From grothausmann.roman at mh-hannover.de Wed Oct 1 11:27:57 2014 From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann) Date: Wed, 01 Oct 2014 17:27:57 +0200 Subject: [ITK] [ITK-users] patch to add a global hierarchical watershed segmentation mode to itksnap In-Reply-To: <53E85181.8040607@mh-hannover.de> References: <53E85181.8040607@mh-hannover.de> Message-ID: <542C1D7D.6000904@mh-hannover.de> Dear mailing list members, Finally, I got my idea about an interactive hierarchical Watershed SegmentationEditor realized. The idea originates from the SegmentationEditor of the InsightApplication demonstrated here: http://www.insight-journal.org/browse/publication/70 I decided to add such functionality to itksnap as it is the successor of the SegmentationEditor. The additions consist of a Click'n'Join mode, which either allows to join or split labels of the current segmentation by clicking, or instead uses a Global Watershed label image as a label source. The great feature of the itkWatershedFilter allows the level of the watershed hierarchy to be changed on-the-fly. The patch is against itksnap-3.0.0 and in beta-testing stage. Loading from files and "back" buttons are not yet implemented. Please feel free to test it too! Regards, Roman On 11/08/14 07:15, Dr. Roman Grothausmann wrote: > Dear mailing list members, > > > For a long time now I've been searching for a replacement of the old > SegmentationEditor (part of the InsightApplications) which I could not get to > work even with older ITK-3.x. Somewhere I was told that it was integrated and > maintained within itksnap. However the only tool in itksnap based on watershed > segmentation seems to be the adaptive brush. It is very handy, but > time-consuming in 3D and only for local segmentations. In contrast the > SegmentationEditor used a global hierarchical watershed segmentation to pick > labels from, see e.g. the video linked here: > http://www.insight-journal.org/browse/publication/70 > Quite often now I've stumbled over data, that would likely have profited a lot > of such a tool for segmentation. > > If such a tool working with ITK-4.x does not exist any more, I thought of > implementing it as a global WS segmentation mode in itksnap. That way making the > tool easier to find, to use and to ensure maintenance (should it be integrated > into the itksnap code base in the end) and also avoiding recoding a GUI with > mouse interaction and such. > > My current idea is to start, similar to the snake-tool, with pre-filtering like > smoothing and optional edge-detection. > Then the main edit mode to consist of the usual 4 subwindows showing an overlay > of the grey-image and the watershed segmentation of the hierarchical WS-filter > (hWS), side-by-side to another label-dataset (loaded like a tiled overlay) which > consist of the actually chosen labels from the hWS as the final data (FD). > The interaction I'm considering would be to LMB click on a label in the hWS > which is then added to the FD as the current fg label, or removed with a RMB. > The hierachrchy level of the hWS could be controlled by a slider or the mouse > wheel + Shift in nearly real time if some region demands higher or lower > detailed segmentation. When the fg label is changed, the segmentation added or > removed with further mouse interactions would modify the new fg label. > When all is done and the global WS mode is left, the FD label-dataset is added > to the main segmentation of itksnap. > > Would that be possible to implement in itksnap 3.x? > What source files of the itksnap code base should I look at for: > - the pre-filtering mode of the snake (for the smoothing and edge detection) > - the mouse interactions (for e.g. adding the whell + Shift interaction) > - possible examples for the dual layout > > Thanks for any comments, help or hints. > Roman > -- Dr. Roman Grothausmann Tomographie und Digitale Bildverarbeitung Tomography and Digital Image Analysis Institut f?r Funktionelle und Angewandte Anatomie, OE 4120 Medizinische Hochschule Hannover Carl-Neuberg-Str. 1 D-30625 Hannover Tel. +49 511 532-9574 -------------- next part -------------- A non-text attachment was scrubbed... Name: itksnap-3.0.0_gWS_53.diff Type: text/x-patch Size: 151111 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Oct 1 15:40:44 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 1 Oct 2014 15:40:44 -0400 Subject: [ITK] [ANNOUNCE] ITK 4.6.1 has been released! Message-ID: On behalf of the Insight Toolkit Community, we are happy to announce the release of ITK 4.6.1! This is a patch release that addresses critical issues. The 4.6.1 release fixes DICOM, MetaIO, TIFF, and PNG IO issues, 32-bit WrapITK build errors, Python wrapping warnings, CMake configuration with COMPONENTS, performance and memory consumption of the ITKv4 implementation of the mutual information matching metric, and a many other issues. Congratulations and thanks to everyone who contributed to this release. We are particularly grateful for the collaborations with the 3D Slicer, Debian, GDCM, and MINC communities to address these issues. Questions and comments are welcome on the ITK mailing lists. The release files can be downloaded from: http://itk.org/ITK/resources/software.html The next feature release of 4.6.0 is scheduled for June. Enjoy ITK! Changes from v4.6.0 to v4.6.1: Arnaud Gelas (5): BUG: fix gdcm version in GDCMImageIO. COMP: missing cast when calling gdcm::DataElement::SetByteValue BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false BUG: split include directories into appropriate cmake variables HDF5 BUG: missing gdcm libraries when using system GDCM Brad