like you found a bug! Can you please test the change and submit a patch for review? https://itk.org/Wiki/ITK/Git/Develop Thanks, Brad > On Jun 15, 2016, at 9:36 AM, Pierre Barbier de Reuille wrote: > > Hey, > > I just compiled the latest version of ITK (4.10.0) with MinGW under windows and I had a problem. > > I compiled it with FFTW compiled with double precision, but in the file Module/Filtering/FFT/src/itkFFTWGlobalConfiguration.cxx the function fftwf_import_wisdom_from_file is used twice when fftw_import_wisdom_from_file should be used: on lines 632 and 709. > > Otherwise, everything compiled just fine. > > Cheers, > > Pierre > > -- > Dr. Barbier de Reuille, Pierre > Institute of Plant Sciences > University of Bern > Altenbergrain 21, CH-3013 Bern, Switzerland > > _______________________________________________ > Powered by www.kitware.com > > 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 michkapopoff at gmail.com Wed Jun 15 17:12:06 2016 From: michkapopoff at gmail.com (Michka Popoff) Date: Wed, 15 Jun 2016 23:12:06 +0200 Subject: [ITK] [ITK-users] Build errors in python wrapping of 4.10.0 In-Reply-To: References: Message-ID: Hi I think this bug is not known. I had a look and could reproduce it with gcc 6.0.0, Cmake 3.5.2, Python 3.5.1 on OS X. GCC 6 is using c++14 by default, but even with c++11 you would probably get the problem. The problem is also there with the latest commit from the master branch. Please note that we probably never tested Python Wrappings with c++11, even not speaking of c++14. The problem seems to have appeared with this patch: https://github.com/InsightSoftwareConsortium/ITK/commit/b6b9a8e8849da1edbf75f88e11adb8d8d15bb395 I removed the ITK_DELETE_FUNCTION macro from the itkTriangleHelper copy constructor, and was able to compile with gcc 6. But it may just a side effect of that patch which is now only appearing with c++ >= 11. It is weird that the problem seems to be only for the itkTriangleHelper class. I will have to look what is the difference in the files generated for swig and what is exactly failing, though I do not know how long it will take me. I hope I can do this this weekend. Thanks Michka > On 09 Jun 2016, at 16:14, Christopher Mullins wrote: > > Hi all, > > Apparently my subscription to this list has lapsed and my first email was rejected (despite receiving the list in my inbox every day). Sorry if there's a double post. > > I'm getting the following build errors when building ITK 4.10.0 with the WRAP_PYTHON option ON[1], [3]. Is this a known issue, or is there a configuration setting I've set improperly? > > Platform is Arch linux, GCC v6.1.1, Python v3.5.1, CMake v3.5.2. There are no warnings. See all output details for this machine here [2], and please let me know if I can provide any others. > > The faster I fix this the faster I'll feel comfortable updating the Arch linux AUR PKGBUILD for ITK, so I appreciate any help you can offer. > > Thanks, > Chris > > > > [1] https://open.cdash.org/viewBuildError.php?buildid=4403379 > [2] https://open.cdash.org/buildSummary.php?buildid=4403379 > > [3] To save you a click, and for the sake of archiving, the error is: > /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp: In function 'PyObject* _wrap_new_itkTriangleHelperPD2(PyObject*, PyObject*)': /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5854:65: error: no matching function for call to 'itk::TriangleHelper >::TriangleHelper()' result = (itkTriangleHelperPD2 *)new itkTriangleHelperPD2(); > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 hans-johnson at uiowa.edu Wed Jun 15 17:22:06 2016 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Wed, 15 Jun 2016 21:22:06 +0000 Subject: [ITK] [ITK-users] Build errors in python wrapping of 4.10.0 In-Reply-To: References: Message-ID: <45356B32-0D4F-4FE9-9157-630919E381EA@uiowa.edu> I?m trying to reproduce now. Hans -- On 6/15/16, 4:12 PM, "Insight-users on behalf of Michka Popoff" wrote: >Hi > >I think this bug is not known. I had a look and could reproduce it with gcc 6.0.0, Cmake 3.5.2, Python 3.5.1 on OS X. >GCC 6 is using c++14 by default, but even with c++11 you would probably get the problem. >The problem is also there with the latest commit from the master branch. > >Please note that we probably never tested Python Wrappings with c++11, even not speaking of c++14. > >The problem seems to have appeared with this patch: >https://github.com/InsightSoftwareConsortium/ITK/commit/b6b9a8e8849da1edbf75f88e11adb8d8d15bb395 > >I removed the ITK_DELETE_FUNCTION macro from the itkTriangleHelper copy constructor, and was able to compile >with gcc 6. But it may just a side effect of that patch which is now only appearing with c++ >= 11. >It is weird that the problem seems to be only for the itkTriangleHelper class. > >I will have to look what is the difference in the files generated for swig and what is exactly failing, >though I do not know how long it will take me. I hope I can do this this weekend. > >Thanks > >Michka > > >> On 09 Jun 2016, at 16:14, Christopher Mullins wrote: >> >> Hi all, >> >> Apparently my subscription to this list has lapsed and my first email was rejected (despite receiving the list in my inbox every day). Sorry if there's a double post. >> >> I'm getting the following build errors when building ITK 4.10.0 with the WRAP_PYTHON option ON[1], [3]. Is this a known issue, or is there a configuration setting I've set improperly? >> >> Platform is Arch linux, GCC v6.1.1, Python v3.5.1, CMake v3.5.2. There are no warnings. See all output details for this machine here [2], and please let me know if I can provide any others. >> >> The faster I fix this the faster I'll feel comfortable updating the Arch linux AUR PKGBUILD for ITK, so I appreciate any help you can offer. >> >> Thanks, >> Chris >> >> >> >> [1] https://open.cdash.org/viewBuildError.php?buildid=4403379 >> [2] https://open.cdash.org/buildSummary.php?buildid=4403379 >> >> [3] To save you a click, and for the sake of archiving, the error is: >> /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp: In function 'PyObject* _wrap_new_itkTriangleHelperPD2(PyObject*, PyObject*)': /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5854:65: error: no matching function for call to 'itk::TriangleHelper >::TriangleHelper()' result = (itkTriangleHelperPD2 *)new itkTriangleHelperPD2(); >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 paniwani at gmail.com Fri Jun 17 02:28:08 2016 From: paniwani at gmail.com (paniwani) Date: Thu, 16 Jun 2016 23:28:08 -0700 (MST) Subject: [ITK] [ITK-users] Simple ITK Python not working on Mac El Capitan (10.11) Message-ID: <1466144888365-37265.post@n7.nabble.com> Hi, I was using simple ITK with python in my application with no problems until I recently upgraded to El Capitan on my Mac. Since then, I have received error messages regarding 64-bit issues. I've tried to reinstall simple ITK multiple times using the python binaries as stated here https://itk.org/Wiki/SimpleITK/GettingStarted#Python_binary_files with both pip and easy_install. However, I continue to run into issues running simpleITK. I am on OSX El Capitan (10.11) and Python 2.7. Here is the output when I try to install the latest via pip and and use it: I also tried to download a separate binary which I thought would be more applicable for El Capitan (Mac OSX v10.11): SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl However, I received the same error message: Any help to get simpleITK in python working again would be appreciated. Thanks in advance! Neil -- View this message in context: http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265.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 pierre.barbierdereuille at gmail.com Fri Jun 17 05:21:05 2016 From: pierre.barbierdereuille at gmail.com (Pierre Barbier de Reuille) Date: Fri, 17 Jun 2016 09:21:05 +0000 Subject: [ITK] [ITK-dev] Error using fftwf_* functions when FFTW is compiled with double In-Reply-To: References: Message-ID: Hello, sorry for the delay, but it took a while to test everything correctly. So I created a topic called fix_fftwf_used_with_fftwd and made the modification. I tested it with the FFTW compiled by ITK itself and all FFTW-related tests passed without problem. There are some tests failing, but they are unrelated to the modification. For completeness, here is the list of tests that failed: The following tests FAILED: 79 - vnl_algo_test_convolve (Failed) 824 - itkHDF5ImageIOTest (Failed) 825 - itkHDF5ImageIOStreamingReadWriteTest (Failed) 1177 - itkCastImageFilterTest (Failed) Cheers, Pierre On Wed, 15 Jun 2016 at 20:35 Bradley Lowekamp wrote: > Hello, > > Looks like you found a bug! > > Can you please test the change and submit a patch for review? > https://itk.org/Wiki/ITK/Git/Develop > > Thanks, > Brad > > On Jun 15, 2016, at 9:36 AM, Pierre Barbier de Reuille < > pierre.barbierdereuille at gmail.com> wrote: > > Hey, > > I just compiled the latest version of ITK (4.10.0) with MinGW under > windows and I had a problem. > > I compiled it with FFTW compiled with double precision, but in the file > Module/Filtering/FFT/src/itkFFTWGlobalConfiguration.cxx the function > fftwf_import_wisdom_from_file is used twice when > fftw_import_wisdom_from_file should be used: on lines 632 and 709. > > Otherwise, everything compiled just fine. > > Cheers, > > Pierre > > -- > > Dr. Barbier de Reuille, Pierre > Institute of Plant Sciences > University of Bern > Altenbergrain 21, CH-3013 Bern, Switzerland > > _______________________________________________ > Powered by www.kitware.com > > 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 > > > -- Dr. Barbier de Reuille, Pierre Institute of Plant Sciences University of Bern Altenbergrain 21, CH-3013 Bern, Switzerland -------------- 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 blowekamp at mail.nih.gov Fri Jun 17 07:54:46 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Fri, 17 Jun 2016 11:54:46 +0000 Subject: [ITK] [ITK-dev] Error using fftwf_* functions when FFTW is compiled with double In-Reply-To: References: Message-ID: <7743F9E5-6F51-4F7F-B7B9-A8C10A4DD550@mail.nih.gov> Nice! Thank you for your contribution. There is already a patch out for the HDF5 issue here: http://review.source.kitware.com/#/c/21231/ You could checkout that patch out, test it and review it, to ensure it addresses your issue. Thanks, Brad On Jun 17, 2016, at 5:21 AM, Pierre Barbier de Reuille > wrote: Hello, sorry for the delay, but it took a while to test everything correctly. So I created a topic called fix_fftwf_used_with_fftwd and made the modification. I tested it with the FFTW compiled by ITK itself and all FFTW-related tests passed without problem. There are some tests failing, but they are unrelated to the modification. For completeness, here is the list of tests that failed: The following tests FAILED: 79 - vnl_algo_test_convolve (Failed) 824 - itkHDF5ImageIOTest (Failed) 825 - itkHDF5ImageIOStreamingReadWriteTest (Failed) 1177 - itkCastImageFilterTest (Failed) Cheers, Pierre On Wed, 15 Jun 2016 at 20:35 Bradley Lowekamp > wrote: Hello, Looks like you found a bug! Can you please test the change and submit a patch for review? https://itk.org/Wiki/ITK/Git/Develop Thanks, Brad On Jun 15, 2016, at 9:36 AM, Pierre Barbier de Reuille > wrote: Hey, I just compiled the latest version of ITK (4.10.0) with MinGW under windows and I had a problem. I compiled it with FFTW compiled with double precision, but in the file Module/Filtering/FFT/src/itkFFTWGlobalConfiguration.cxx the function fftwf_import_wisdom_from_file is used twice when fftw_import_wisdom_from_file should be used: on lines 632 and 709. Otherwise, everything compiled just fine. Cheers, Pierre -- Dr. Barbier de Reuille, Pierre Institute of Plant Sciences University of Bern Altenbergrain 21, CH-3013 Bern, Switzerland _______________________________________________ Powered by www.kitware.com 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 -- Dr. Barbier de Reuille, Pierre Institute of Plant Sciences University of Bern Altenbergrain 21, CH-3013 Bern, Switzerland -------------- 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 blowekamp at mail.nih.gov Fri Jun 17 08:05:49 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Fri, 17 Jun 2016 12:05:49 +0000 Subject: [ITK] [ITK-users] Simple ITK Python not working on Mac El Capitan (10.11) In-Reply-To: <1466144888365-37265.post@n7.nabble.com> References: <1466144888365-37265.post@n7.nabble.com> Message-ID: <7CB5F016-E3E0-4782-BC8D-ACCED31DFB3A@mail.nih.gov> Hello, You probably what this file: https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl Also you probably didn?t have the latest version of pip, try using updating to the latest version. It is recommended not to change the system version but instead use a virtual environment as described in the wiki documentation. Aside from that general advice, I can?t help specifically because you did not provide sufficient details. Such as which python you are using ( system, anaconda) or it?s version, nor do you provide the command to install SimpleITK or the output. HTH, Brad > On Jun 17, 2016, at 2:28 AM, paniwani wrote: > > Hi, > > I was using simple ITK with python in my application with no problems until > I recently upgraded to El Capitan on my Mac. Since then, I have received > error messages regarding 64-bit issues. I've tried to reinstall simple ITK > multiple times using the python binaries as stated here > https://itk.org/Wiki/SimpleITK/GettingStarted#Python_binary_files with both > pip and easy_install. However, I continue to run into issues running > simpleITK. > > I am on OSX El Capitan (10.11) and Python 2.7. > > Here is the output when I try to install the latest via pip and and use it: > > > > I also tried to download a separate binary which I thought would be more > applicable for El Capitan (Mac OSX v10.11): > > SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl > > However, I received the same error message: > > > > Any help to get simpleITK in python working again would be appreciated. > Thanks in advance! > > Neil > > > > > > > > -- > View this message in context: http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265.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 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 paniwani at gmail.com Fri Jun 17 11:20:28 2016 From: paniwani at gmail.com (paniwani) Date: Fri, 17 Jun 2016 08:20:28 -0700 (MST) Subject: [ITK] [ITK-users] Simple ITK Python not working on Mac El Capitan (10.11) In-Reply-To: <7CB5F016-E3E0-4782-BC8D-ACCED31DFB3A@mail.nih.gov> References: <1466144888365-37265.post@n7.nabble.com> <7CB5F016-E3E0-4782-BC8D-ACCED31DFB3A@mail.nih.gov> Message-ID: <1466176828948-37268.post@n7.nabble.com> Hi, It appears the code that I pasted did not show up in the email version of the mailing list. I've re-pasted below. I'm using system Python 2.7 and Mac OSX El Capitan. Thank you! ----- I was using simple ITK with python in my application with no problems until I recently upgraded to El Capitan on my Mac. Since then, I have received error messages regarding 64-bit issues. I've tried to reinstall simple ITK multiple times using the python binaries as stated here https://itk.org/Wiki/SimpleITK/GettingStarted#Python_binary_files with both pip and easy_install. However, I continue to run into issues running simpleITK. I am on OSX El Capitan (10.11) and Python 2.7. Here is the output when I try to install the latest via pip and and use it: ? Downloads sudo pip install --trusted-host www.simpleitk.org -f http://www.simpleitk.org/SimpleITK/resources/software.html --timeout 30 SimpleITK The directory '/Users/neil/Library/Caches/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag. The directory '/Users/neil/Library/Caches/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag. Collecting SimpleITK Downloading https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl (72.6MB) 100% |????????????????????????????????| 72.6MB 41.9MB/s Installing collected packages: SimpleITK Successfully installed SimpleITK-0.9.1 ? Downloads python Python 2.7.10 (default, Oct 23 2015, 19:19:21) [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import SimpleITK as sitk Traceback (most recent call last): File "", line 1, in File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line 1, in from .SimpleITK import * File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 28, in _SimpleITK = swig_import_helper() File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 24, in swig_import_helper _mod = imp.load_module('_SimpleITK', fp, pathname, description) ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python: no appropriate 64-bit architecture (see "man python" for running in 32-bit mode) >>> I also tried to download a separate binary which I thought would be more applicable for El Capitan (Mac OSX v10.11): SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl However, I received the same error message: ? Downloads sudo pip install SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl The directory '/Users/neil/Library/Caches/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag. The directory '/Users/neil/Library/Caches/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag. Processing ./SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl Installing collected packages: SimpleITK Successfully installed SimpleITK-0.9.0 ? Downloads python Python 2.7.10 (default, Oct 23 2015, 19:19:21) [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import SimpleITK as sitk Traceback (most recent call last): File "", line 1, in File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line 1, in from .SimpleITK import * File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 28, in _SimpleITK = swig_import_helper() File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 24, in swig_import_helper _mod = imp.load_module('_SimpleITK', fp, pathname, description) ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python: no appropriate 64-bit architecture (see "man python" for running in 32-bit mode) >>> Any help to get simpleITK in python working again would be appreciated. Thanks in advance! Neil -- View this message in context: http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265p37268.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 Fri Jun 17 14:05:25 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Fri, 17 Jun 2016 18:05:25 +0000 Subject: [ITK] [ITK-users] Simple ITK Python not working on Mac El Capitan (10.11) In-Reply-To: <1466176828948-37268.post@n7.nabble.com> References: <1466144888365-37265.post@n7.nabble.com> <7CB5F016-E3E0-4782-BC8D-ACCED31DFB3A@mail.nih.gov> <1466176828948-37268.post@n7.nabble.com> Message-ID: Hi, Where did you get you python from? You are using a version from /Library/Framework/Python.frameworks, which is not the system version. The error with the first command gives you a suggestion on how to solve the problem. The second error appears to be a binary compatibility issue with the distribution you have of python. Please read the guidance on the wiki with the different distributions of python, along with following the recommendation to setup a virtual environment. https://itk.org/Wiki/SimpleITK/GettingStarted Good luck, Brad > On Jun 17, 2016, at 11:20 AM, paniwani wrote: > > Hi, > > It appears the code that I pasted did not show up in the email version of > the mailing list. I've re-pasted below. I'm using system Python 2.7 and Mac > OSX El Capitan. Thank you! > > ----- > > I was using simple ITK with python in my application with no problems until > I recently upgraded to El Capitan on my Mac. Since then, I have received > error messages regarding 64-bit issues. I've tried to reinstall simple ITK > multiple times using the python binaries as stated here > https://itk.org/Wiki/SimpleITK/GettingStarted#Python_binary_files with both > pip and easy_install. However, I continue to run into issues running > simpleITK. > > I am on OSX El Capitan (10.11) and Python 2.7. > > Here is the output when I try to install the latest via pip and and use it: > > ? Downloads sudo pip install --trusted-host www.simpleitk.org -f > http://www.simpleitk.org/SimpleITK/resources/software.html --timeout 30 > SimpleITK > The directory '/Users/neil/Library/Caches/pip/http' or its parent directory > is not owned by the current user and the cache has been disabled. Please > check the permissions and owner of that directory. If executing pip with > sudo, you may want sudo's -H flag. > The directory '/Users/neil/Library/Caches/pip' or its parent directory is > not owned by the current user and caching wheels has been disabled. check > the permissions and owner of that directory. If executing pip with sudo, you > may want sudo's -H flag. > Collecting SimpleITK > Downloading > https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl > (72.6MB) > 100% |????????????????????????????????| 72.6MB 41.9MB/s > Installing collected packages: SimpleITK > Successfully installed SimpleITK-0.9.1 > ? Downloads python > Python 2.7.10 (default, Oct 23 2015, 19:19:21) > [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin > Type "help", "copyright", "credits" or "license" for more information. >>>> import SimpleITK as sitk > Traceback (most recent call last): > File "", line 1, in > File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line 1, in > > from .SimpleITK import * > File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 28, > in > _SimpleITK = swig_import_helper() > File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 24, > in swig_import_helper > _mod = imp.load_module('_SimpleITK', fp, pathname, description) > ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python: no > appropriate 64-bit architecture (see "man python" for running in 32-bit > mode) >>>> > > I also tried to download a separate binary which I thought would be more > applicable for El Capitan (Mac OSX v10.11): > > SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl > > However, I received the same error message: > > ? Downloads sudo pip install > SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl > The directory '/Users/neil/Library/Caches/pip/http' or its parent directory > is not owned by the current user and the cache has been disabled. Please > check the permissions and owner of that directory. If executing pip with > sudo, you may want sudo's -H flag. > The directory '/Users/neil/Library/Caches/pip' or its parent directory is > not owned by the current user and caching wheels has been disabled. check > the permissions and owner of that directory. If executing pip with sudo, you > may want sudo's -H flag. > Processing > ./SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl > Installing collected packages: SimpleITK > Successfully installed SimpleITK-0.9.0 > ? Downloads python > Python 2.7.10 (default, Oct 23 2015, 19:19:21) > [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin > Type "help", "copyright", "credits" or "license" for more information. >>>> import SimpleITK as sitk > Traceback (most recent call last): > File "", line 1, in > File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line 1, in > > from .SimpleITK import * > File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 28, > in > _SimpleITK = swig_import_helper() > File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line 24, > in swig_import_helper > _mod = imp.load_module('_SimpleITK', fp, pathname, description) > ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python: no > appropriate 64-bit architecture (see "man python" for running in 32-bit > mode) >>>> > > Any help to get simpleITK in python working again would be appreciated. > Thanks in advance! > > Neil > > > > -- > View this message in context: http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265p37268.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 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 paniwani at gmail.com Fri Jun 17 14:55:26 2016 From: paniwani at gmail.com (paniwani) Date: Fri, 17 Jun 2016 11:55:26 -0700 (MST) Subject: [ITK] [ITK-users] Simple ITK Python not working on Mac El Capitan (10.11) In-Reply-To: References: <1466144888365-37265.post@n7.nabble.com> <7CB5F016-E3E0-4782-BC8D-ACCED31DFB3A@mail.nih.gov> <1466176828948-37268.post@n7.nabble.com> Message-ID: I had several versions of Python installed. I removed the version at /Library/Frameworks and reinstalled Python 2.7 using Homebrew. I then followed the advice of the guide and setup a virtual environment within my project (called ecvenv), installed pip, upgraded pip, and used it to install SimpleITK. It installed the one you recommended earlier, v0.9.1. (ecvenv) *? **econtour* *git:(**master**) **?* pip install --trusted-host www.simpleitk.org -f http://www.simpleitk.org/SimpleITK/resources/software.html --timeout 30 SimpleITK Collecting SimpleITK Downloading https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl (72.6MB) 100% |????????????????????????????????| 72.6MB 43.5MB/s Installing collected packages: SimpleITK Successfully installed SimpleITK-0.9.1 However, I continue to run into a "Fatal Python Error" when trying to load simple itk from within python. See below: (ecvenv) *? **econtour* *git:(**master**) **?* which python /Users/neil/work/Meteor/econtour/ecvenv/bin/python (ecvenv) *? **econtour* *git:(**master**) **?* which pip /Users/neil/work/Meteor/econtour/ecvenv/bin/pip (ecvenv) *? **econtour* *git:(**master**) **?* pip list pip (8.1.2) setuptools (23.0.0) SimpleITK (0.9.1) wheel (0.29.0) (ecvenv) *? **econtour* *git:(**master**) **?* python Python 2.7.11 (default, Jan 22 2016, 08:29:18) [GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import SimpleITK as sitk Fatal Python error: PyThreadState_Get: no current thread [1] 2805 abort python On Fri, Jun 17, 2016 at 9:56 AM, Bradley Lowekamp [via ITK - Users] < ml-node+s7n37269h95 at n7.nabble.com> wrote: > Hi, > > Where did you get you python from? You are using a version from > /Library/Framework/Python.frameworks, which is not the system version. > > The error with the first command gives you a suggestion on how to solve > the problem. > > The second error appears to be a binary compatibility issue with the > distribution you have of python. > > Please read the guidance on the wiki with the different distributions of > python, along with following the recommendation to setup a virtual > environment. > > https://itk.org/Wiki/SimpleITK/GettingStarted > > Good luck, > Brad > > > > > > On Jun 17, 2016, at 11:20 AM, paniwani <[hidden email] > > wrote: > > > > Hi, > > > > It appears the code that I pasted did not show up in the email version > of > > the mailing list. I've re-pasted below. I'm using system Python 2.7 and > Mac > > OSX El Capitan. Thank you! > > > > ----- > > > > I was using simple ITK with python in my application with no problems > until > > I recently upgraded to El Capitan on my Mac. Since then, I have received > > error messages regarding 64-bit issues. I've tried to reinstall simple > ITK > > multiple times using the python binaries as stated here > > https://itk.org/Wiki/SimpleITK/GettingStarted#Python_binary_files with > both > > pip and easy_install. However, I continue to run into issues running > > simpleITK. > > > > I am on OSX El Capitan (10.11) and Python 2.7. > > > > Here is the output when I try to install the latest via pip and and use > it: > > > > ? Downloads sudo pip install --trusted-host www.simpleitk.org -f > > http://www.simpleitk.org/SimpleITK/resources/software.html --timeout 30 > > SimpleITK > > The directory '/Users/neil/Library/Caches/pip/http' or its parent > directory > > is not owned by the current user and the cache has been disabled. Please > > check the permissions and owner of that directory. If executing pip with > > sudo, you may want sudo's -H flag. > > The directory '/Users/neil/Library/Caches/pip' or its parent directory > is > > not owned by the current user and caching wheels has been disabled. > check > > the permissions and owner of that directory. If executing pip with sudo, > you > > may want sudo's -H flag. > > Collecting SimpleITK > > Downloading > > > https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl > > (72.6MB) > > 100% |????????????????????????????????| 72.6MB 41.9MB/s > > Installing collected packages: SimpleITK > > Successfully installed SimpleITK-0.9.1 > > ? Downloads python > > Python 2.7.10 (default, Oct 23 2015, 19:19:21) > > [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin > > Type "help", "copyright", "credits" or "license" for more information. > >>>> import SimpleITK as sitk > > Traceback (most recent call last): > > File "", line 1, in > > File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line 1, > in > > > > from .SimpleITK import * > > File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line > 28, > > in > > _SimpleITK = swig_import_helper() > > File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line > 24, > > in swig_import_helper > > _mod = imp.load_module('_SimpleITK', fp, pathname, description) > > ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python: > no > > appropriate 64-bit architecture (see "man python" for running in 32-bit > > mode) > >>>> > > > > I also tried to download a separate binary which I thought would be more > > applicable for El Capitan (Mac OSX v10.11): > > > > > SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl > > > > > However, I received the same error message: > > > > ? Downloads sudo pip install > > > SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl > > > The directory '/Users/neil/Library/Caches/pip/http' or its parent > directory > > is not owned by the current user and the cache has been disabled. Please > > check the permissions and owner of that directory. If executing pip with > > sudo, you may want sudo's -H flag. > > The directory '/Users/neil/Library/Caches/pip' or its parent directory > is > > not owned by the current user and caching wheels has been disabled. > check > > the permissions and owner of that directory. If executing pip with sudo, > you > > may want sudo's -H flag. > > Processing > > > ./SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl > > > Installing collected packages: SimpleITK > > Successfully installed SimpleITK-0.9.0 > > ? Downloads python > > Python 2.7.10 (default, Oct 23 2015, 19:19:21) > > [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin > > Type "help", "copyright", "credits" or "license" for more information. > >>>> import SimpleITK as sitk > > Traceback (most recent call last): > > File "", line 1, in > > File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line 1, > in > > > > from .SimpleITK import * > > File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line > 28, > > in > > _SimpleITK = swig_import_helper() > > File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line > 24, > > in swig_import_helper > > _mod = imp.load_module('_SimpleITK', fp, pathname, description) > > ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python: > no > > appropriate 64-bit architecture (see "man python" for running in 32-bit > > mode) > >>>> > > > > Any help to get simpleITK in python working again would be appreciated. > > Thanks in advance! > > > > Neil > > > > > > > > -- > > View this message in context: > http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265p37268.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 > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265p37269.html > To unsubscribe from Simple ITK Python not working on Mac El Capitan > (10.11), click here > > . > NAML > > -- Neil Panjwani Duke University | B.S.E. 2010 Tel: (760) 486-0765 -- View this message in context: http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265p37270.html Sent from the ITK - Users mailing list archive at Nabble.com. -------------- 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 paniwani at gmail.com Fri Jun 17 16:11:49 2016 From: paniwani at gmail.com (paniwani) Date: Fri, 17 Jun 2016 13:11:49 -0700 (MST) Subject: [ITK] [ITK-users] Simple ITK Python not working on Mac El Capitan (10.11) In-Reply-To: References: <1466144888365-37265.post@n7.nabble.com> <7CB5F016-E3E0-4782-BC8D-ACCED31DFB3A@mail.nih.gov> <1466176828948-37268.post@n7.nabble.com> Message-ID: I eventually got it working by re-installing python as above and then using homebrew to install simple itk. Thanks for your help! Neil On Fri, Jun 17, 2016 at 1:03 PM, Neil Panjwani wrote: > I had several versions of Python installed. I removed the version at > /Library/Frameworks and reinstalled Python 2.7 using Homebrew. I then > followed the advice of the guide and setup a virtual environment within my > project (called ecvenv), installed pip, upgraded pip, and used it to > install SimpleITK. It installed the one you recommended earlier, v0.9.1. > > (ecvenv) *? **econtour* *git:(**master**) **?* pip install > --trusted-host www.simpleitk.org -f > http://www.simpleitk.org/SimpleITK/resources/software.html --timeout 30 > SimpleITK > > Collecting SimpleITK > > Downloading > https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl > (72.6MB) > > 100% |????????????????????????????????| 72.6MB 43.5MB/s > > Installing collected packages: SimpleITK > > Successfully installed SimpleITK-0.9.1 > > > However, I continue to run into a "Fatal Python Error" when trying to load > simple itk from within python. See below: > > (ecvenv) *? **econtour* *git:(**master**) **?* which python > > /Users/neil/work/Meteor/econtour/ecvenv/bin/python > > (ecvenv) *? **econtour* *git:(**master**) **?* which pip > > /Users/neil/work/Meteor/econtour/ecvenv/bin/pip > > (ecvenv) *? **econtour* *git:(**master**) **?* pip list > > pip (8.1.2) > > setuptools (23.0.0) > > SimpleITK (0.9.1) > > wheel (0.29.0) > > (ecvenv) *? **econtour* *git:(**master**) **?