King (2): COMP: Fix vxl_config_macros usage of CMake check macros BUG: Fix itk_module_config for repeated calls Bradley Lowekamp (8): ENH: Adding License file from upstream MetaIO ENH: Adding script to update MetaIO from upstream ENH: Remove ITK MetaIO to prepare for upstream import COMP: Fix variable type for Set/Get macros BUG: Use METER of sCAL scale unit BUG: Use PNG_SCALE_METER for PNG sCAL unit BUG: Fix overflows computing size of read tiff image BUG: Use array delete operator for array new allocations Christopher Mullins (2): COMP: Allows latex to compile for ITKSoftwareGuide COMP: Wrap MeshBase templates David T. Chen (1): DOC: Fixed HistogramThresholdImageFitler Gert Wollny (1): COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) Girish Mallya (1): BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. Hans Johnson (12): COMP: Add tolerance for comparing floating point PERF: Remove non-threadable algorithm components PERF: Remove large foot print of PDF derivatives. PERF: Revert Remove large foot print of PDF derivatives. STYLE: Test against almost equal for floating point values STYLE: Non-exact floating point testing PERF: Distribute initialization per thread buffers ENH: Remove unnecessary mutable qualifier. STYLE: Remove comment with no meaning. ENH: Moved accumlator logic to main MI class ENH: Allow staggering of accumulations per thread. PERF: Zero reset thread buffers during finalize Matthew McCormick (31): BUG: ArchiveTestingData.py future imports must occur at the beginning. DOC: Remove Image2.cxx reference from Book 2. DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. DOC: Remove references to Book 1 sections from Book 2. DOC: Make BinaryThresholdImageFilter not floating. DOC: Fix Software Guide figure caption for FlipImageFilter. DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. DOC: Remove duplicate figure in LaplacianRecursiveGaussianImageFilter2.cxx. DOC: ImageRandomConstIteratorWithIndex table reference. BUG: Bump GCCXML to 2014-08-06. BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. BUG: Fix alpha assignment for RGBA TIFF. BUG: Fix Nifti IO read with large images. BUG: Improve thread-safety and performance of PCAShapeSignedDistanceFunction. DOC: itk::statistics -> itk::Statistics. DOC: Remove duplicate text in LaplacianRecursiveGaussian example. DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. BUG: TransformFileReader does not clear its TransformList. BUG: Prevent dangling pointer in HDF5TransformIO. COMP: Fix missing prefix in ITKv3ImageRegistration20Test. BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform STYLE: Improve style in BinaryImageToLabelMapFilter. BUG: Fix BinaryImageToLabelMapFilter on 1D image. ENH: Improve precision of the joint PDF sum BUG: Fix BinShrinkImageFilter for different input/output image types. COMP: Fix transform type for ITKv3/IterativeClosestPoint2. COMP: Add missing wrapping for TransformIOBaseTemplate. BUG: gdcm::StringFilter recognizes backslash delimiter. ENH: Bump ITK version to 4.6.1. MetaIO Maintainers (1): MetaIO (reduced) Michka Popoff (4): BUG: Improve SWIG version check BUG: Add VTK_VERSION for older VTK versions BUG: Update VTK minimum version (for release) BUG: Fix memory leak in MetaImageIO after exception Vladimir S. FONOV (1): BUG: Fixing incorrect MINC style inverse transform From matt.mccormick at kitware.com Wed Oct 1 15:50:33 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 1 Oct 2014 15:50:33 -0400 Subject: [ITK] [ANNOUNCE] ITK 4.6.1 has been released! In-Reply-To: References: Message-ID: Minor correction: > > The next feature release of 4.6.0 is scheduled for June. > The next feature release of 4.7.0 is scheduled for December. From matt.mccormick at kitware.com Wed Oct 1 18:40:32 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 1 Oct 2014 18:40:32 -0400 Subject: [ITK] Opportunity to share, discuss, design, and learn with other ITK community members Message-ID: On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/u/0/events/c2284tfm9u9t6ft6ghp5u8546mc For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 To get regular invites to these events, join the ITK Bar Camp G+ Community: https://plus.google.com/u/0/communities/111375098792764998322 All are welcome. Hope to talk to you then! From joel.schaerer at laposte.net Thu Oct 2 05:33:06 2014 From: joel.schaerer at laposte.net (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=) Date: Thu, 02 Oct 2014 11:33:06 +0200 Subject: [ITK] [ITK-users] Proper chaining of filters Message-ID: <542D1BD2.40801@laposte.net> Hi all, I've noticed a couple times that when building a pipeline with ITK, you need to keep a reference to all filters before the pipeline is updated. This seems a little counter-intuitive to me, so I would like to better understand the issue and see if there is a way around it. As an example, the following code doesn't work: DilateType::Pointer dilate = DilateType::New(); dilate->SetInput(thresh->GetOutput()); dilate->SetKernel(kernel); dilate_filters.push_back(dilate); for (int i=0; i<14; ++i) { DilateType::Pointer temp = DilateType::New(); temp->SetInput(dilate->GetOutput()); temp->SetKernel(kernel); dilate = temp; } dilate->Update(); Regions don't get propagated properly and I get the following exception when writing the output: C++ exception with description "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not fully contain requested paste IO regionPaste IO region: ImageIORegion (0x7fff9bb72cc0) Dimension: 3 Index: 0 0 0 Size: 0 0 0 Largest possible region: ImageRegion (0x7fff9bb72bc0) Dimension: 3 Index: [0, 0, 0] Size: [0, 0, 0] " thrown in the test