* python > > Python 2.7.11 (default, Jan 22 2016, 08:29:18) > > [GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)] on darwin > > Type "help", "copyright", "credits" or "license" for more information. > > >>> import SimpleITK as sitk > > Fatal Python error: PyThreadState_Get: no current thread > > [1] 2805 abort python > > > > > On Fri, Jun 17, 2016 at 9:56 AM, Bradley Lowekamp [via ITK - Users] < > ml-node+s7n37269h95 at n7.nabble.com> wrote: > >> Hi, >> >> Where did you get you python from? You are using a version from >> /Library/Framework/Python.frameworks, which is not the system version. >> >> The error with the first command gives you a suggestion on how to solve >> the problem. >> >> The second error appears to be a binary compatibility issue with the >> distribution you have of python. >> >> Please read the guidance on the wiki with the different distributions of >> python, along with following the recommendation to setup a virtual >> environment. >> >> https://itk.org/Wiki/SimpleITK/GettingStarted >> >> Good luck, >> Brad >> >> >> >> >> > On Jun 17, 2016, at 11:20 AM, paniwani <[hidden email] >> > wrote: >> > >> > Hi, >> > >> > It appears the code that I pasted did not show up in the email version >> of >> > the mailing list. I've re-pasted below. I'm using system Python 2.7 and >> Mac >> > OSX El Capitan. Thank you! >> > >> > ----- >> > >> > I was using simple ITK with python in my application with no problems >> until >> > I recently upgraded to El Capitan on my Mac. Since then, I have >> received >> > error messages regarding 64-bit issues. I've tried to reinstall simple >> ITK >> > multiple times using the python binaries as stated here >> > https://itk.org/Wiki/SimpleITK/GettingStarted#Python_binary_files with >> both >> > pip and easy_install. However, I continue to run into issues running >> > simpleITK. >> > >> > I am on OSX El Capitan (10.11) and Python 2.7. >> > >> > Here is the output when I try to install the latest via pip and and use >> it: >> > >> > ? Downloads sudo pip install --trusted-host www.simpleitk.org -f >> > http://www.simpleitk.org/SimpleITK/resources/software.html --timeout >> 30 >> > SimpleITK >> > The directory '/Users/neil/Library/Caches/pip/http' or its parent >> directory >> > is not owned by the current user and the cache has been disabled. >> Please >> > check the permissions and owner of that directory. If executing pip >> with >> > sudo, you may want sudo's -H flag. >> > The directory '/Users/neil/Library/Caches/pip' or its parent directory >> is >> > not owned by the current user and caching wheels has been disabled. >> check >> > the permissions and owner of that directory. If executing pip with >> sudo, you >> > may want sudo's -H flag. >> > Collecting SimpleITK >> > Downloading >> > >> https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/Python/SimpleITK-0.9.1-cp27-none-macosx_10_6_intel.whl >> > (72.6MB) >> > 100% |????????????????????????????????| 72.6MB 41.9MB/s >> > Installing collected packages: SimpleITK >> > Successfully installed SimpleITK-0.9.1 >> > ? Downloads python >> > Python 2.7.10 (default, Oct 23 2015, 19:19:21) >> > [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin >> > Type "help", "copyright", "credits" or "license" for more information. >> >>>> import SimpleITK as sitk >> > Traceback (most recent call last): >> > File "", line 1, in >> > File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line >> 1, in >> > >> > from .SimpleITK import * >> > File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line >> 28, >> > in >> > _SimpleITK = swig_import_helper() >> > File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line >> 24, >> > in swig_import_helper >> > _mod = imp.load_module('_SimpleITK', fp, pathname, description) >> > ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python: >> no >> > appropriate 64-bit architecture (see "man python" for running in 32-bit >> > mode) >> >>>> >> > >> > I also tried to download a separate binary which I thought would be >> more >> > applicable for El Capitan (Mac OSX v10.11): >> > >> > >> SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl >> >> > >> > However, I received the same error message: >> > >> > ? Downloads sudo pip install >> > >> SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl >> >> > The directory '/Users/neil/Library/Caches/pip/http' or its parent >> directory >> > is not owned by the current user and the cache has been disabled. >> Please >> > check the permissions and owner of that directory. If executing pip >> with >> > sudo, you may want sudo's -H flag. >> > The directory '/Users/neil/Library/Caches/pip' or its parent directory >> is >> > not owned by the current user and caching wheels has been disabled. >> check >> > the permissions and owner of that directory. If executing pip with >> sudo, you >> > may want sudo's -H flag. >> > Processing >> > >> ./SimpleITK-0.9.0-cp27-none-macosx_10_6_intel.macosx_10_7_intel.macosx_10_8_intel.macosx_10_9_intel.macosx_10_10_intel.whl >> >> > Installing collected packages: SimpleITK >> > Successfully installed SimpleITK-0.9.0 >> > ? Downloads python >> > Python 2.7.10 (default, Oct 23 2015, 19:19:21) >> > [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin >> > Type "help", "copyright", "credits" or "license" for more information. >> >>>> import SimpleITK as sitk >> > Traceback (most recent call last): >> > File "", line 1, in >> > File "/Library/Python/2.7/site-packages/SimpleITK/__init__.py", line >> 1, in >> > >> > from .SimpleITK import * >> > File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line >> 28, >> > in >> > _SimpleITK = swig_import_helper() >> > File "/Library/Python/2.7/site-packages/SimpleITK/SimpleITK.py", line >> 24, >> > in swig_import_helper >> > _mod = imp.load_module('_SimpleITK', fp, pathname, description) >> > ImportError: /Library/Frameworks/Python.framework/Versions/2.7/Python: >> no >> > appropriate 64-bit architecture (see "man python" for running in 32-bit >> > mode) >> >>>> >> > >> > Any help to get simpleITK in python working again would be appreciated. >> > Thanks in advance! >> > >> > Neil >> > >> > >> > >> > -- >> > View this message in context: >> http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265p37268.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 >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265p37269.html >> To unsubscribe from Simple ITK Python not working on Mac El Capitan >> (10.11), click here >> >> . >> NAML >> >> > > > > -- > Neil Panjwani > Duke University | B.S.E. 2010 > Tel: (760) 486-0765 > -- Neil Panjwani Duke University | B.S.E. 2010 Tel: (760) 486-0765 -- View this message in context: http://itk-users.7.n7.nabble.com/Simple-ITK-Python-not-working-on-Mac-El-Capitan-10-11-tp37265p37271.html Sent from the ITK - Users mailing list archive at Nabble.com. -------------- 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 javij1 at gmail.com Sat Jun 18 19:59:34 2016 From: javij1 at gmail.com (=?UTF-8?Q?Javier_Juan_Albarrac=c3=adn?=) Date: Sun, 19 Jun 2016 01:59:34 +0200 Subject: [ITK] [ITK-users] ImageI iterators same walk order simultaneously Message-ID: <3b8ffc92-0aeb-11ba-d4c1-a946ee8ee3c1@gmail.com> Hello, I want to traverse an image that points to an intra-cranial mask, and perform an operation on other image only in the voxels where the intra-cranial mask are true. I wrote the following code: itk::ImageRegionConstIterator iteratorMask(mask, mask->GetLargestPossibleRegion()); itk::ImageRegionIterator iteratorMap(map, map->GetLargestPossibleRegion()); iteratorMask.GoToBegin(); iteratorMap.GoToBegin(); while (!iteratorMask.IsAtEnd()) { if (iteratorMask.Get()) { iteratorMap.Set(i); ++i; } ++iteratorMask; ++iteratorMap; } My question is: can I be sure that, with this implementation both iterators point to the same voxel of the image simultaneously? Or should I use itk::ImageRegionConstIteratorWithIndex on "mask" and modify "map" through the "SetPixel" method? I have read that "SetPixel" and "GetPixel" methods are slow and not preferred against iterators. It is possible to implement this operation only with iterators? Thank you very much Regards. Javier. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 sg.ele.eng at gmail.com Sun Jun 19 22:22:47 2016 From: sg.ele.eng at gmail.com (Sara Gh) Date: Sun, 19 Jun 2016 22:22:47 -0400 Subject: [ITK] SimpleITK - Resizing MRI scan with slice thickness and slice gap parameters Message-ID: Hello experts, I have two MRI scans: axial (256x256x56) and coronal (68x256x256). For both of them, slice thickness and slice gap parameters are 2 and 1, respectively. I have re-arranged the coronal scan to be in the axial view. Therefore, the new coronal scan (with the axial view) is 256x256x68. Now, I am trying to use SimpleITK to resize/upsample both scans to 256x256x256. Considering *slice gap and slice thickness parameters*, how can I perform this 3D-resizing in SimpleITK? Thanks, Sara Gh -------------- next part -------------- An HTML attachment was scrubbed... URL: From tevain at telecom-paristech.fr Mon Jun 20 04:41:42 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Mon, 20 Jun 2016 10:41:42 +0200 (CEST) Subject: [ITK] [ITK-users] ImageI iterators same walk order simultaneously In-Reply-To: <3b8ffc92-0aeb-11ba-d4c1-a946ee8ee3c1@gmail.com> References: <3b8ffc92-0aeb-11ba-d4c1-a946ee8ee3c1@gmail.com> Message-ID: <166575769.10455174.1466412102217.JavaMail.zimbra@enst.fr> Hi Javier, You can use iterators to do so without problems, given that you ensure that: - The two images are in the same reference frame (i.e. axes represent the same directions in both). - The ImageRegions to parse are identical . Otherwise you will lose the correpondence between the images. HTH, Tim ----- Mail original ----- De: "Javier Juan Albarrac?n" ?: insight-users at itk.org Envoy?: Dimanche 19 Juin 2016 01:59:34 Objet: [ITK] [ITK-users] ImageI iterators same walk order simultaneously Hello, I want to traverse an image that points to an intra-cranial mask, and perform an operation on other image only in the voxels where the intra-cranial mask are true. I wrote the following code: itk::ImageRegionConstIterator iteratorMask(mask, mask->GetLargestPossibleRegion()); itk::ImageRegionIterator iteratorMap(map, map->GetLargestPossibleRegion()); iteratorMask.GoToBegin(); iteratorMap.GoToBegin(); while (!iteratorMask.IsAtEnd()) { if (iteratorMask.Get()) { iteratorMap.Set(i); ++i; } ++iteratorMask; ++iteratorMap; } My question is: can I be sure that, with this implementation both iterators point to the same voxel of the image simultaneously? Or should I use itk::ImageRegionConstIteratorWithIndex on "mask" and modify "map" through the "SetPixel" method? I have read that "SetPixel" and "GetPixel" methods are slow and not preferred against iterators. It is possible to implement this operation only with iterators? Thank you very much Regards. Javier. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 hebennink at gmail.com Mon Jun 20 09:49:58 2016 From: hebennink at gmail.com (Edwin Bennink) Date: Mon, 20 Jun 2016 15:49:58 +0200 Subject: [ITK] [ITK-users] WrapITK question: how to cast images with RGB or complex float pixel types to a Numpy array? Message-ID: Hello, I am searching for a way to access pixel data of unsigned char RGBPixel images and complex float images in Numpy through PyBuffer. I guess that it should be possible to cast these images to a vector type and access the data without copying, but I can't figure out how. PyBuffer doesn't support RGB or complex images, and it feels stupid to decompose and recompose into a vector image. What would be a neat solution to this problem? Thanks! Edwin Bennink -------------- 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 scapegoat.sarthak at gmail.com Mon Jun 20 10:31:59 2016 From: scapegoat.sarthak at gmail.com (Scapegoat Sarthak) Date: Mon, 20 Jun 2016 10:31:59 -0400 Subject: [ITK] [ITK-users] ResampleDICOM Assertion Error Message-ID: Hello All, I have been trying (unsuccessfully) to write a DICOM series with non-integer slopes. I have seen in an earlier community post (reference - http://public.kitware.com/pipermail/community/2014-September/007143.html) about the exact same issue and it is still not resolved (I am running version 4.9.0. Can someone from the moderators' side confirm in which version this has been taken care of (if at all)? Thanks, Sarthak -------------- 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 brad at lowekamp.net Mon Jun 20 10:57:25 2016 From: brad at lowekamp.net (Bradley Lowekamp) Date: Mon, 20 Jun 2016 10:57:25 -0400 Subject: [ITK] [ITK-dev] A couple critical patches for the release branch Message-ID: Hello, Can a couple critical patches for SimpleITK be merged into the release branch: commit 679b23d1513732b020fb04b7e28d69e3daaed833 Author: Bradley Lowekamp Date: Fri Jun 10 13:35:51 2016 -0400 COMP: Fix undefined NumericTraits::Zero and One errors with mingw64 This correct the preproces variable checked to be specific for Microsofts compiler. Change-Id: I67d295fef24b31b0ab24a8894565fbc249b39292 commit b177530b5d4ceab8097b3fb47376c433e09bfdc8 Author: Bradley Lowekamp Date: Thu May 26 11:34:50 2016 -0400 COMP: Address VS9 ambiguous std::abs call in Haung calculator When using 64-bit indexes with MS Visual Studio 9, std::abs of __int64 is not implemented. We use the concise tri-nary operator to implement abs. Change-Id: I91bb0878f8289144de7ddc61c01f44a0f58ca962 Thanks! Brad -------------- 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 shawn.sa.zhang at gmail.com Mon Jun 20 11:05:51 2016 From: shawn.sa.zhang at gmail.com (Shawn SA Zhang) Date: Mon, 20 Jun 2016 11:05:51 -0400 Subject: [ITK] ITK MorphologicalWatershed failed on simple test image Message-ID: <033801d1cb05$3cb98040$b62c80c0$@gmail.com> Hi Dear fellow ITK/SimpleITK developers, I encountered a strange issue where the attached simple test image fails in MorphologicalWatershed filter. The following python code produces an image with all "1"s, using the attached input_inv.vtk file. Import SimpleITK as sitk input_inv = sitk.ReadImage("input_inv.vtk") input_watershed = sitk.MorphologicalWatershed(input_inv) sitk.WriteImage(input_watershed, "input_watershed.vtk") For quick diagnosis, I attached the visualization of the input_inv.vtk file. Any suggestion will be greatly appreciated. Many thanks for your attention and help! -Shawn Independent Image Processing Consultant -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: input_inv.vtk Type: application/octet-stream Size: 147838 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: input_visualization.png Type: image/png Size: 11301 bytes Desc: not available URL: From blowekamp at mail.nih.gov Mon Jun 20 11:12:27 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Mon, 20 Jun 2016 15:12:27 +0000 Subject: [ITK] SimpleITK - Resizing MRI scan with slice thickness and slice gap parameters In-Reply-To: References: Message-ID: <58981452-D9C9-4E16-8F42-6CF989F9E370@mail.nih.gov> Hello, I am not sure what you mean by you ?re-arranged the coronal scan to be in the axial view?. I hope you did it in a way to preserve the meta-data and the direction cosine matrix. You should be able to do this all in what step with the resample filter. You need to use the input?s direction matrix for the OutputDirection of the resample filter. Next set the OutputSize, and then correctly calculate the OutputSpacing so that the result has the same physical extent as the input. If you need further help, perhaps sharing a snip-it of code would help. HTH, Brad On Jun 19, 2016, at 10:22 PM, Sara Gh > wrote: Hello experts, I have two MRI scans: axial (256x256x56) and coronal (68x256x256). For both of them, slice thickness and slice gap parameters are 2 and 1, respectively. I have re-arranged the coronal scan to be in the axial view. Therefore, the new coronal scan (with the axial view) is 256x256x68. Now, I am trying to use SimpleITK to resize/upsample both scans to 256x256x256. Considering slice gap and slice thickness parameters, how can I perform this 3D-resizing in SimpleITK? Thanks, Sara Gh _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Mon Jun 20 11:18:24 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Mon, 20 Jun 2016 15:18:24 +0000 Subject: [ITK] [ITK-users] WrapITK question: how to cast images with RGB or complex float pixel types to a Numpy array? In-Reply-To: References: Message-ID: <0E306F74-4017-4F1F-BFE4-CD0624909082@mail.nih.gov> Hello, In C++ ITK I would just use the CastImageFilter inplace to convert from RGBPixel to a vector type. But that doesn?t seemed to be wrapped: https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Filtering/ImageFilterBase/wrapping/itkCastImageFilter.wrap I would look into extending the pyBuffer to support the RGBPixel type: https://github.com/tobiasmaier/itkPyBuffer/blob/master/wrapping/itkPyBuffer.wrap There should be some information documenting this in the ITK software guide: https://itk.org/ITK/help/documentation.html HTH, Brad On Jun 20, 2016, at 9:49 AM, Edwin Bennink > wrote: Hello, I am searching for a way to access pixel data of unsigned char RGBPixel images and complex float images in Numpy through PyBuffer. I guess that it should be possible to cast these images to a vector type and access the data without copying, but I can't figure out how. PyBuffer doesn't support RGB or complex images, and it feels stupid to decompose and recompose into a vector image. What would be a neat solution to this problem? Thanks! Edwin Bennink _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 blowekamp at mail.nih.gov Mon Jun 20 11:25:17 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Mon, 20 Jun 2016 15:25:17 +0000 Subject: [ITK] ITK MorphologicalWatershed failed on simple test image In-Reply-To: <033801d1cb05$3cb98040$b62c80c0$@gmail.com> References: <033801d1cb05$3cb98040$b62c80c0$@gmail.com> Message-ID: <87D56173-1C08-4F56-B388-C6BC62F7AFA0@mail.nih.gov> Hello, I think your expectations for the algorithm are not correct. Here is a Jupyter notebooks which may help: http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/32_Watersheds_Segmentation.html The input to the algorithms is expected to be a ?feature? image, which is usually and edge map, or a distance field. I think you are trying to run a ?binary watershed? algorithm as opposed to a ?grayscale watershed? algorithm, so a distance field is likely what you want. There should be plenty of information out there about this common algorithm and different way to use it. HTH, Brad On Jun 20, 2016, at 11:05 AM, Shawn SA Zhang > wrote: Hi Dear fellow ITK/SimpleITK developers, I encountered a strange issue where the attached simple test image fails in MorphologicalWatershed filter. The following python code produces an image with all ?1?s, using the attached input_inv.vtk file. Import SimpleITK as sitk input_inv = sitk.ReadImage(?input_inv.vtk?) input_watershed = sitk.MorphologicalWatershed(input_inv) sitk.WriteImage(input_watershed, "input_watershed.vtk") For quick diagnosis, I attached the visualization of the input_inv.vtk file. Any suggestion will be greatly appreciated. Many thanks for your attention and help! -Shawn Independent Image Processing Consultant _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Tue Jun 21 08:48:16 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Tue, 21 Jun 2016 12:48:16 +0000 Subject: [ITK] [ITK-dev] A couple critical patches for the release branch In-Reply-To: References: Message-ID: Hello, Can these patches pleased be merged into the release branch. Thanks, Brad On Jun 20, 2016, at 10:57 AM, Bradley Lowekamp > wrote: Hello, Can a couple critical patches for SimpleITK be merged into the release branch: commit 679b23d1513732b020fb04b7e28d69e3daaed833 Author: Bradley Lowekamp > Date: Fri Jun 10 13:35:51 2016 -0400 COMP: Fix undefined NumericTraits::Zero and One errors with mingw64 This correct the preproces variable checked to be specific for Microsofts compiler. Change-Id: I67d295fef24b31b0ab24a8894565fbc249b39292 commit b177530b5d4ceab8097b3fb47376c433e09bfdc8 Author: Bradley Lowekamp > Date: Thu May 26 11:34:50 2016 -0400 COMP: Address VS9 ambiguous std::abs call in Haung calculator When using 64-bit indexes with MS Visual Studio 9, std::abs of __int64 is not implemented. We use the concise tri-nary operator to implement abs. Change-Id: I91bb0878f8289144de7ddc61c01f44a0f58ca962 Thanks! Brad _______________________________________________ Powered by www.kitware.com 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 _______________________________________________ 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://kitware.com/products/protraining.php Please keep messages on-topic and check 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 kolin9105 at gmail.com Tue Jun 21 11:52:31 2016 From: kolin9105 at gmail.com (meikolin saimara) Date: Tue, 21 Jun 2016 22:52:31 +0700 Subject: [ITK] [ITK-users] help me Message-ID: hello everyone.. I need your help. I am a beginner in itk and I need confidence connected for my riset. now I am very confused about a function SeedX and SeedY in confidence connected. can you give what is the usefulness of SeedX and SeedY because when I set Seed X and seed Y in confidence connected segmentation the picture would be change. -------------- 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 sg.ele.eng at gmail.com Tue Jun 21 14:29:05 2016 From: sg.ele.eng at gmail.com (Sara Gh) Date: Tue, 21 Jun 2016 14:29:05 -0400 Subject: [ITK] SimpleITK - Resizing MRI scan with slice thickness and slice gap parameters In-Reply-To: <58981452-D9C9-4E16-8F42-6CF989F9E370@mail.nih.gov> References: <58981452-D9C9-4E16-8F42-6CF989F9E370@mail.nih.gov> Message-ID: Dear Brad, Thank you for your time and helpful email. Here is my edited code for the first part which tries to resmaple Coronal image using the direction of Axial image: # imageA : Axial MRI scan, size : 256x256x56 , spacing: 1,1,3, slice gap : 1 # imageC : Coronal MRI scan, size : 256x256x68 , spacing: 1,1,3, slice gap : 1 resample = sitk.ResampleImageFilter() resample.SetReferenceImage(imageC) resample.SetOutputDirection(imageA.GetDirection()) resample.SetOutputOrigin(imageA.GetOrigin()) imageCA = resample.Execute(imageC) sitk.Show(imageCA) # imageCA: size : 256x256x68 I believe I have missed something here because the size of resampled coronal image (imageCA) should be 68x256x256. Should I change the OutputSpacing to [3,1,1]? For resizing the imageCA considering slice thickness and slice gap parameters, should I use something like "resample.SetSize([256,256,256)"? How should I calculate and specify OutputSpacing? Best regards, Sara On Mon, Jun 20, 2016 at 11:12 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] < blowekamp at mail.nih.gov> wrote: > Hello, > > I am not sure what you mean by you ?re-arranged the coronal scan to be in > the axial view?. I hope you did it in a way to preserve the meta-data and > the direction cosine matrix. You should be able to do this all in what step > with the resample filter. > > You need to use the input?s direction matrix for the OutputDirection of > the resample filter. Next set the OutputSize, and then correctly calculate > the OutputSpacing so that the result has the same physical extent as the > input. > > If you need further help, perhaps sharing a snip-it of code would help. > > HTH, > Brad > > On Jun 19, 2016, at 10:22 PM, Sara Gh wrote: > > Hello experts, > > I have two MRI scans: axial (256x256x56) and coronal (68x256x256). For > both of them, slice thickness and slice gap parameters are 2 and 1, > respectively. > I have re-arranged the coronal scan to be in the axial view. Therefore, > the new coronal scan (with the axial view) is 256x256x68. > Now, I am trying to use SimpleITK to resize/upsample both scans to > 256x256x256. Considering *slice gap and slice thickness parameters*, how > can I perform this 3D-resizing in SimpleITK? > > Thanks, > Sara Gh > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.paik at elucidbio.com Tue Jun 21 15:15:32 2016 From: david.paik at elucidbio.com (David S. Paik (Elucid Bioimaging)) Date: Tue, 21 Jun 2016 19:15:32 +0000 Subject: [ITK] Level Sets v4 CFL calculation Message-ID: <67143F71-E5EF-4CC8-949A-D2EDA835124D@elucidbio.com> I am going through the level sets v4 code and finding different areas of the code that appear to be dead cruft yet still in the code making understanding of the code difficult for a new comer. LevelSetEquationTermContainer (which represents a single equation), stores its CFL contributions in a std::map for each term. No problem. However, LevelSetEquationTermBase also has m_CFLContribution which is set to zero (in constructor and SetUp) and no other code seems to ever change. So I?m guessing that in this class, it is some leftover dead code but it makes the code very confusing if you happen to start looking at this class first. But much more seriously, in LevelSetEvolution::ComputeTimeStepForNextiteration specialized for LevelSetDenseImage (itkLevelSetEvolution.hxx line 128-130), there are the following two lines: LevelSetOutputRealType contribution = this->m_EquationContainer->ComputeCFLContribution(); contribution = 1; This negates the whole CFL computation and instead chooses a totally arbitrary value. Perhaps this was accidentally left in the code? I seem to recall seeing something similar in the v3 level set framework. If the true value was actually larger, this can lead to too large a time step and thus severe numerical instability. Does anybody who maintains any of the level set v4 code read this? Is there anybody I should be contacting directly? David From jhlegarreta at vicomtech.org Tue Jun 21 17:19:47 2016 From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta) Date: Tue, 21 Jun 2016 23:19:47 +0200 Subject: [ITK] [ITK-users] help me In-Reply-To: References: Message-ID: Hi Miekolin, the itk::ConfidenceConnectedImageFilter [1] (if that is the one you are using) requires a seed (or point inside the structure of interest in your image) to start developing its segmentation algorihm. Having a look at the implementation itself [2], there are no such SeedX or SeedY functions, but rather one named SetSeed, which makes sense given that ITK is a toolkit to deal with N-dimensional images. Reading the software guide [3] is a must when beginning to work with ITK. The filter you are supposedly using is explained in section 4.1.4, p.354. HTH JON HAITZ [1] https://itk.org/Doxygen/html/classitk_1_1ConfidenceConnectedImageFilter.html [2] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Segmentation/RegionGrowing/include/itkConfidenceConnectedImageFilter.hxx [3] https://itk.org/ItkSoftwareGuide.pdf _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 marco.giord at gmail.com Wed Jun 22 04:38:06 2016 From: marco.giord at gmail.com (marco giordano) Date: Wed, 22 Jun 2016 10:38:06 +0200 Subject: [ITK] [ITK-users] Read 4D CT cardiac dicom series and save it as a single 4D nifti file In-Reply-To: References: <1465484786789-7588963.post@n2.nabble.com> Message-ID: Dear Andras, all, I did try with 3D Slicer but the 4D sequence is not loaded correctly (slices are not loaded in the right order). One issue that I see is that each Dicom series is actually a semi-volume (e.g. the upper or lower part of a volume) thus it requires some merging of the data before writing. I am writing some code even though I thought there would be more examples of similar import routine developed in the past. I will keep you posted if i make any progress regards 2016-06-11 6:25 GMT+02:00 Andras Lasso : > 3D Slicer can load some 4D CTs a 3D+t sequence and you cab save it as a 4D > nrrd. You may give it a try. If it doesn't work for your sequence then > report the problem on the slicer-users mailing list. If you can provide a > sample data set then slicer developers most likely will be able to make it > work. > > > > Andras > > > > *From: *marco giordano > *Sent: *June 10, 2016 17:32 > *To: *Scapegoat Sarthak > *Cc: *insight-users at itk.org > *Subject: *Re: [ITK] [ITK-users] Read 4D CT cardiac dicom series and save > it as a single 4D nifti file > > > Hi there, > > Thanks for the suggestions. VV is not really an option since I have to > analyze many cases. I even tried to use VV but it gives me the wrong order > of the slices. > > I am trying the "itk::ImageSeriesReader" (right?) but it is complaining > that "Position is not unique". I think it refers to the fact that the > slices in my "series" have the "same location". Not sure this is meant to > transform 2D into 4D if it expects different locations, maybe it is for 2D > into 3D. Any idea? > > Regards > > 2016-06-09 17:21 GMT+02:00 Scapegoat Sarthak > : > >> You can do it pretty easily: >> >> Read DICOM using SeriesFileReader and then connect output to a FileWriter >> with the file name of your choice (in this case, it would be >> "output.nii.gz"). >> >> >> On 9 June 2016 at 11:06, Mohammad Varasteh wrote: >> >>> Dear Marco, >>> >>> Actually I do not know how to do it in the ITK but for such cases (if it >>> is >>> few cases) I normally use "VV: the 4D slicer". You can find it in the >>> following link: >>> >>> http://www.creatis.insa-lyon.fr/rio/vv >>> >>> I hope this will be of some use. >>> >>> Varasteh >>> >>> >>> >>> -- >>> View this message in context: >>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Read-4D-CT-cardiac-dicom-series-and-save-it-as-a-single-4D-nifti-file-tp7588962p7588963.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 >> >> > > > -- > Marco Giordano > SKYPE:marcogiord81 > -- Marco Giordano SKYPE:marcogiord81 -------------- 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 Jun 22 06:30:47 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 22 Jun 2016 12:30:47 +0200 Subject: [ITK] Redudancy in LevelSetBase hierarchy In-Reply-To: <7B2A0371-4D8A-473C-B201-54267261DA68@elucidbio.com> References: <7B2A0371-4D8A-473C-B201-54267261DA68@elucidbio.com> Message-ID: Hans, I think you were involved with refactoring registration framework for V4. Can you pitch in? Regards On Sat, Jun 11, 2016 at 1:24 AM, David S. Paik (Elucid Bioimaging) < david.paik at elucidbio.com> wrote: > I am going through the level set v4 classes in 4.9.1 and I noticed a few > things. > > In itk::LevelSetBase > > - EvaluateMeanCurvature( const InputType& iP ) is declared pure virtual > (.h line 75) but a definition is provided (.hxx line 88). While > syntactically permissible, this seems more likely an oversight rather than > an intentional design. (see below) > > - Both versions of EvaluateLaplacian are pure virtual even though they > could be computed at this point in the hierarchy as the trace of the > Hessian matrix. This is analogous to how EvaluateGradientNorm is > calculated even though EvaluateGradient is still pure virtual in this > class. (see below) > > > In itk::DiscreteLevelSetImage > > - EvaluateLaplacian (both versions) do their own redundant calculation of > second derivatives even though they may have already been calculated in the > Hessian matrix. There?s probably a design tradeoff between redundantly > computing the Laplacian (as it is now) vs. Laplacian triggering a full > Hessian computation even if the off diagonal elements of the Hessian are > not used. One possibility is to check to see if Hessian has been computed > and if so use it but not trigger a full Hessian computation. > > - EvaluateMeanCurvature (both versions) override itk::LevelSetBase?s > version but they appear to be exactly the same. The virtual function calls > should work from the base class. Not a bug but this seems to be an > unnecessary redundancy. Am I missing something? > > > David > > _______________________________________________ > 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 Wed Jun 22 06:33:41 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 22 Jun 2016 12:33:41 +0200 Subject: [ITK] [ITK-users] Fast image creation from a signed distance function In-Reply-To: <1465984814443-7588969.post@n2.nabble.com> References: <1465984814443-7588969.post@n2.nabble.com> Message-ID: Hi Yurii, if you can provide 0 level pixels, the rest can be computed using e.g. Maurer filter. Regards On Wed, Jun 15, 2016 at 12:00 PM, Yurii Borokh wrote: > Hi all,I'm searching for a filter that could effectively create an image > from > a signed distance function.Of course, it can be done straightforwardly by > calculation of distance in each pixel. But I would like to minimize the > number of calls to distance function since it's implemented via RBF and > calls are rather expensive. Does ITK has some kind of such > functionality?Any > hints would be appreciated.Regards,Yurii > > > > -- > View this message in context: > http://itk-insight-users.2283740.n2.nabble.com/Fast-image-creation-from-a-signed-distance-function-tp7588969.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 > _______________________________________________ > 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 dzenanz at gmail.com Wed Jun 22 06:46:05 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 22 Jun 2016 12:46:05 +0200 Subject: [ITK] [ITK-users] Licensing question In-Reply-To: <1039149860.11159873.1466490799507.JavaMail.yahoo@mail.yahoo.com> References: <1039149860.11159873.1466490799507.JavaMail.yahoo.ref@mail.yahoo.com> <1039149860.11159873.1466490799507.JavaMail.yahoo@mail.yahoo.com> Message-ID: TL;DR version: http://www.apache.org/foundation/license-faq.html#WhatDoesItMEAN Regards, D?enan On Tue, Jun 21, 2016 at 8:33 AM, Malsoaz James via Insight-users < insight-users at itk.org> wrote: > Hi, > > I would like to use ITK in a commercial application but I have some > questions about the Apache2 license. > Should I include somewhere the ITK copyright in my application? In source > code? In related documents? > > Currently I'm using version 4.8. I made minor modifications in source file > of ITK to fit my needs. Should I publish these changes? > > Thank you for your answer. > Best regards, > > James > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 david.paik at elucidbio.com Wed Jun 22 10:57:15 2016 From: david.paik at elucidbio.com (David S. Paik (Elucid Bioimaging)) Date: Wed, 22 Jun 2016 14:57:15 +0000 Subject: [ITK] Redudancy in LevelSetBase hierarchy In-Reply-To: References: <7B2A0371-4D8A-473C-B201-54267261DA68@elucidbio.com> Message-ID: D?enan, Thank you for your response! Although it really is more the level set segmentation framework for V4 that this applies to. If either of you can point me to someone who?s done work on that, it?d be appreciated. Thanks! David On Jun 22, 2016, at 3:30 AM, D?enan Zuki? > wrote: Hans, I think you were involved with refactoring registration framework for V4. Can you pitch in? Regards On Sat, Jun 11, 2016 at 1:24 AM, David S. Paik (Elucid Bioimaging) > wrote: I am going through the level set v4 classes in 4.9.1 and I noticed a few things. In itk::LevelSetBase - EvaluateMeanCurvature( const InputType& iP ) is declared pure virtual (.h line 75) but a definition is provided (.hxx line 88). While syntactically permissible, this seems more likely an oversight rather than an intentional design. (see below) - Both versions of EvaluateLaplacian are pure virtual even though they could be computed at this point in the hierarchy as the trace of the Hessian matrix. This is analogous to how EvaluateGradientNorm is calculated even though EvaluateGradient is still pure virtual in this class. (see below) In itk::DiscreteLevelSetImage - EvaluateLaplacian (both versions) do