body. My guess is that the filters get destroyed before they get a chance to be executed. If I explicitely keep references to each filter, it works: DilateType::Pointer dilate = DilateType::New(); dilate->SetInput(thresh->GetOutput()); dilate->SetKernel(kernel); // We need to keep a reference to each filter in the pipeline before it is updated std::vector dilate_filters; dilate_filters.push_back(dilate); for (int i=0; i<14; ++i) { DilateType::Pointer temp = DilateType::New(); temp->SetInput(dilate_filters.back()->GetOutput()); temp->SetKernel(kernel); dilate = temp; dilate_filters.push_back(temp); } dilate_filters.back()->Update(); My question is, why doesn't a filter keep a reference to the previous filter in the pipeline? Is there a way around this? Thanks! Jo?l _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 pola_88 at hotmail.it Thu Oct 2 05:45:10 2014 From: pola_88 at hotmail.it (Paola Volonghi) Date: Thu, 2 Oct 2014 11:45:10 +0200 Subject: [ITK] (no subject) Message-ID: Hi all, we developed a python program on ubuntu 13.10 using vtk library ver. 5.8.0 and itk library ver. 3.20.1. In our program we used also these command lines: itk.VTKImageToImageFilter.IF3.New() itk.ImageToVTKImageFilter[image_type].New() itk.PyBuffer[image_type].GetArrayFromImage( ?. ) but we discovered that they don't work on itk ver. 4.x. Is there another way to convert images from itk to vtk and vice versa, using the newest versions of vtk and itk? Thanks! Paola -------------- next part -------------- An HTML attachment was scrubbed... URL: From michkapopoff at gmail.com Thu Oct 2 07:11:13 2014 From: michkapopoff at gmail.com (Michka Popoff) Date: Thu, 2 Oct 2014 13:11:13 +0200 Subject: [ITK] (no subject) In-Reply-To: References: Message-ID: <0978546B-55C4-470A-9BE2-C5DD20455818@gmail.com> Hi for the moment, the PyBuffer module has been moved out of ITK, and is no more maintained. There was a port done for ITK4, but it is not tested so I don?t know how well it is working [1] I plan to work a little bit on it one day if I can find some time. The way to move images from itk to vtk is to use the ITKVTKGlue module. You need to build ITK with: Module_ITKVtkGlue=ON Then you can do something like this (for a 2d image for example): image_type = itk.Image[itk.UC, 2] reader = itk.ImageFileReader[image_type].New() reader.SetFileName(?PATH/TO/FILE?) reader.Update() vtk_image = itk.ImageToVTKImageFilter[image_type].New() vtk_image.SetInput(reader.GetOutput()) vtk_image.Update() Then you can use the vtk_image as a vtk object, that you can render or work on. Is there a specific error message you get ? Michka [1] https://github.com/InsightSoftwareConsortium/itkPyBuffer On 2 oct. 2014, at 11:45, Paola Volonghi wrote: > Hi all, > we developed a python program on ubuntu 13.10 using vtk library ver. 5.8.0 and itk library ver. 3.20.1. In our program we used also these command lines: > itk.VTKImageToImageFilter.IF3.New() > itk.ImageToVTKImageFilter[image_type].New() > itk.PyBuffer[image_type].GetArrayFromImage( ?. ) > but we discovered that they don't work on itk ver. 4.x. > Is there another way to convert images from itk to vtk and vice versa, using the newest versions of vtk and itk? > > Thanks! > > Paola > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Thu Oct 2 10:16:08 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 2 Oct 2014 10:16:08 -0400 Subject: [ITK] [ITK-users] Proper chaining of filters In-Reply-To: <542D1BD2.40801@laposte.net> References: <542D1BD2.40801@laposte.net> Message-ID: Hi Jo?l, Calling temp->SetInput(dilate->GetOutput()); Connects the DataObject generated by dilate to the temp filter. temp does not increment dilate's reference count, and it would be difficult to do since the SetInput input is the DataObject, not the ProcessObject. As a consequence, at least one SmartPointer needs to be kept in scope as with your second example. HTH, Matt On Thu, Oct 2, 2014 at 5:33 AM, Jo?l Schaerer wrote: > Hi all, > > I've noticed a couple times that when building a pipeline with ITK, you need > to keep a reference to all filters before the pipeline is updated. This > seems a little counter-intuitive to me, so I would like to better understand > the issue and see if there is a way around it. > > As an example, the following code doesn't work: > > DilateType::Pointer dilate = DilateType::New(); > dilate->SetInput(thresh->GetOutput()); > dilate->SetKernel(kernel); > > dilate_filters.push_back(dilate); > for (int i=0; i<14; ++i) { > DilateType::Pointer temp = DilateType::New(); > temp->SetInput(dilate->GetOutput()); > temp->SetKernel(kernel); > dilate = temp; > } > dilate->Update(); > > Regions don't get propagated properly and I get the following exception when > writing the output: > > C++ exception with description > "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: > itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not > fully contain requested paste IO regionPaste IO region: ImageIORegion > (0x7fff9bb72cc0) > Dimension: 3 > Index: 0 0 0 > Size: 0 0 0 > Largest possible region: ImageRegion (0x7fff9bb72bc0) > Dimension: 3 > Index: [0, 0, 0] > Size: [0, 0, 0] > " thrown in the test body. > > My guess is that the filters get destroyed before they get a chance to be > executed. If I explicitely keep references to each filter, it works: > > DilateType::Pointer dilate = DilateType::New(); > dilate->SetInput(thresh->GetOutput()); > dilate->SetKernel(kernel); > // We need to keep a reference to each filter in the pipeline before it is > updated > std::vector dilate_filters; > dilate_filters.push_back(dilate); > for (int i=0; i<14; ++i) { > DilateType::Pointer temp = DilateType::New(); > temp->SetInput(dilate_filters.back()->GetOutput()); > temp->SetKernel(kernel); > dilate = temp; > dilate_filters.push_back(temp); > } > dilate_filters.back()->Update(); > > My question is, why doesn't a filter keep a reference to the previous filter > in the pipeline? Is there a way around this? > > Thanks! > > Jo?l > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 joel.schaerer at laposte.net Thu Oct 2 10:22:24 2014 From: joel.schaerer at laposte.net (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=) Date: Thu, 02 Oct 2014 16:22:24 +0200 Subject: [ITK] [ITK-users] Proper chaining of filters In-Reply-To: References: <542D1BD2.40801@laposte.net> Message-ID: <542D5FA0.8070903@laposte.net> Hi Matt, Thanks for the confirmation. I was thinking there might be another mechanism I wasn't aware of. Jo?l On 10/02/2014 04:16 PM, Matt McCormick wrote: > Hi Jo?l, > > Calling > > temp->SetInput(dilate->GetOutput()); > > Connects the DataObject generated by dilate to the temp filter. temp > does not increment dilate's reference count, and it would be difficult > to do since the SetInput input is the DataObject, not the > ProcessObject. > > As a consequence, at least one SmartPointer needs to be kept in scope > as with your second example. > > HTH, > Matt > > On Thu, Oct 2, 2014 at 5:33 AM, Jo?l Schaerer wrote: >> Hi all, >> >> I've noticed a couple times that when building a pipeline with ITK, you need >> to keep a reference to all filters before the pipeline is updated. This >> seems a little counter-intuitive to me, so I would like to better understand >> the issue and see if there is a way around it. >> >> As an example, the following code doesn't work: >> >> DilateType::Pointer dilate = DilateType::New(); >> dilate->SetInput(thresh->GetOutput()); >> dilate->SetKernel(kernel); >> >> dilate_filters.push_back(dilate); >> for (int i=0; i<14; ++i) { >> DilateType::Pointer temp = DilateType::New(); >> temp->SetInput(dilate->GetOutput()); >> temp->SetKernel(kernel); >> dilate = temp; >> } >> dilate->Update(); >> >> Regions don't get propagated properly and I get the following exception when >> writing the output: >> >> C++ exception with description >> "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: >> itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not >> fully contain requested paste IO regionPaste IO region: ImageIORegion >> (0x7fff9bb72cc0) >> Dimension: 3 >> Index: 0 0 0 >> Size: 0 0 0 >> Largest possible region: ImageRegion (0x7fff9bb72bc0) >> Dimension: 3 >> Index: [0, 0, 0] >> Size: [0, 0, 0] >> " thrown in the test body. >> >> My guess is that the filters get destroyed before they get a chance to be >> executed. If I explicitely keep references to each filter, it works: >> >> DilateType::Pointer dilate = DilateType::New(); >> dilate->SetInput(thresh->GetOutput()); >> dilate->SetKernel(kernel); >> // We need to keep a reference to each filter in the pipeline before it is >> updated >> std::vector dilate_filters; >> dilate_filters.push_back(dilate); >> for (int i=0; i<14; ++i) { >> DilateType::Pointer temp = DilateType::New(); >> temp->SetInput(dilate_filters.back()->GetOutput()); >> temp->SetKernel(kernel); >> dilate = temp; >> dilate_filters.push_back(temp); >> } >> dilate_filters.back()->Update(); >> >> My question is, why doesn't a filter keep a reference to the previous filter >> in the pipeline? Is there a way around this? >> >> Thanks! >> >> Jo?l >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 pedromorais-17 at hotmail.com Thu Oct 2 12:24:31 2014 From: pedromorais-17 at hotmail.com (Pedro Morais) Date: Thu, 2 Oct 2014 09:24:31 -0700 (PDT) Subject: [ITK] [ITK-users] 3D generalized hough transform Message-ID: <1412267071841-7586297.post@n2.nabble.com> Hi all, I'm wonder if ITK has an implementation of a 3D generalized hough transform. Do you have any idea? Regards, Pedro -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/3D-generalized-hough-transform-tp7586297.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 llliu at umich.edu Thu Oct 2 20:40:16 2014 From: llliu at umich.edu (Lianli Liu) Date: Thu, 2 Oct 2014 20:40:16 -0400 Subject: [ITK] [ITK-users] vector image registration Message-ID: Hi all, I wonder if ITK is supporting vector image registration now? If not, any suggestions to achieve this goal? Thanks! Lianli -------------- 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 ggigi78 at gmail.com Fri Oct 3 05:05:29 2014 From: ggigi78 at gmail.com (Gianluigi Caddeo) Date: Fri, 3 Oct 2014 10:05:29 +0100 Subject: [ITK] [ITK-users] help installing ITK Message-ID: Hi all, during my installation on an ubuntu machine I had this problem: *[100%] Built target ITKv3ThinPlateSplineWarp/bin/sh: 1: DOXYGEN_EXECUTABLE-NOTFOUND: not foundmake[2]: *** [Utilities/Doxygen/CMakeFiles/Documentation] Errore 127make[1]: *** [Utilities/Doxygen/CMakeFiles/Documentation.dir/all] Errore 2make: *** [all] Errore* But doxygen exist and stay in my */usr/bin* directory How can I to force ITK to search doxygen in that directory? thanks a lot Gg -------------- 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 fitz at zhaw.ch Fri Oct 3 09:04:49 2014 From: fitz at zhaw.ch (Fitze Thomas (fitz)) Date: Fri, 3 Oct 2014 13:04:49 +0000 Subject: [ITK] Using filters with images of different dimensions Message-ID: <1BBE26F3-BB10-4BAE-BCFB-B30A2FE8448D@zhaw.ch> Hi all My current situation: 1. 