their own redundant calculation of second derivatives even though they may have already been calculated in the Hessian matrix. There?s probably a design tradeoff between redundantly computing the Laplacian (as it is now) vs. Laplacian triggering a full Hessian computation even if the off diagonal elements of the Hessian are not used. One possibility is to check to see if Hessian has been computed and if so use it but not trigger a full Hessian computation. - EvaluateMeanCurvature (both versions) override itk::LevelSetBase?s version but they appear to be exactly the same. The virtual function calls should work from the base class. Not a bug but this seems to be an unnecessary redundancy. Am I missing something? David _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From shrikantvc at gmail.com Wed Jun 22 11:50:48 2016 From: shrikantvc at gmail.com (shrikant) Date: Wed, 22 Jun 2016 08:50:48 -0700 (MST) Subject: [ITK] [ITK-users] image registration in MATALAB vs ITK. Message-ID: <1466610648735-7588990.post@n2.nabble.com> Hi, I am new to ITK, i have working MATLAB registration as a below code. Please note that here I am registering fixed image with high features and moving image with very low signal. [optimizer,metric]=imregconfig('multimodal'); tr1 = imregtform(movingImage, fixedImageResized, 'translation', optimizer, metric); I need to convert into ITK 4 code. I am using below ITK code typedef itk::ImageRegistrationMethodv4 RegistrationType; RegistrationType::Pointer registration = RegistrationType::New(); RegistrationType::ShrinkFactorsArrayType shrinkFactorsPerLevel; RegistrationType::SmoothingSigmasArrayType smoothingSigmasPerLevel; MetricType::Pointer metric = MetricType::New(); metric->SetNumberOfHistogramBins(50); metric->SetUseMovingImageGradientFilter(true); metric->SetUseFixedImageGradientFilter(true); registration->SetMetric(metric); RSGDOptimizerType::Pointer smartOptimizer = RSGDOptimizerType::New(); smartOptimizer->SetLearningRate(0.5); smartOptimizer->SetMaximumStepSizeInPhysicalUnits(0.001); smartOptimizer->SetMinimumStepLength(0.0001); smartOptimizer->SetNumberOfIterations(100); smartOptimizer->ReturnBestParametersAndValueOn(); smartOptimizer->SetRelaxationFactor(0.5); registration->SetOptimizer(smartOptimizer); registration->SetNumberOfLevels(1); shrinkFactorsPerLevel.SetSize(1); shrinkFactorsPerLevel[0] = 1; registration->SetShrinkFactorsPerLevel(shrinkFactorsPerLevel); smoothingSigmasPerLevel.SetSize(1); smoothingSigmasPerLevel[0] = 0; registration->SetSmoothingSigmasPerLevel(smoothingSigmasPerLevel); registration->SetMetricSamplingStrategy(RegistrationType::REGULAR); registration->SetMetricSamplingPercentage(100); registration->Update(); TransformType::ParametersType finalParameters = registration->GetOutput()->Get()->GetParameters(); yTranslation = finalParameters[1]; Here I am getting huge differences like, -0.33 (ITK) vs -1.20(MATLAB) mm. If I see visually then matlab results look more correct. Any idea what is going wrong here? Any help would be highly appreciated. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/image-registration-in-MATALAB-vs-ITK-tp7588990.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 chinander at gmail.com Wed Jun 22 13:40:11 2016 From: chinander at gmail.com (Mike Chinander) Date: Wed, 22 Jun 2016 12:40:11 -0500 Subject: [ITK] [ITK-users] Wrap new filter for CSharp Message-ID: Are the instructions here [1] applicable to wrapping filters for CSharp? I'd like to use the SiddonJacobsRayCastInterpolateImageFunction in C# from a SimpleITK Superbuild. Thanks, --Mike Chinander [1] https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch9.html#x50-1500009.5 -------------- 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 dan.muel at gmail.com Wed Jun 22 23:27:36 2016 From: dan.muel at gmail.com (Dan Mueller) Date: Thu, 23 Jun 2016 12:57:36 +0930 Subject: [ITK] [ITK-users] Wrap new filter for CSharp In-Reply-To: References: Message-ID: Hi Mike, No, the link you reference is for ITK wrappers, not SimpleITK (ITK and SimpleITK are different -- SimpleITK is built on top of ITK). If you want to wrap this filter in SimpleITK, the following links may be helpful: https://itk.org/SimpleITKDoxygen/html/FilterTemplatesPage.html http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874546/ Cheers, Dan On 23 Jun 2016 3:10 am, "Mike Chinander" wrote: > Are the instructions here [1] applicable to wrapping filters for CSharp? > I'd like to use the SiddonJacobsRayCastInterpolateImageFunction in C# from > a SimpleITK Superbuild. > > Thanks, > > --Mike Chinander > > [1] > https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch9.html#x50-1500009.5 > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 Francois.GIRINON at ensam.eu Thu Jun 23 05:55:36 2016 From: Francois.GIRINON at ensam.eu (Francois.GIRINON at ensam.eu) Date: Thu, 23 Jun 2016 09:55:36 +0000 Subject: [ITK] update dynamically images in the registration pipeline Message-ID: Hello everyone, I'd like to suit the registration pipeline to a particular use: 1) I have two fixed target images 2) I have an itk transform which generates an itk mesh, and from this mesh two images are dynamically generated 3) Using the metric methods of ITK I want to optimize the above transform parameters to minimize the metric As a matter of fact, I don't really need any interpolation method since the generated images already have the same resolution and size. However I can still use a nearest-neighbor interpolation if required. The real question is where and how to update the dynamically generated images ? One of my ideas was to create a kind of wrapper like https://itk.org/Doxygen/html/classitk_1_1ObjectToObjectMultiMetricv4.html and starting the GetValue method with an update of my images. The problem is more about the GetValueAndDerivative which I guess tries to evaluate the metric for closest parameters values. I don't know here where should I put my update method. Thanks! Fran?ois. From tevain at telecom-paristech.fr Thu Jun 23 07:37:28 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Thu, 23 Jun 2016 13:37:28 +0200 (CEST) Subject: [ITK] update dynamically images in the registration pipeline In-Reply-To: References: Message-ID: <462815471.13619268.1466681848742.JavaMail.zimbra@enst.fr> Hello Fran?ois, One solution for you could be to create your own cost function to optimize through an itk optimizer. In your case, the comparison between the two mesh-based images and fixed images seems quite easy so you should be able to have a single-valued cost function. You can find examples of custom CFs in the optimizers tests, like here : https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Numerics/Optimizers/test/itkRegularStepGradientDescentOptimizerTest.cxx It basically consist in redefining the GetValue and GetDerivative methods, the later being used in some optimizers which need access to derivatives (like the gradient descent). Then, you just have to plug this custom function to an ordinary itk optimization pipeline to get your best transformation. HTH, Tim ----- Mail original ----- De: "Francois GIRINON" ?: community at itk.org Envoy?: Jeudi 23 Juin 2016 11:55:36 Objet: [ITK] update dynamically images in the registration pipeline Hello everyone, I'd like to suit the registration pipeline to a particular use: 1) I have two fixed target images 2) I have an itk transform which generates an itk mesh, and from this mesh two images are dynamically generated 3) Using the metric methods of ITK I want to optimize the above transform parameters to minimize the metric As a matter of fact, I don't really need any interpolation method since the generated images already have the same resolution and size. However I can still use a nearest-neighbor interpolation if required. The real question is where and how to update the dynamically generated images ? One of my ideas was to create a kind of wrapper like https://itk.org/Doxygen/html/classitk_1_1ObjectToObjectMultiMetricv4.html and starting the GetValue method with an update of my images. The problem is more about the GetValueAndDerivative which I guess tries to evaluate the metric for closest parameters values. I don't know here where should I put my update method. Thanks! Fran?ois. _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From marco.giord at gmail.com Thu Jun 23 09:15:44 2016 From: marco.giord at gmail.com (marco giordano) Date: Thu, 23 Jun 2016 15:15:44 +0200 Subject: [ITK] [ITK-users] Read 4D CT cardiac dicom series and save it as a single 4D nifti file In-Reply-To: References: <1465484786789-7588963.post@n2.nabble.com> Message-ID: Hi there, I managed to read the 4D CT cardiac dataset by importing each volume separately and writing it in a 4D image with an iterator. It assumes the origin of the first series is the correct one. With some adaptations it can read also semi-volumes and stitch them together (still in progress) .I share the routine here, maybe it is useful to someone: https://github.com/marcogiord/esercizi/blob/master/itk/DicomRead4DTimeSeries_SingleDicomVolumes.cpp Marco -------------- 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 Thu Jun 23 09:56:34 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 23 Jun 2016 13:56:34 +0000 Subject: [ITK] [ITK-dev] A couple critical patches for the release branch In-Reply-To: References: Message-ID: <854C012C-E5E9-4EB5-8E02-A10811EEC51A@mail.nih.gov> Can someone please help me by merging these patches into the ITK release branch? Thanks! Brad On Jun 21, 2016, at 8:48 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] > wrote: Hello, Can these patches pleased be merged into the release branch. Thanks, Brad On Jun 20, 2016, at 10:57 AM, Bradley Lowekamp > wrote: Hello, Can a couple critical patches for SimpleITK be merged into the release branch: commit 679b23d1513732b020fb04b7e28d69e3daaed833 Author: Bradley Lowekamp > Date: Fri Jun 10 13:35:51 2016 -0400 COMP: Fix undefined NumericTraits::Zero and One errors with mingw64 This correct the preproces variable checked to be specific for Microsofts compiler. Change-Id: I67d295fef24b31b0ab24a8894565fbc249b39292 commit b177530b5d4ceab8097b3fb47376c433e09bfdc8 Author: Bradley Lowekamp > Date: Thu May 26 11:34:50 2016 -0400 COMP: Address VS9 ambiguous std::abs call in Haung calculator When using 64-bit indexes with MS Visual Studio 9, std::abs of __int64 is not implemented. We use the concise tri-nary operator to implement abs. Change-Id: I91bb0878f8289144de7ddc61c01f44a0f58ca962 Thanks! Brad _______________________________________________ Powered by www.kitware.com 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 _______________________________________________ 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://kitware.com/products/protraining.php Please keep messages on-topic and check 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 brad.king at kitware.com Thu Jun 23 10:10:25 2016 From: brad.king at kitware.com (Brad King) Date: Thu, 23 Jun 2016 10:10:25 -0400 Subject: [ITK] [ITK-dev] A couple critical patches for the release branch In-Reply-To: <854C012C-E5E9-4EB5-8E02-A10811EEC51A@mail.nih.gov> References: <854C012C-E5E9-4EB5-8E02-A10811EEC51A@mail.nih.gov> Message-ID: <576BEDD1.3030900@kitware.com> On 06/23/2016 09:56 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote: > Can someone please help me by merging these patches into the ITK release branch? Done. Sorry for the delay. Your previous messages seemed to be about SimpleITK rather than ITK. -Brad K _______________________________________________ Powered by www.kitware.com 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 blowekamp at mail.nih.gov Thu Jun 23 10:13:21 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 23 Jun 2016 14:13:21 +0000 Subject: [ITK] [ITK-dev] A couple critical patches for the release branch In-Reply-To: <576BEDD1.3030900@kitware.com> References: <854C012C-E5E9-4EB5-8E02-A10811EEC51A@mail.nih.gov> <576BEDD1.3030900@kitware.com> Message-ID: Thank you very much! I thought that might have been a source of confusion when I re-read the original message. Brad > On Jun 23, 2016, at 10:10 AM, Brad King wrote: > > On 06/23/2016 09:56 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote: >> Can someone please help me by merging these patches into the ITK release branch? > > Done. Sorry for the delay. Your previous messages seemed to be > about SimpleITK rather than ITK. > > -Brad K > _______________________________________________ Powered by www.kitware.com 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 blowekamp at mail.nih.gov Thu Jun 23 10:21:44 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Thu, 23 Jun 2016 14:21:44 +0000 Subject: [ITK] [ITK-users] image registration in MATALAB vs ITK. In-Reply-To: <1466610648735-7588990.post@n2.nabble.com> References: <1466610648735-7588990.post@n2.nabble.com> Message-ID: Hello, One key feature of ITK is that is does just about everything with respect to physical space, as opposed to considering things just a matrix of numbers. This can make setting up the parameters data dependent and tricker. There is the scales estimator which can be used to help certain aspects of this [1], but this then interacts with your learning rate. Also make sure to use the callbacks to print the parameters and metric value during the optimization [2]. You need to study the optimization process and algorithm to determine why its not covering correctly. HTH, Brad [1] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/RegistrationITKv4/ImageRegistration1.cxx#L442-L450 [2] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Examples/RegistrationITKv4/ImageRegistration1.cxx#L469-L471 > On Jun 22, 2016, at 11:50 AM, shrikant wrote: > > Hi, > > I am new to ITK, i have working MATLAB registration as a below code. Please > note that here I am registering fixed image with high features and moving > image with very low signal. > > [optimizer,metric]=imregconfig('multimodal'); > tr1 = imregtform(movingImage, fixedImageResized, 'translation', optimizer, > metric); > > I need to convert into ITK 4 code. I am using below ITK code > > typedef itk::ImageRegistrationMethodv4 TransformType> RegistrationType; > RegistrationType::Pointer registration = RegistrationType::New(); > RegistrationType::ShrinkFactorsArrayType shrinkFactorsPerLevel; > RegistrationType::SmoothingSigmasArrayType smoothingSigmasPerLevel; > MetricType::Pointer metric = MetricType::New(); > > metric->SetNumberOfHistogramBins(50); > metric->SetUseMovingImageGradientFilter(true); > metric->SetUseFixedImageGradientFilter(true); > registration->SetMetric(metric); > > > RSGDOptimizerType::Pointer smartOptimizer = RSGDOptimizerType::New(); > smartOptimizer->SetLearningRate(0.5); > smartOptimizer->SetMaximumStepSizeInPhysicalUnits(0.001); > smartOptimizer->SetMinimumStepLength(0.0001); > smartOptimizer->SetNumberOfIterations(100); > smartOptimizer->ReturnBestParametersAndValueOn(); > smartOptimizer->SetRelaxationFactor(0.5); > registration->SetOptimizer(smartOptimizer); > > > registration->SetNumberOfLevels(1); > > shrinkFactorsPerLevel.SetSize(1); > shrinkFactorsPerLevel[0] = 1; > registration->SetShrinkFactorsPerLevel(shrinkFactorsPerLevel); > smoothingSigmasPerLevel.SetSize(1); > smoothingSigmasPerLevel[0] = 0; > registration->SetSmoothingSigmasPerLevel(smoothingSigmasPerLevel); > > > registration->SetMetricSamplingStrategy(RegistrationType::REGULAR); > registration->SetMetricSamplingPercentage(100); > > registration->Update(); > > TransformType::ParametersType finalParameters = > registration->GetOutput()->Get()->GetParameters(); > yTranslation = finalParameters[1]; > > Here I am getting huge differences like, -0.33 (ITK) vs -1.20(MATLAB) mm. If > I see visually then matlab results look more correct. > > Any idea what is going wrong here? > > Any help would be highly appreciated. > > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/image-registration-in-MATALAB-vs-ITK-tp7588990.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 tevain at telecom-paristech.fr Fri Jun 24 04:08:53 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Fri, 24 Jun 2016 10:08:53 +0200 (CEST) Subject: [ITK] update dynamically images in the registration pipeline In-Reply-To: References: Message-ID: <669536405.14264375.1466755733048.JavaMail.zimbra@enst.fr> Since I do not know what is your cost function, I can't really help you. >From a generic point of view, you should compute the partial derivative of the cost function for each parameter. Tim ----- Mail original ----- De: "Francois GIRINON" ?: tevain at telecom-paristech.fr Envoy?: Jeudi 23 Juin 2016 18:52:29 Objet: RE:[ITK] update dynamically images in the registration pipeline Hello Tim, I'm finally following your advice. I'm writing a specific costFunction class with a new registration pipeline : itkPointSetToMultiImagesRegistrationMethod. I thought the derivative in the metric classes was approximated which is not. Do you know any way to approximate it by the way ? Thanks for your help. ________________________________________ De : Timothee Evain [tevain at telecom-paristech.fr] Envoy? : jeudi 23 juin 2016 13:37 ? : GIRINON Fran?ois Cc : community at itk.org Objet : Re: [ITK] update dynamically images in the registration pipeline Hello Fran?ois, One solution for you could be to create your own cost function to optimize through an itk optimizer. In your case, the comparison between the two mesh-based images and fixed images seems quite easy so you should be able to have a single-valued cost function. You can find examples of custom CFs in the optimizers tests, like here : https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Numerics/Optimizers/test/itkRegularStepGradientDescentOptimizerTest.cxx It basically consist in redefining the GetValue and GetDerivative methods, the later being used in some optimizers which need access to derivatives (like the gradient descent). Then, you just have to plug this custom function to an ordinary itk optimization pipeline to get your best transformation. HTH, Tim ----- Mail original ----- De: "Francois GIRINON" ?: community at itk.org Envoy?: Jeudi 23 Juin 2016 11:55:36 Objet: [ITK] update dynamically images in the registration pipeline Hello everyone, I'd like to suit the registration pipeline to a particular use: 1) I have two fixed target images 2) I have an itk transform which generates an itk mesh, and from this mesh two images are dynamically generated 3) Using the metric methods of ITK I want to optimize the above transform parameters to minimize the metric As a matter of fact, I don't really need any interpolation method since the generated images already have the same resolution and size. However I can still use a nearest-neighbor interpolation if required. The real question is where and how to update the dynamically generated images ? One of my ideas was to create a kind of wrapper like https://itk.org/Doxygen/html/classitk_1_1ObjectToObjectMultiMetricv4.html and starting the GetValue method with an update of my images. The problem is more about the GetValueAndDerivative which I guess tries to evaluate the metric for closest parameters values. I don't know here where should I put my update method. Thanks! Fran?ois. _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From tevain at telecom-paristech.fr Fri Jun 24 08:11:02 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Fri, 24 Jun 2016 14:11:02 +0200 (CEST) Subject: [ITK] update dynamically images in the registration pipeline In-Reply-To: References: <669536405.14264375.1466755733048.JavaMail.zimbra@enst.fr> Message-ID: <932767876.14472644.1466770262215.JavaMail.zimbra@enst.fr> Please remind to keep the discussion posted to the mail list for record. There are plenty of ways to numerically estimate the gradient magnitude, you could use : -itkGradientMagnitudeImageFilter -itkGradientMagnitudeRecursiveGaussianImageFilter -itkDerivativeImageFilter -with your own Sobel operator ... Then use this image gradient in your cost function regarding the image contribution to partial derivatives. That's how ITK does it (e.g. https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Registration/Common/include/itkMeanSquaresImageToImageMetric.hxx , lines 150-200). Tim ----- Mail original ----- De: "Francois GIRINON" ?: tevain at telecom-paristech.fr Envoy?: Vendredi 24 Juin 2016 11:45:27 Objet: RE:[ITK] update dynamically images in the registration pipeline Xrays are generated from the meshes and compared to the original ones using a metric. The thing is, it must be really hard and maybe impossible to compute explicitely the derivative of the cost function. That's why I'd like to know if there is any way in ITK to estimate the gradient like dlib does : http://dlib.net/optimization.html#find_min_using_approximate_derivatives Thanks again. Fran?ois. ________________________________________ De : Timothee Evain [tevain at telecom-paristech.fr] Envoy? : vendredi 24 juin 2016 10:08 ? : GIRINON Fran?ois Cc : community at itk.org Objet : Re: [ITK] update dynamically images in the registration pipeline Since I do not know what is your cost function, I can't really help you. >From a generic point of view, you should compute the partial derivative of the cost function for each parameter. Tim ----- Mail original ----- De: "Francois GIRINON" ?: tevain at telecom-paristech.fr Envoy?: Jeudi 23 Juin 2016 18:52:29 Objet: RE:[ITK] update dynamically images in the registration pipeline Hello Tim, I'm finally following your advice. I'm writing a specific costFunction class with a new registration pipeline : itkPointSetToMultiImagesRegistrationMethod. I thought the derivative in the metric classes was approximated which is not. Do you know any way to approximate it by the way ? Thanks for your help. ________________________________________ De : Timothee Evain [tevain at telecom-paristech.fr] Envoy? : jeudi 23 juin 2016 13:37 ? : GIRINON Fran?ois Cc : community at itk.org Objet : Re: [ITK] update dynamically images in the registration pipeline Hello Fran?ois, One solution for you could be to create your own cost function to optimize through an itk optimizer. In your case, the comparison between the two mesh-based images and fixed images seems quite easy so you should be able to have a single-valued cost function. You can find examples of custom CFs in the optimizers tests, like here : https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Numerics/Optimizers/test/itkRegularStepGradientDescentOptimizerTest.cxx It basically consist in redefining the GetValue and GetDerivative methods, the later being used in some optimizers which need access to derivatives (like the gradient descent). Then, you just have to plug this custom function to an ordinary itk optimization pipeline to get your best transformation. HTH, Tim ----- Mail original ----- De: "Francois GIRINON" ?: community at itk.org Envoy?: Jeudi 23 Juin 2016 11:55:36 Objet: [ITK] update dynamically images in the registration pipeline Hello everyone, I'd like to suit the registration pipeline to a particular use: 1) I have two fixed target images 2) I have an itk transform which generates an itk mesh, and from this mesh two images are dynamically generated 3) Using the metric methods of ITK I want to optimize the above transform parameters to minimize the metric As a matter of fact, I don't really need any interpolation method since the generated images already have the same resolution and size. However I can still use a nearest-neighbor interpolation if required. The real question is where and how to update the dynamically generated images ? One of my ideas was to create a kind of wrapper like https://itk.org/Doxygen/html/classitk_1_1ObjectToObjectMultiMetricv4.html and starting the GetValue method with an update of my images. The problem is more about the GetValueAndDerivative which I guess tries to evaluate the metric for closest parameters values. I don't know here where should I put my update method. Thanks! Fran?ois. _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From Francois.GIRINON at ensam.eu Fri Jun 24 09:22:01 2016 From: Francois.GIRINON at ensam.eu (Francois.GIRINON at ensam.eu) Date: Fri, 24 Jun 2016 13:22:01 +0000 Subject: [ITK] update dynamically images in the registration pipeline In-Reply-To: <932767876.14472644.1466770262215.JavaMail.zimbra@enst.fr> References: <669536405.14264375.1466755733048.JavaMail.zimbra@enst.fr> , <932767876.14472644.1466770262215.JavaMail.zimbra@enst.fr> Message-ID: Sure, I've already had a look to this but it would be wrong to compute the derivative that way because it involves x' = T(p,x) [the x pixel location transformed by T with parameters p] has the same intensity than x. It would be right if the transformed pixel kept the same intensity value. In my case, the image is generated each time. ________________________________________ De : Timothee Evain [tevain at telecom-paristech.fr] Envoy? : vendredi 24 juin 2016 14:11 ? : GIRINON Fran?ois Cc : community at itk.org Objet : Re: [ITK] update dynamically images in the registration pipeline Please remind to keep the discussion posted to the mail list for record. There are plenty of ways to numerically estimate the gradient magnitude, you could use : -itkGradientMagnitudeImageFilter -itkGradientMagnitudeRecursiveGaussianImageFilter -itkDerivativeImageFilter -with your own Sobel operator ... Then use this image gradient in your cost function regarding the image contribution to partial derivatives. That's how ITK does it (e.g. https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Registration/Common/include/itkMeanSquaresImageToImageMetric.hxx , lines 150-200). Tim ----- Mail original ----- De: "Francois GIRINON" ?: tevain at telecom-paristech.fr Envoy?: Vendredi 24 Juin 2016 11:45:27 Objet: RE:[ITK] update dynamically images in the registration pipeline Xrays are generated from the meshes and compared to the original ones using a metric. The thing is, it must be really hard and maybe impossible to compute explicitely the derivative of the cost function. That's why I'd like to know if there is any way in ITK to estimate the gradient like dlib does : http://dlib.net/optimization.html#find_min_using_approximate_derivatives Thanks again. Fran?ois. ________________________________________ De : Timothee Evain [tevain at telecom-paristech.fr] Envoy? : vendredi 24 juin 2016 10:08 ? : GIRINON Fran?ois Cc : community at itk.org Objet : Re: [ITK] update dynamically images in the registration pipeline Since I do not know what is your cost function, I can't really help you. >From a generic point of view, you should compute the partial derivative of the cost function for each parameter. Tim ----- Mail original ----- De: "Francois GIRINON" ?: tevain at telecom-paristech.fr Envoy?: Jeudi 23 Juin 2016 18:52:29 Objet: RE:[ITK] update dynamically images in the registration pipeline Hello Tim, I'm finally following your advice. I'm writing a specific costFunction class with a new registration pipeline : itkPointSetToMultiImagesRegistrationMethod. I thought the derivative in the metric classes was approximated which is not. Do you know any way to approximate it by the way ? Thanks for your help. ________________________________________ De : Timothee Evain [tevain at telecom-paristech.fr] Envoy? : jeudi 23 juin 2016 13:37 ? : GIRINON Fran?ois Cc : community at itk.org Objet : Re: [ITK] update dynamically images in the registration pipeline Hello Fran?ois, One solution for you could be to create your own cost function to optimize through an itk optimizer. In your case, the comparison between the two mesh-based images and fixed images seems quite easy so you should be able to have a single-valued cost function. You can find examples of custom CFs in the optimizers tests, like here : https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Numerics/Optimizers/test/itkRegularStepGradientDescentOptimizerTest.cxx It basically consist in redefining the GetValue and GetDerivative methods, the later being used in some optimizers which need access to derivatives (like the gradient descent). Then, you just have to plug this custom function to an ordinary itk optimization pipeline to get your best transformation. HTH, Tim ----- Mail original ----- De: "Francois GIRINON" ?: community at itk.org Envoy?: Jeudi 23 Juin 2016 11:55:36 Objet: [ITK] update dynamically images in the registration pipeline Hello everyone, I'd like to suit the registration pipeline to a particular use: 1) I have two fixed target images 2) I have an itk transform which generates an itk mesh, and from this mesh two images are dynamically generated 3) Using the metric methods of ITK I want to optimize the above transform parameters to minimize the metric As a matter of fact, I don't really need any interpolation method since the generated images already have the same resolution and size. However I can still use a nearest-neighbor interpolation if required. The real question is where and how to update the dynamically generated images ? One of my ideas was to create a kind of wrapper like https://itk.org/Doxygen/html/classitk_1_1ObjectToObjectMultiMetricv4.html and starting the GetValue method with an update of my images. The problem is more about the GetValueAndDerivative which I guess tries to evaluate the metric for closest parameters values. I don't know here where should I put my update method. Thanks! Fran?ois. _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From tevain at telecom-paristech.fr Fri Jun 24 10:44:12 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Fri, 24 Jun 2016 16:44:12 +0200 (CEST) Subject: [ITK] update dynamically images in the registration pipeline In-Reply-To: References: <669536405.14264375.1466755733048.JavaMail.zimbra@enst.fr> <932767876.14472644.1466770262215.JavaMail.zimbra@enst.fr> Message-ID: <187242741.14617891.1466779452233.JavaMail.zimbra@enst.fr> Well, if it's impossible to have the derivative of the projection generation, I would go with a non gradient-based optimization scheme. I have very little knowledge on the topic, so you should have a look to the optimizer section of the ITK manuel (Amoeba or SPSA schemes for example). Tim ----- Mail original ----- De: "Francois GIRINON" ?: tevain at telecom-paristech.fr Cc: community at itk.org Envoy?: Vendredi 24 Juin 2016 15:22:01 Objet: RE:[ITK] update dynamically images in the registration pipeline Sure, I've already had a look to this but it would be wrong to compute the derivative that way because it involves x' = T(p,x) [the x pixel location transformed by T with parameters p] has the same intensity than x. It would be right if the transformed pixel kept the same intensity value. In my case, the image is generated each time. ________________________________________ De : Timothee Evain [tevain at telecom-paristech.fr] Envoy? : vendredi 24 juin 2016 14:11 ? : GIRINON Fran?ois Cc : community at itk.org Objet : Re: [ITK] update dynamically images in the registration pipeline Please remind to keep the discussion posted to the mail list for record. There are plenty of ways to numerically estimate the gradient magnitude, you could use : -itkGradientMagnitudeImageFilter -itkGradientMagnitudeRecursiveGaussianImageFilter -itkDerivativeImageFilter -with your own Sobel operator ... Then use this image gradient in your cost function regarding the image contribution to partial derivatives. That's how ITK does it (e.g. https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Registration/Common/include/itkMeanSquaresImageToImageMetric.hxx , lines 150-200). Tim ----- Mail original ----- De: "Francois GIRINON" ?: tevain at telecom-paristech.fr Envoy?: Vendredi 24 Juin 2016 11:45:27 Objet: RE:[ITK] update dynamically images in the registration pipeline Xrays are generated from the meshes and compared to the original ones using a metric. The thing is, it must be really hard and maybe impossible to compute explicitely the derivative of the cost function. That's why I'd like to know if there is any way in ITK to estimate the gradient like dlib does : http://dlib.net/optimization.html#find_min_using_approximate_derivatives Thanks again. Fran?ois. ________________________________________ De : Timothee Evain [tevain at telecom-paristech.fr] Envoy? : vendredi 24 juin 2016 10:08 ? : GIRINON Fran?ois Cc : community at itk.org Objet : Re: [ITK] update dynamically images in the registration pipeline Since I do not know what is your cost function, I can't really help you. >From a generic point of view, you should compute the partial derivative of the cost function for each parameter. Tim ----- Mail original ----- De: "Francois GIRINON" ?: tevain at telecom-paristech.fr Envoy?: Jeudi 23 Juin 2016 18:52:29 Objet: RE:[ITK] update dynamically images in the registration pipeline Hello Tim, I'm finally following your advice. I'm writing a specific costFunction class with a new registration pipeline : itkPointSetToMultiImagesRegistrationMethod. I thought the derivative in the metric classes was approximated which is not. Do you know any way to approximate it by the way ? Thanks for your help. ________________________________________ De : Timothee Evain [tevain at telecom-paristech.fr] Envoy? : jeudi 23 juin 2016 13:37 ? : GIRINON Fran?ois Cc : community at itk.org Objet : Re: [ITK] update dynamically images in the registration pipeline Hello Fran?ois, One solution for you could be to create your own cost function to optimize through an itk optimizer. In your case, the comparison between the two mesh-based images and fixed images seems quite easy so you should be able to have a single-valued cost function. You can find examples of custom CFs in the optimizers tests, like here : https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Numerics/Optimizers/test/itkRegularStepGradientDescentOptimizerTest.cxx It basically consist in redefining the GetValue and GetDerivative methods, the later being used in some optimizers which need access to derivatives (like the gradient descent). Then, you just have to plug this custom function to an ordinary itk optimization pipeline to get your best transformation. HTH, Tim ----- Mail original ----- De: "Francois GIRINON" ?: community at itk.org Envoy?: Jeudi 23 Juin 2016 11:55:36 Objet: [ITK] update dynamically images in the registration pipeline Hello everyone, I'd like to suit the registration pipeline to a particular use: 1) I have two fixed target images 2) I have an itk transform which generates an itk mesh, and from this mesh two images are dynamically generated 3) Using the metric methods of ITK I want to optimize the above transform parameters to minimize the metric As a matter of fact, I don't really need any interpolation