3D inputImage 2. calculate hessian matrix for the image 3. calculate trace of hessian matrix for each voxel 4. use GetAverageSliceImagefilter to get an average (along 1 dimension) of the hessian trace for each voxel in a slice. This reduces the size of this dimension to 1. I will call this the ?averageTracePlane?. Now i want to use the averageTracePlane as a sort of lookup table for my inputImage and apply the corresponding averageTrace value. Or in pseudo code: inputImage(x,y,z) = some_constant * averageTracePlane(x,y,1) How do i set up a image filter that iterates over my inputImage and cycles through the averageTracePlane? I tried using a BinaryFunctorImageFilter, but could not figure out how to get it to ?cycle" trough my averageTracePlane with dimension size 1. Thanks a lot, Thomas From blowekamp at mail.nih.gov Fri Oct 3 09:41:14 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 3 Oct 2014 09:41:14 -0400 Subject: [ITK] Using filters with images of different dimensions (Image broadcast operators?) In-Reply-To: <1BBE26F3-BB10-4BAE-BCFB-B30A2FE8448D@zhaw.ch> References: <1BBE26F3-BB10-4BAE-BCFB-B30A2FE8448D@zhaw.ch> Message-ID: <8BBBA5D3-F1B0-4DC2-8DE3-99F3070B5BDD@mail.nih.gov> Hello, On Oct 3, 2014, at 9:04 AM, Fitze Thomas (fitz) wrote: > Hi all > > My current situation: > 1. 3D inputImage > 2. calculate hessian matrix for the image > 3. calculate trace of hessian matrix for each voxel > 4. use GetAverageSliceImagefilter to get an average (along 1 dimension) of the hessian trace for each voxel in a slice. This reduces the size of this dimension to 1. I will call this the ?averageTracePlane?. Did you consider using a couple MeanProjectionImageFilters[1] to achieve this? > > Now i want to use the averageTracePlane as a sort of lookup table for my inputImage and apply the corresponding averageTrace value. Or in pseudo code: > inputImage(x,y,z) = some_constant * averageTracePlane(x,y,1) > > How do i set up a image filter that iterates over my inputImage and cycles through the averageTracePlane? I tried using a BinaryFunctorImageFilter, but could not figure out how to get it to ?cycle" trough my averageTracePlane with dimension size 1. > You are not going to be able to use any of the Functor based filters as they will expect the images to be the same dimensions. You will need to create a custom filter to do this. You may find the ImageSliceConstItearatorWithIndex[2] use full in combination with a region iterator. Something like this: ImageSliceConstIteratorWithIndex it( image, image->GetRequestedRegion() ); ImageRegionIteratorType it2(projectedImage, projectedImage->GetRequestedRegion() ); it.SetFirstDirection(0); it.SetSecondDirection(1); it.GoToBegin(); it2.GoToBegin(); while( !it.IsAtEnd() && !it2.IsAtEnd() ) { while( !it.IsAtEndOfSlice() ) { while( !it.IsAtEndOfLine() ) { value = it.Get() * it2.Get(); ++it; } it.NextLine(); } it.NextSlice(); ++it2; } This concept of doing operations on different sized images is common in numerical environments such as Matlab, numpy[3] etc..., we don't currently have it in ITK, and I'm not aware of any Insight Journal Article which contributes it either. I think this could be quite a useful filter, say BroadcastingBinaryFunctorImageFilter. Brad > Thanks a lot, > Thomas [1] http://www.itk.org/Doxygen/html/classitk_1_1MeanProjectionImageFilter.html [2] http://www.itk.org/Doxygen/html/classitk_1_1ImageSliceConstIteratorWithIndex.html [3] http://docs.scipy.org/doc/numpy/user/basics.broadcasting.html > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From nicgallego at gmail.com Fri Oct 3 10:29:00 2014 From: nicgallego at gmail.com (Nicolas Gallego) Date: Fri, 3 Oct 2014 16:29:00 +0200 Subject: [ITK] Using filters with images of different dimensions In-Reply-To: <1BBE26F3-BB10-4BAE-BCFB-B30A2FE8448D@zhaw.ch> References: <1BBE26F3-BB10-4BAE-BCFB-B30A2FE8448D@zhaw.ch> Message-ID: Hi Fitze, It seams that what you need is an image iterator. Find some information on classes like itkImageRegionIterator [1] and further information on the software guide [2] on iterators chapter 6. There are different flavors depending on what you need. You may consider the WithIndex iterators since you mentioned you intent to use that image as a lookup table. I hope that helps, [1] http://www.itk.org/Doxygen46/html/classitk_1_1ImageRegionIterator.html [2] http://www.itk.org/ItkSoftwareGuide.pdf Nicol?s Gallego-Ortiz Universit? catholique de Louvain, Belgium 2014-10-03 15:04 GMT+02:00 Fitze Thomas (fitz) : > Hi all > > My current situation: > 1. 3D inputImage > 2. calculate hessian matrix for the image > 3. calculate trace of hessian matrix for each voxel > 4. use GetAverageSliceImagefilter to get an average (along 1 dimension) of > the hessian trace for each voxel in a slice. This reduces the size of this > dimension to 1. I will call this the ?averageTracePlane?. > > Now i want to use the averageTracePlane as a sort of lookup table for my > inputImage and apply the corresponding averageTrace value. Or in pseudo > code: > inputImage(x,y,z) = some_constant * averageTracePlane(x,y,1) > > How do i set up a image filter that iterates over my inputImage and cycles > through the averageTracePlane? I tried using a BinaryFunctorImageFilter, > but could not figure out how to get it to ?cycle" trough my > averageTracePlane with dimension size 1. > > Thanks a lot, > Thomas > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Oct 3 12:57:27 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 3 Oct 2014 12:57:27 -0400 Subject: [ITK] [ITK-dev] Missing "gdcmImageHelper.h" "gdcmSerieHelper.h" on Debian-sid-gcc4-64bit Message-ID: Hi Steve, Mathieu, I noticed that the Debian-sid-gcc4-64bit is having build failures due to missing gdcmImageHelper.h, gdcmSerieHelper.h, since Tuesday, September 30th. Debian-sid-gcc4-32bit ?seems fine. Any ideas on what is happening? Thanks, Matt _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check 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 mathieu.malaterre at gmail.com Sat Oct 4 08:11:09 2014 From: mathieu.malaterre at gmail.com (Mathieu Malaterre) Date: Sat, 4 Oct 2014 14:11:09 +0200 Subject: [ITK] [ITK-dev] Missing "gdcmImageHelper.h" "gdcmSerieHelper.h" on Debian-sid-gcc4-64bit In-Reply-To: <3257282.IFWIHhm9zD@riemann> References: <3257282.IFWIHhm9zD@riemann> Message-ID: On Fri, Oct 3, 2014 at 10:15 PM, Steve M. Robbins wrote: > On October 3, 2014 12:57:27 PM Matt McCormick wrote: >> Hi Steve, Mathieu, >> >> I noticed that the Debian-sid-gcc4-64bit is having build failures due >> to missing gdcmImageHelper.h, gdcmSerieHelper.h, since Tuesday, >> September 30th. Debian-sid-gcc4-32bit seems fine. Any ideas on what >> is happening? > > Well, the difference between the two systems is that I update "Debian-sid- > gcc4-64bit" very regularly, and update "-32bit" very rarely. In particular, > "-64bit" has "gdcm (2.4.4-2)" updated on Sept 30th. > > I'll start looking into the build failure. Thanks for pointing it out. It's there: https://packages.debian.org/sid/amd64/libgdcm2-dev/filelist I guess the cmake cache is still using /usr/include/gdcm-2.2 instead of /usr/include/gdcm-2.4 2cts -- Mathieu _______________________________________________ Powered by www.kitware.com 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 arnaudgelas at gmail.com Mon Oct 6 03:58:09 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Mon, 6 Oct 2014 09:58:09 +0200 Subject: [ITK] [ITK-users] How to remove a tag from MetaDataDictionary? Message-ID: Hi all, I am trying to write a DICOM file in which, the orientation (among others) has changed in my pipeline... 1- After having a look https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919 It appears to me that if the orientation is in the MetaDataDictionary, it is saved anyway into the DICOM image, there is no way to force the ImageIO to recompute it from the image and save it ??? If there is, can anyone give me a pointer? 2- Since I can't find a way to update the image orientation in itk::GDCMImageIO, I have been looking at removing the corresponding tag from the MetaDataDictionary. I could not find any method or any way to do it??? If there is, can anyone give me a pointer? I wish I would not have to copy the dictionary and add if statement to avoid copying the direction... Thanks in advance, Arnaud -------------- 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 emmasaunders123 at gmail.com Mon Oct 6 07:31:03 2014 From: emmasaunders123 at gmail.com (Emma Saunders) Date: Mon, 6 Oct 2014 12:31:03 +0100 Subject: [ITK] [ITK-users] Overlap_image registration metrics Message-ID: Hello all, When computing metrics for image registration, does ITK calculated the metric for only the regions in the image that overlap? If so is this performed on just the initial regions that overlap or will this region of overlap increase during registration and thus require the region in which the metric is calculated to alter? Thanks for any help Emma -------------- 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.ulge at gmail.com Mon Oct 6 09:20:27 2014 From: marco.ulge at gmail.com (Marco Ulge) Date: Mon, 6 Oct 2014 06:20:27 -0700 (MST) Subject: [ITK] [ITK-users] Texture Features extraction Message-ID: <1412601627242-34642.post@n7.nabble.com> Hello, i'm currently working on texture feature extraction and I'm following this examle: http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures It works fine and basically it's all i need. The only problem is that i need to able to specify an arbitrary window size (which is 3 in this example) but as soon as i try to assign it a different value this won't work anymore and i can't figure out why. Can anyone help me with this please? Thanks. Marco -- View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.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 dominique at toepfer-web.de Mon Oct 6 09:47:12 2014 From: dominique at toepfer-web.de (=?ISO-8859-1?Q?Dominique_T=F6pfer?=) Date: Mon, 06 Oct 2014 15:47:12 +0200 Subject: [ITK] [ITK-users] Texture Features extraction In-Reply-To: <1412601627242-34642.post@n7.nabble.com> References: <1412601627242-34642.post@n7.nabble.com> Message-ID: <54329D60.9030004@toepfer-web.de> Hi Marco, you probably forgot to adjust the range of the for-loops. They are running from 1 to size-2 so that the window will not "leave" the image at its boundaries. HTH Dominique On 06.10.2014 15:20, Marco Ulge wrote: > Hello, > > i'm currently working on texture feature extraction and I'm following this > examle: > http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures > > > It works fine and basically it's all i need. The only problem is that i need > to able to specify an arbitrary window size (which is 3 in this example) but > as soon as i try to assign it a different value this won't work anymore and > i can't figure out why. > > Can anyone help me with this please? > > Thanks. > > Marco > > > > -- > View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.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 marco.ulge at gmail.com Mon Oct 6 10:18:26 2014 From: marco.ulge at gmail.com (Marco Ulge) Date: Mon, 6 Oct 2014 07:18:26 -0700 (MST) Subject: [ITK] [ITK-users] Texture Features extraction In-Reply-To: <54329D60.9030004@toepfer-web.de> References: <1412601627242-34642.post@n7.nabble.com> <54329D60.9030004@toepfer-web.de> Message-ID: <1412605106652-34644.post@n7.nabble.com> Thanks for your reply, so if i wanted to specify a window size of 5 (for example) i should iterate from 1 to size - 4? Thanks. Marco -- View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642p34644.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 wjhzwy at gmail.com Mon Oct 6 10:27:10 2014 From: wjhzwy at gmail.com (Jiahui Wang) Date: Mon, 6 Oct 2014 10:27:10 -0400 Subject: [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer Message-ID: Dear All, I modified ImageRegistration8.cxx to run my own rigid registration. However, I found that the processing time of ITKv4 based RegularStepGradientDescentOptimizer is almost 10 times more than that of ITKv3 based one. The program was run on the same machine. The only difference is the ITK libraries. Could anyone give me some suggestions to solve this issue? Thanks, JW -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Mon Oct 6 11:08:10 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 6 Oct 2014 11:08:10 -0400 Subject: [ITK] [ITK-users] How to remove a tag from MetaDataDictionary? In-Reply-To: References: Message-ID: Hi Arnaud, > I am trying to write a DICOM file in which, the orientation (among others) > has changed in my pipeline... > > 1- After having a look > https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919 > > It appears to me that if the orientation is in the MetaDataDictionary, it is > saved anyway into the DICOM image, there is no way to force the ImageIO to > recompute it from the image and save it ??? > If there is, can anyone give me a pointer? If there is a Direction on the input image, it should use it [1]. But the DICOM tag 0020|0037 cannot be present. > 2- Since I can't find a way to update the image orientation in > itk::GDCMImageIO, I have been looking at removing the corresponding tag from > the MetaDataDictionary. I could not find any method or any way to do it??? > If there is, can anyone give me a pointer? > > I wish I would not have to copy the dictionary and add if statement to avoid > copying the direction... This is the method I usually apply... Sorry for the lack of new tricks! Matt [1] https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L816-L828 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Mon Oct 6 11:12:52 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 6 Oct 2014 11:12:52 -0400 Subject: [ITK] [ITK-users] Overlap_image registration metrics In-Reply-To: References: Message-ID: Hi Emma, > When computing metrics for image registration, does ITK calculated the > metric for only the regions in the image that overlap? Yes. See, for example, [1]. > If so is this performed on just the initial regions that overlap or will > this region of overlap increase during registration and thus require the > region in which the metric is calculated to alter? Yes. Ideally, as the registration progresses, the overlap increases, and the registration becomes progressively better. HTH, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.hxx;h=8a6069dde32309a214229968294a14911c701dd0;hb=HEAD#l312 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From lasso at queensu.ca Mon Oct 6 11:44:08 2014 From: lasso at queensu.ca (Andras Lasso) Date: Mon, 6 Oct 2014 15:44:08 +0000 Subject: [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer In-Reply-To: References: Message-ID: See this long thread about this issue: http://slicer-devel.65872.n3.nabble.com/BRAINS-rigid-registration-td4032229.html Short summary: There were some performance regressions in mutual information metric computation, threading, etc. that have been recently fixed, so use the latest ITK version. ITKv4 uses a slightly slower but more accurate optimizer, but if you adjust the number of samples and stopping condition then usually the registration time only increases by about 30-50% (and you might get better quality results). You can see all the changes that have been done in 3D Slicer and BRAINS repositories to go from a 10x-100x slowdown to an approximately equivalent registration speed with ITKv4 compared to ITKv3. Andras From: Community [mailto:community-bounces at itk.org] On Behalf Of Jiahui Wang Sent: Monday, October 06, 2014 10:27 AM To: insight-users at itk.org Subject: [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer Dear All, I modified ImageRegistration8.cxx to run my own rigid registration. However, I found that the processing time of ITKv4 based RegularStepGradientDescentOptimizer is almost 10 times more than that of ITKv3 based one. The program was run on the same machine. The only difference is the ITK libraries. Could anyone give me some suggestions to solve this issue? Thanks, JW -------------- 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 dae.wong at gmail.com Tue Oct 7 03:38:49 2014 From: dae.wong at gmail.com (Fabian Torres) Date: Tue, 7 Oct 2014 15:38:49 +0800 Subject: [ITK] [ITK-users] region inside points Message-ID: Hi all. I have an image that represents some pixels over the surface of an object. Pixels in the surface have value of 1 while any other pixel has value of 0. The pixels are not a continuous line, there are some gaps between pixels. I want to know the region surrounded by the white pixels in my image. I will be working with 2D and 3D data. Is there any class implemented in ITK that I can use? Thanks -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.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 g.bogle at auckland.ac.nz Tue Oct 7 03:40:40 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 7 Oct 2014 07:40:40 +0000 Subject: [ITK] [ITK-users] region inside points In-Reply-To: References: Message-ID: Maybe you could do something with BinaryImageDilateFilter. ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian Torres [dae.wong at gmail.com] Sent: Tuesday, 7 October 2014 8:38 p.m. To: insight-users Subject: [ITK-users] region inside points Hi all. I have an image that represents some pixels over the surface of an object. Pixels in the surface have value of 1 while any other pixel has value of 0. The pixels are not a continuous line, there are some gaps between pixels. I want to know the region surrounded by the white pixels in my image. I will be working with 2D and 3D data. Is there any class implemented in ITK that I can use? Thanks -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.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 g.bogle at auckland.ac.nz Tue Oct 7 03:46:17 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 7 Oct 2014 07:46:17 +0000 Subject: [ITK] [ITK-users] region inside points In-Reply-To: References: , Message-ID: Sorry, I misread your post Fabian - I read it as you wanting the region _surrounding_ the white pixels. But dilate might be usable to fill the gaps, followed by skeletonization. ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Tuesday, 7 October 2014 8:40 p.m. To: Fabian Torres; insight-users Subject: Re: [ITK-users] region inside points Maybe you could do something with BinaryImageDilateFilter. ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian Torres [dae.wong at gmail.com] Sent: Tuesday, 7 October 2014 8:38 p.m. To: insight-users Subject: [ITK-users] region inside points Hi all. I have an image that represents some pixels over the surface of an object. Pixels in the surface have value of 1 while any other pixel has value of 0. The pixels are not a continuous line, there are some gaps between pixels. I want to know the region surrounded by the white pixels in my image. I will be working with 2D and 3D data. Is there any class implemented in ITK that I can use? Thanks -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.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 pola_88 at hotmail.it Tue Oct 7 04:02:39 2014 From: pola_88 at hotmail.it (Paola Volonghi) Date: Tue, 7 Oct 2014 10:02:39 +0200 Subject: [ITK] (no subject) In-Reply-To: <0978546B-55C4-470A-9BE2-C5DD20455818@gmail.com> References: , <0978546B-55C4-470A-9BE2-C5DD20455818@gmail.com> Message-ID: Thanks for your reply.We have just tried before to do what you suggested.Any other idea??ThanksPaola Subject: Re: [ITK] (no subject) From: michkapopoff at gmail.com Date: Thu, 2 Oct 2014 13:11:13 +0200 CC: community at itk.org To: pola_88 at hotmail.it Hi for the moment, the PyBuffer module has been moved out of ITK, and is no more maintained.There was a port done for ITK4, but it is not tested so I don?t know how well it is working [1]I plan to work a little bit on it one day if I can find some time. The way to move images from itk to vtk is to use the ITKVTKGlue module.You need to build ITK with:Module_ITKVtkGlue=ON Then you can do something like this (for a 2d image for example): image_type = itk.Image[itk.UC, 2]reader = itk.ImageFileReader[image_type].New()reader.SetFileName(?PATH/TO/FILE?)reader.Update()vtk_image = itk.ImageToVTKImageFilter[image_type].New()vtk_image.SetInput(reader.GetOutput())vtk_image.Update() Then you can use the vtk_image as a vtk object, that you can render or work on. Is there a specific error message you get ? Michka [1] https://github.com/InsightSoftwareConsortium/itkPyBuffer On 2 oct. 2014, at 11:45, Paola Volonghi wrote:Hi all,we developed a python program on ubuntu 13.10 using vtk library ver. 5.8.0 and itk library ver. 3.20.1. In our program we used also these command lines:itk.VTKImageToImageFilter.IF3.New()itk.ImageToVTKImageFilter[image_type].New()itk.PyBuffer[image_type].GetArrayFromImage( ?. )but we discovered that they don't work on itk ver. 4.x.Is there another way to convert images from itk to vtk and vice versa, using the newest versions of vtk and itk? Thanks! Paola _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From michkapopoff at gmail.com Tue Oct 7 04:04:52 2014 From: michkapopoff at gmail.com (Michka Popoff) Date: Tue, 7 Oct 2014 10:04:52 +0200 Subject: [ITK] (no subject) In-Reply-To: References: , <0978546B-55C4-470A-9BE2-C5DD20455818@gmail.com> Message-ID: What error message are you getting or what is happening ? It?s not really clear to me. When you say ?It doesn?t work?, I need more details to be able to help you. Michka On 7 oct. 2014, at 10:02, Paola Volonghi wrote: > Thanks for your reply. > We have just tried before to do what you suggested. > Any other idea?? > Thanks > Paola > > Subject: Re: [ITK] (no subject) > From: michkapopoff at gmail.com > Date: Thu, 2 Oct 2014 13:11:13 +0200 > CC: community at itk.org > To: pola_88 at hotmail.it > > Hi > > for the moment, the PyBuffer module has been moved out of ITK, and is no more maintained. > There was a port done for ITK4, but it is not tested so I don?t know how well it is working [1] > I plan to work a little bit on it one day if I can find some time. > > The way to move images from itk to vtk is to use the ITKVTKGlue module. > You need to build ITK with: > Module_ITKVtkGlue=ON > > Then you can do something like this (for a 2d image for example): > > image_type = itk.Image[itk.UC, 2] > reader = itk.ImageFileReader[image_type].New() > reader.SetFileName(?PATH/TO/FILE?) > reader.Update() > vtk_image = itk.ImageToVTKImageFilter[image_type].New() > vtk_image.SetInput(reader.GetOutput()) > vtk_image.Update() > > Then you can use the vtk_image as a vtk object, that you can render or work on. > > Is there a specific error message you get ? > > Michka > > [1] https://github.com/InsightSoftwareConsortium/itkPyBuffer > > On 2 oct. 2014, at 11