method since the generated images already have the same resolution and size. However I can still use a nearest-neighbor interpolation if required. The real question is where and how to update the dynamically generated images ? One of my ideas was to create a kind of wrapper like https://itk.org/Doxygen/html/classitk_1_1ObjectToObjectMultiMetricv4.html and starting the GetValue method with an update of my images. The problem is more about the GetValueAndDerivative which I guess tries to evaluate the metric for closest parameters values. I don't know here where should I put my update method. Thanks! Fran?ois. _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community From sg.ele.eng at gmail.com Sun Jun 26 01:57:16 2016 From: sg.ele.eng at gmail.com (Sara Gh) Date: Sun, 26 Jun 2016 01:57:16 -0400 Subject: [ITK] [ITK-users] SimpleITK - Resampling Coronal Image in the Axial View Message-ID: Hello experts, I have two MRI scans: Axial and Coronal # *imageA* : Axial MRI scan, size : 256x256x56 (256mmx256mmx168mm) , spacing: 1,1,3 ( slice gap : 1 => slice thickness : 2) # *imageC* : Coronal MRI scan, size : 256x256x68 (256mmx256mmx204mm) , spacing: 1,1,3 ( slice gap : 1 => slice thickness : 2) I am trying to view Coronal image from the axial view i.e. resampling Coronal image using the direction of Axial image. Here is my code: resample = sitk.ResampleImageFilter() resample.SetReferenceImage(imageC) resample.SetOutputDirection(imageA.GetDirection()) resample.SetOutputOrigin(imageA.GetOrigin()) imageCA = resample.Execute(imageC) sitk.Show(imageCA) # Result: imageCA: size : 256x256x68 (256mmx256mmx204mm), spacing: 1,1,3 I believe I have missed something because, in my idea, the size of resampled coronal image (imageCA) should be 68x256x256 (204mmx256mmx256mm) with the spacing [3,1,1]. I also tried to set the OutputSpacing to [3,1,1], but the size of the imageCA changes to 256x256x68 (768mmx256mmx68mm). I would be thankful if someone could help me in this regard. Best regards, Sara Gh -------------- 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 cervellone at gmail.com Sun Jun 26 16:07:46 2016 From: cervellone at gmail.com (cervellone at gmail.com) Date: Sun, 26 Jun 2016 22:07:46 +0200 Subject: [ITK] [ITK-users] Import itk always takes ages and results in warnings Message-ID: Hello all, Is there a way to speed up the import of itk in an application and the suppression of the warnings I get every time I run the python script ? Thank you all JP Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 3,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface' -------------- 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 Mon Jun 27 05:40:01 2016 From: tevain at telecom-paristech.fr (Timothee Evain) Date: Mon, 27 Jun 2016 11:40:01 +0200 (CEST) Subject: [ITK] [ITK-users] SimpleITK - Resampling Coronal Image in the Axial View In-Reply-To: References: Message-ID: <1561329490.15991909.1467020401395.JavaMail.zimbra@enst.fr> Hello, First of all, it depends on the patient position in the data, but usually the X axis describe the left/right direction, the Y axis the anterior/posterior direction and the Z axis the top/bottom one. So I would expect the resampled imageC size to be 256x68x256 rather than 68x256x256. Then, I think you should try to transform your imageC to be in the imageA orientation. Let say the imageA have a LPS coordinate system. If the imageC : -first direction represents the axis going from the patient's right to the patient's left -second direction represents the axis going from the patient's top to the patient's bottom -third direction represents the axis going from the patient's front to the patient's rear Then you should rotate the imageC by a -pi/2 angle around the X axis. You could use the Euler3DTransform to get this rotation. Then you feed the resample filter with this transform, plus the needed parameters (origin, spacing, size,...), and you should be able to have your resampled data. Just be sure to fully understand the transformation you're making (I recommend the ResampleImageFilter part of the ITK guide which is quite useful). HTH, Tim ----- Mail original ----- De: "Sara Gh" ?: insight-users at itk.org Envoy?: Dimanche 26 Juin 2016 07:57:16 Objet: [ITK] [ITK-users] SimpleITK - Resampling Coronal Image in the Axial View Hello experts, I have two MRI scans: Axial and Coronal # imageA : Axial MRI scan, size : 256x256x56 (256mmx256mmx168mm) , spacing: 1,1,3 ( slice gap : 1 => slice thickness : 2 ) # imageC : Coronal MRI scan, size : 256x256x68 (256mmx256mmx204mm) , spacing: 1,1,3 ( slice gap : 1 => slice thickness : 2 ) I am trying to view Coronal image from the axial view i.e. resampling Coronal image using the direction of Axial image. Here is my code: resample = sitk.ResampleImageFilter() resample.SetReferenceImage(imageC) resample.SetOutputDirection(imageA.GetDirection()) resample.SetOutputOrigin(imageA.GetOrigin()) imageCA = resample.Execute(imageC) sitk.Show(imageCA) # Result: imageCA: size : 256x256x68 (256mmx256mmx204mm), spacing: 1,1,3 I believe I have missed something because, in my idea, the size of resampled coronal image (imageCA) should be 68x256x256 ( 204mmx256mmx256mm) with the spacing [3,1,1] . I also tried to set the OutputSpacing to [3,1,1], but the size of the imageCA changes to 256x256x68 (768mmx256mmx68mm). I would be thankful if someone could help me in this regard. Best regards, Sara Gh _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 michkapopoff at gmail.com Mon Jun 27 16:03:30 2016 From: michkapopoff at gmail.com (Michka Popoff) Date: Mon, 27 Jun 2016 22:03:30 +0200 Subject: [ITK] [ITK-users] Import itk always takes ages and results in warnings In-Reply-To: References: Message-ID: Hi to reduce the import time, one solution would be to reduce the number of wrapped modules and types (and image/vector dimensions). If you re-build ITK by disabling the things you don?t need, there will be less things to load. I have some ideas on how to improve the import situation but never came to it, so not sure anybody has been working intensively on that. For the warnings, we need to fix them in ITK. The QuadEdgeMeshCellTraitsInfo class is probably not be usable as is. If you want to hide the warnings, you can use (like for other python warnings): import warnings warnings.simplefilter(?ignore", Warning) You can reset the filter after the import. That should to it. Michka > On 26 Jun 2016, at 22:07, cervellone at gmail.com wrote: > > Hello all, > > Is there a way to speed up the import of itk in an application and the suppression of the warnings I get every time I run the python script ? > > Thank you all > JP > > > Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 3,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface' > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 michkapopoff at gmail.com Mon Jun 27 16:25:05 2016 From: michkapopoff at gmail.com (Michka Popoff) Date: Mon, 27 Jun 2016 22:25:05 +0200 Subject: [ITK] [ITK-users] Issue on itk.QuadEdgeMeshCellTraitsInfo In-Reply-To: <1465709590989.57546@sphic.org.cn> References: <1465709590989.57546@sphic.org.cn> Message-ID: Hi thanks for reporting this. I also could reproduce the warnings. I opened a bug for this here so we can keep track of it: https://issues.itk.org/jira/browse/ITK-3448 The same error was also reported on the mailing list yesterday. If you just want to hide the warning you can use: import warnings warnings.simplefilter(?ignore", Warning) If you need to use QuadEdgeMeshCellTraitsInfo with Python, somebody will need to fix this. I already gave it a shot, but this may take some time. Not sure I will be able to look at this until next week. Thanks Michka > On 12 Jun 2016, at 07:33, ??? wrote: > > ?Hi all, > > When I used python-supported ITK 4.10.0 to get the types of itk.QuadEdgeMeshCellTraitsInfo for the first time, I got two warnings > > Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 2,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,2,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,2,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface' > Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 3,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface' > > Options: > > > If I run itk.QuadEdgeMeshCellTraitsInfo.GetTypes() again or use ITK 4.9.1 instead, it just displays > > > Options: > > > So what's the problem? What is the unknown parameter? Has someone met this issue? Thanks. > > > Regards, > > Zhuangming Shen > > > > > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 cervellone at gmail.com Tue Jun 28 04:59:08 2016 From: cervellone at gmail.com (cervellone at gmail.com) Date: Tue, 28 Jun 2016 10:59:08 +0200 Subject: [ITK] [ITK-users] Import itk always takes ages and results in warnings In-Reply-To: References: Message-ID: Dear Michka Thank you for your reply. I will take that into consideration when building ITK next time. Unfortunately there is little comprehensive guide to what all those options in cmake really mean or do, so id rather build more than less. Also VTK is pretty heavy in term of modules, and I have the impression that it is noticeably faster. Best JP On Mon, Jun 27, 2016 at 10:03 PM, Michka Popoff wrote: > Hi > > to reduce the import time, one solution would be to reduce the number of > wrapped modules > and types (and image/vector dimensions). If you re-build ITK by disabling > the things you > don?t need, there will be less things to load. > > I have some ideas on how to improve the import situation but never came to > it, so > not sure anybody has been working intensively on that. > > For the warnings, we need to fix them in ITK. > The QuadEdgeMeshCellTraitsInfo class is probably not be usable as is. > > If you want to hide the warnings, you can use (like for other python > warnings): > > import warnings > warnings.simplefilter(?ignore", Warning) > > You can reset the filter after the import. > > That should to it. > > > Michka > > > On 26 Jun 2016, at 22:07, cervellone at gmail.com wrote: > > > > Hello all, > > > > Is there a way to speed up the import of itk in an application and the > suppression of the warnings I get every time I run the python script ? > > > > Thank you all > > JP > > > > > > Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< > 3,float,float,unsigned long,unsigned long,unsigned > char,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned > long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned > long,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned > long,unsigned long,bool,bool,true > > >,std::set< unsigned long > >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' > in template 'itk::CellInterface' > > > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the 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 Tue Jun 28 08:47:07 2016 From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C]) Date: Tue, 28 Jun 2016 12:47:07 +0000 Subject: [ITK] [ITK-users] Import itk always takes ages and results in warnings In-Reply-To: References: Message-ID: <53A818A2-9662-45F8-BFEE-39FB05A28A5D@mail.nih.gov> Hi JP, Native ITK wrapping has a powerful set of features which include using template like classes. This allows for easy customization of the build and direct control over the input and output type of many filter. This does come at the cost of having a very large interface and currently long import time. Have you looked into SimpleITK? It has a smaller interface, and less flexibility but it does load quite quickly (.3s) into Python. HTH, Brad On Jun 28, 2016, at 4:59 AM, cervellone at gmail.com wrote: Dear Michka Thank you for your reply. I will take that into consideration when building ITK next time. Unfortunately there is little comprehensive guide to what all those options in cmake really mean or do, so id rather build more than less. Also VTK is pretty heavy in term of modules, and I have the impression that it is noticeably faster. Best JP On Mon, Jun 27, 2016 at 10:03 PM, Michka Popoff > wrote: Hi to reduce the import time, one solution would be to reduce the number of wrapped modules and types (and image/vector dimensions). If you re-build ITK by disabling the things you don?t need, there will be less things to load. I have some ideas on how to improve the import situation but never came to it, so not sure anybody has been working intensively on that. For the warnings, we need to fix them in ITK. The QuadEdgeMeshCellTraitsInfo class is probably not be usable as is. If you want to hide the warnings, you can use (like for other python warnings): import warnings warnings.simplefilter(?ignore", Warning) You can reset the filter after the import. That should to it. Michka > On 26 Jun 2016, at 22:07, cervellone at gmail.com wrote: > > Hello all, > > Is there a way to speed up the import of itk in an application and the suppression of the warnings I get every time I run the python script ? > > Thank you all > JP > > > Warning: Unknown parameter 'itk::QuadEdgeMeshCellTraitsInfo< 3,float,float,unsigned long,unsigned long,unsigned char,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long, unsigned long,bool,bool,true > >,itk::MapContainer< unsigned long,itk::QuadEdgeMeshPoint< float,3,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > > >,std::set< unsigned long >,itk::GeometricalQuadEdge< unsigned long,unsigned long,bool,bool,true > >' in template 'itk::CellInterface' > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 tobias.wood at kcl.ac.uk Tue Jun 28 08:57:27 2016 From: tobias.wood at kcl.ac.uk (Wood, Tobias) Date: Tue, 28 Jun 2016 12:57:27 +0000 Subject: [ITK] N4BiasFieldCorrectionImageFilter units for FWHM? Message-ID: Hello, What are the units for SetBiasFieldFullWidthAtHalfMaximum() method on N4BiasFieldCorrectionImageFilter? mm? Voxels? Something else entirely? I am trying to bias-correct some pre-clinical images that have small voxels (100 micron isotropic), and reducing the FWHM by a factor of 10 makes quite a difference to the output bias field. Best wishes, Toby From dzenanz at gmail.com Tue Jun 28 11:23:56 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Tue, 28 Jun 2016 11:23:56 -0400 Subject: [ITK] N4BiasFieldCorrectionImageFilter units for FWHM? In-Reply-To: References: Message-ID: Hi Toby, it is perhaps expressed in terms of Gaussian kernel widths ? Regards On Tue, Jun 28, 2016 at 8:57 AM, Wood, Tobias wrote: > Hello, > > What are the units for SetBiasFieldFullWidthAtHalfMaximum() method on > N4BiasFieldCorrectionImageFilter? mm? Voxels? Something else entirely? > > I am trying to bias-correct some pre-clinical images that have small > voxels (100 micron isotropic), and reducing the FWHM by a factor of 10 > makes quite a difference to the output bias field. > > Best wishes, > Toby > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -------------- next part -------------- An HTML attachment was scrubbed... URL: From scorpiuni at gmail.com Tue Jun 28 15:52:09 2016 From: scorpiuni at gmail.com (Robert) Date: Tue, 28 Jun 2016 12:52:09 -0700 (MST) Subject: [ITK] [ITK-users] Filters in 3D Message-ID: <1467143529556-7589004.post@n2.nabble.com> Hello, I have a general question about 3D filters, especially about the SignedDanielssonDistanceMapImageFilter. Does this filter work Slice by Slice when using 3-dimensional data, or does the calculation of the euclidian distance take into account the 3 coordinates of a voxel? I guess sometimes the result would be quite similar, but I constructed some examples on paper where there would be a difference. Is there any place where this is marked down for the different filters? Thanks in advance, Robert -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Filters-in-3D-tp7589004.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 basafa at clearguidemedical.com Tue Jun 28 16:08:00 2016 From: basafa at clearguidemedical.com (ebasafa) Date: Tue, 28 Jun 2016 13:08:00 -0700 (MST) Subject: [ITK] [ITK-users] Filters in 3D In-Reply-To: <1467143529556-7589004.post@n2.nabble.com> References: <1467143529556-7589004.post@n2.nabble.com> Message-ID: <1467144480931-7589005.post@n2.nabble.com> Hi Robert, As far as I know, all ITK filters are templated over the input/output image type(s), which means you set the dimensions as you define the image types to work with. I don't have experience with that particular filter, but seems like it's no exception. That being said, there is a filter that lets you apply a filter or a bunch of filters on individual slices of an input volume (itkSliceBySliceImageFilter). Basically you assign to it input image(s) and filter(s) and it applies those filter(s) on individual slices of those image(s). Obviously, those filters need to be able to work with images of one dimension less than your input image. I presume the results will differ if a filter that calculates distances is applied on 2D vs 3D images. HTH Ehsan Robert wrote > Hello, > > I have a general question about 3D filters, especially about the > SignedDanielssonDistanceMapImageFilter. > Does this filter work Slice by Slice when using 3-dimensional data, or > does the calculation of the euclidian distance take into account the 3 > coordinates of a voxel? I guess sometimes the result would be quite > similar, but I constructed some examples on paper where there would be a > difference. Is there any place where this is marked down for the different > filters? > > Thanks in advance, > Robert -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Filters-in-3D-tp7589004p7589005.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 scorpiuni at gmail.com Tue Jun 28 16:21:44 2016 From: scorpiuni at gmail.com (Robert) Date: Tue, 28 Jun 2016 13:21:44 -0700 (MST) Subject: [ITK] [ITK-users] Filters in 3D In-Reply-To: <1467144480931-7589005.post@n2.nabble.com> References: <1467143529556-7589004.post@n2.nabble.com> <1467144480931-7589005.post@n2.nabble.com> Message-ID: <1467145304984-7589006.post@n2.nabble.com> Thanks for the fast reply, however, this does not yet quite answer my question. I used the filter, as you said, with dimension 3 inside my code. I know about the Slice by Slice Filter, however, I want to know how it works specifically when using the template for dimension 3. I mean, I could apply it slice by slice, then apply it with dimension 3 and then calculate the difference, but I thought that maybe someone already tested this once ;) Basically, my question is if the template for dimension 3 uses the Slice by Slice approach, or if it uses "real" 3d coordinates. Thanks for you reply however. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Filters-in-3D-tp7589004p7589006.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 Tue Jun 28 18:16:17 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 28 Jun 2016 18:16:17 -0400 Subject: [ITK] [ITK-users] ResampleDICOM Assertion Error In-Reply-To: References: Message-ID: Hi Sarthak, ITK 4.10.0 was updated to use the GDCM release branch. Please try 4.10.0 and let us know how it goes. Thanks, Matt On Mon, Jun 20, 2016 at 10:31 AM, Scapegoat Sarthak wrote: > Hello All, > > I have been trying (unsuccessfully) to write a DICOM series with non-integer > slopes. I have seen in an earlier community post (reference - > http://public.kitware.com/pipermail/community/2014-September/007143.html) > about the exact same issue and it is still not resolved (I am running > version 4.9.0. > > Can someone from the moderators' side confirm in which version this has been > taken care of (if at all)? > > Thanks, > Sarthak > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 dzenanz at gmail.com Wed Jun 29 09:52:06 2016 From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=) Date: Wed, 29 Jun 2016 09:52:06 -0400 Subject: [ITK] [ITK-users] Filters in 3D In-Reply-To: <1467145304984-7589006.post@n2.nabble.com> References: <1467143529556-7589004.post@n2.nabble.com> <1467144480931-7589005.post@n2.nabble.com> <1467145304984-7589006.post@n2.nabble.com> Message-ID: Hi Robert, Danielsson's and Maurer's filters use real 3D coordinates for distances. Regards, D?enan On Tue, Jun 28, 2016 at 4:21 PM, Robert wrote: > Thanks for the fast reply, however, this does not yet quite answer my > question. > I used the filter, as you said, with dimension 3 inside my code. I know > about the Slice by Slice Filter, however, I want to know how it works > specifically when using the template for dimension 3. > I mean, I could apply it slice by slice, then apply it with dimension 3 and > then calculate the difference, but I thought that maybe someone already > tested this once ;) > Basically, my question is if the template for dimension 3 uses the Slice by > Slice approach, or if it uses "real" 3d coordinates. > > Thanks for you reply however. > > > > -- > View this message in context: > http://itk-insight-users.2283740.n2.nabble.com/Filters-in-3D-tp7589004p7589006.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 matt.mccormick at kitware.com Wed Jun 29 11:23:14 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 29 Jun 2016 11:23:14 -0400 Subject: [ITK] Level Sets v4 CFL calculation In-Reply-To: <67143F71-E5EF-4CC8-949A-D2EDA835124D@elucidbio.com> References: <67143F71-E5EF-4CC8-949A-D2EDA835124D@elucidbio.com> Message-ID: Hi David, If there is is dead, patches that remove it would be welcome. Please see https://itk.org/Wiki/ITK/Git/Develop Thanks, Matt On Tue, Jun 21, 2016 at 3:15 PM, David S. Paik (Elucid Bioimaging) wrote: > I am going through the level sets v4 code and finding different areas of the code that appear to be dead cruft yet still in the code making understanding of the code difficult for a new comer. > > LevelSetEquationTermContainer (which represents a single equation), stores its CFL contributions in a std::map for each term. No problem. > > However, LevelSetEquationTermBase also has m_CFLContribution which is set to zero (in constructor and SetUp) and no other code seems to ever change. So I?m guessing that in this class, it is some leftover dead code but it makes the code very confusing if you happen to start looking at this class first. > > But much more seriously, in LevelSetEvolution::ComputeTimeStepForNextiteration specialized for LevelSetDenseImage (itkLevelSetEvolution.hxx line 128-130), there are the following two lines: > > LevelSetOutputRealType contribution = this->m_EquationContainer->ComputeCFLContribution(); > contribution = 1; > > This negates the whole CFL computation and instead chooses a totally arbitrary value. Perhaps this was accidentally left in the code? I seem to recall seeing something similar in the v3 level set framework. If the true value was actually larger, this can lead to too large a time step and thus severe numerical instability. > > Does anybody who maintains any of the level set v4 code read this? Is there anybody I should be contacting directly? > > David > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From matt.mccormick at kitware.com Wed Jun 29 11:30:22 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 29 Jun 2016 11:30:22 -0400 Subject: [ITK] [ITK-users] Licensing question In-Reply-To: References: <1039149860.11159873.1466490799507.JavaMail.yahoo.ref@mail.yahoo.com> <1039149860.11159873.1466490799507.JavaMail.yahoo@mail.yahoo.com> Message-ID: Hi James, If your modifications would be useful to others, your contributions are welcome. Please see https://itk.org/Wiki/ITK/Git/Develop for the process. Thanks, Matt On Wed, Jun 22, 2016 at 6:46 AM, D?enan Zuki? wrote: > TL;DR version: > http://www.apache.org/foundation/license-faq.html#WhatDoesItMEAN > > Regards, > D?enan > > On Tue, Jun 21, 2016 at 8:33 AM, Malsoaz James via Insight-users > wrote: >> >> Hi, >> >> I would like to use ITK in a commercial application but I have some >> questions about the Apache2 license. >> Should I include somewhere the ITK copyright in my application? In source >> code? In related documents? >> >> Currently I'm using version 4.8. I made minor modifications in source file >> of ITK to fit my needs. Should I publish these changes? >> >> Thank you for your answer. >> Best regards, >> >> James >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 matt.mccormick at kitware.com Wed Jun 29 11:34:39 2016 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 29 Jun 2016 11:34:39 -0400 Subject: [ITK] Redudancy in LevelSetBase hierarchy In-Reply-To: References: <7B2A0371-4D8A-473C-B201-54267261DA68@elucidbio.com> Message-ID: Hi David, Arnaud and Kishore are LevelSetsv4 experts, although they may or may not have time to work on the code further. If patches are submitted to Gerrit for review, please add them as reviewers so they have an opportunity to review the changes. Thanks, Matt On Wed, Jun 22, 2016 at 10:57 AM, David S. Paik (Elucid Bioimaging) wrote: > D?enan, > > Thank you for your response! Although it really is more the level set > segmentation framework for V4 that this applies to. If either of you can > point me to someone who?s done work on that, it?d be appreciated. > > Thanks! > David > > > On Jun 22, 2016, at 3:30 AM, D?enan Zuki? wrote: > > Hans, I think you were involved with refactoring registration framework for > V4. Can you pitch in? > > Regards > > On Sat, Jun 11, 2016 at 1:24 AM, David S. Paik (Elucid Bioimaging) > wrote: >> >> I am going through the level set v4 classes in 4.9.1 and I noticed a few >> things. >> >> In itk::LevelSetBase >> >> - EvaluateMeanCurvature( const InputType& iP ) is declared pure virtual >> (.h line 75) but a definition is provided (.hxx line 88). While >> syntactically permissible, this seems more likely an oversight rather than >> an intentional design. (see below) >> >> - Both versions of EvaluateLaplacian are pure virtual even though they >> could be computed at this point in the hierarchy as the trace of the Hessian >> matrix. This is analogous to how EvaluateGradientNorm is calculated even >> though EvaluateGradient is still pure virtual in this class. (see below) >> >> >> In itk::DiscreteLevelSetImage >> >> - EvaluateLaplacian (both versions) do their own redundant calculation of >> second derivatives even though they may have already been calculated in the >> Hessian matrix. There?s probably a design tradeoff between redundantly >> computing the Laplacian (as it is now) vs. Laplacian triggering a full >> Hessian computation even if the off diagonal elements of the Hessian are not >> used. One possibility is to check to see if Hessian has been computed and >> if so use it but not trigger a full Hessian computation. >> >> - EvaluateMeanCurvature (both versions) override itk::LevelSetBase?s >> version but they appear to be exactly the same. The virtual function calls >> should work from the base class. Not a bug but this seems to be an >> unnecessary redundancy. Am I missing something? >> >> >> David >> >> _______________________________________________ >> 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 hans-johnson at uiowa.edu Wed Jun 29 17:24:32 2016 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Wed, 29 Jun 2016 21:24:32 +0000 Subject: [ITK] Redudancy in LevelSetBase hierarchy In-Reply-To: References: <7B2A0371-4D8A-473C-B201-54267261DA68@elucidbio.com> Message-ID: I did not work on level sets. Sent from my iPhone > On Jun 29, 2016, at 11:35 AM, Matt McCormick wrote: > > Hi David, > > Arnaud and Kishore are LevelSetsv4 experts, although they may or may > not have time to work on the code further. If patches are submitted > to Gerrit for review, please add them as reviewers so they have an > opportunity to review the changes. > > Thanks, > Matt > > On Wed, Jun 22, 2016 at 10:57 AM, David S. Paik (Elucid Bioimaging) > wrote: >> D?enan, >> >> Thank you for your response! Although it really is more the level set >> segmentation framework for V4 that this applies to. If either of you can >> point me to someone who?s done work on that, it?d be appreciated. >> >> Thanks! >> David >> >> >> On Jun 22, 2016, at 3:30 AM, D?enan Zuki? wrote: >> >> Hans, I think you were involved with refactoring registration framework for >> V4. Can you pitch in? >> >> Regards >> >> On Sat, Jun 11, 2016 at 1:24 AM, David S. Paik (Elucid Bioimaging) >> wrote: >>> >>> I am going through the level set v4 classes in 4.9.1 and I noticed a few >>> things. >>> >>> In itk::LevelSetBase >>> >>> - EvaluateMeanCurvature( const InputType& iP ) is declared pure virtual >>> (.h line 75) but a definition is provided (.hxx line 88). While >>> syntactically permissible, this seems more likely an oversight rather than >>> an intentional design. (see below) >>> >>> - Both versions of EvaluateLaplacian are pure virtual even though they >>> could be computed at this point in the hierarchy as the trace of the Hessian >>> matrix. This is analogous to how EvaluateGradientNorm is calculated even >>> though EvaluateGradient is still pure virtual in this class. (see below) >>> >>> >>> In itk::DiscreteLevelSetImage >>> >>> - EvaluateLaplacian (both versions) do their own redundant calculation of >>> second derivatives even though they may have already been calculated in the >>> Hessian matrix. There?s probably a design tradeoff between redundantly >>> computing the Laplacian (as it is now) vs. Laplacian triggering a full >>> Hessian computation even if the off diagonal elements of the Hessian are not >>> used. One possibility is to check to see if Hessian has been computed and >>> if so use it but not trigger a full Hessian computation. >>> >>> - EvaluateMeanCurvature (both versions) override itk::LevelSetBase?s >>> version but they appear to be exactly the same. The virtual function calls >>> should work from the base class. Not a bug but this seems to be an >>> unnecessary redundancy. Am I missing something? >>> >>> >>> David >>> >>> _______________________________________________ >>> 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 christopherrmullins at gmail.com Thu Jun 30 11:55:03 2016 From: christopherrmullins at gmail.com (Christopher Mullins) Date: Thu, 30 Jun 2016 11:55:03 -0400 Subject: [ITK] [ITK-users] Build errors in python wrapping of 4.10.0 In-Reply-To: <45356B32-0D4F-4FE9-9157-630919E381EA@uiowa.edu> References: <45356B32-0D4F-4FE9-9157-630919E381EA@uiowa.edu> Message-ID: Hi all, Thanks for the help on this. I've been traveling and haven't had much time to investigate, but I believe Michka is correct. It looks like the build is successful with the -std=c++98 flag, and only one test fails [1]. I'll test the python wrapping and report back if anything terrible happens -- if not I'll bump the AUR PKGBUILD. Thanks again, Chris [1] https://open.cdash.org/buildSummary.php?buildid=4435570 On Wed, Jun 15, 2016 at 5:22 PM, Johnson, Hans J wrote: > I?m trying to reproduce now. > > Hans > > > -- > > > On 6/15/16, 4:12 PM, "Insight-users on behalf of Michka Popoff" < > insight-users-bounces at itk.org on behalf of michkapopoff at gmail.com> wrote: > > >Hi > > > >I think this bug is not known. I had a look and could reproduce it with > gcc 6.0.0, Cmake 3.5.2, Python 3.5.1 on OS X. > >GCC 6 is using c++14 by default, but even with c++11 you would probably > get the problem. > >The problem is also there with the latest commit from the master branch. > > > >Please note that we probably never tested Python Wrappings with c++11, > even not speaking of c++14. > > > >The problem seems to have appeared with this patch: > > > https://github.com/InsightSoftwareConsortium/ITK/commit/b6b9a8e8849da1edbf75f88e11adb8d8d15bb395 > > > >I removed the ITK_DELETE_FUNCTION macro from the itkTriangleHelper copy > constructor, and was able to compile > >with gcc 6. But it may just a side effect of that patch which is now only > appearing with c++ >= 11. > >It is weird that the problem seems to be only for the itkTriangleHelper > class. > > > >I will have to look what is the difference in the files generated for > swig and what is exactly failing, > >though I do not know how long it will take me. I hope I can do this this > weekend. > > > >Thanks > > > >Michka > > > > > >> On 09 Jun 2016, at 16:14, Christopher Mullins < > christopherrmullins at gmail.com> wrote: > >> > >> Hi all, > >> > >> Apparently my subscription to this list has lapsed and my first email > was rejected (despite receiving the list in my inbox every day). Sorry if > there's a double post. > >> > >> I'm getting the following build errors when building ITK 4.10.0 with > the WRAP_PYTHON option ON[1], [3]. Is this a known issue, or is there a > configuration setting I've set improperly? > >> > >> Platform is Arch linux, GCC v6.1.1, Python v3.5.1, CMake v3.5.2. There > are no warnings. See all output details for this machine here [2], and > please let me know if I can provide any others. > >> > >> The faster I fix this the faster I'll feel comfortable updating the > Arch linux AUR PKGBUILD for ITK, so I appreciate any help you can offer. > >> > >> Thanks, > >> Chris > >> > >> > >> > >> [1] https://open.cdash.org/viewBuildError.php?buildid=4403379 > >> [2] https://open.cdash.org/buildSummary.php?buildid=4403379 > >> > >> [3] To save you a click, and for the sake of archiving, the error is: > >> > /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp: > In function 'PyObject* _wrap_new_itkTriangleHelperPD2(PyObject*, > PyObject*)': > /home/chris/projects/MyTests/ITK-build/Wrapping/Modules/ITKCommon/itkTriangleHelperPython.cpp:5854:65: > error: no matching function for call to > 'itk::TriangleHelper >::TriangleHelper()' result = > (itkTriangleHelperPD2 *)new itkTriangleHelperPD2(); > >> _____________________________________ > >> Powered by www.kitware.com > >> > >> Visit other Kitware open-source projects at > >> http://www.kitware.com/opensource/opensource.html > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> http://www.kitware.com/products/protraining.php > >> > >> Please keep messages on-topic and check the 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 rphellan2210 at gmail.com Thu Jun 30 14:40:56 2016 From: rphellan2210 at gmail.com (Renzo Ph) Date: Thu, 30 Jun 2016 12:40:56 -0600 Subject: [ITK] GeodesicActiveContourLevelSetImageFilter aborted Message-ID: Hello, I'm using the GeodesicActiveContourLevelSetImageFilter. The initial level set image looks like a distance map with positive and negative values and an initial contour at the 0 level set. The feature image looks like an inverted gradient image, and the values are between 0 and 1 after applying a sigmoid. However, when I try to execute the filter, it always says "aborted". Has anybody had the same problem. I'm using this filter to segment vessels, so they are thin structures. I can send the code or images of the partial results if required. Thanks, Renzo -------------- next part -------------- An HTML attachment was scrubbed... URL: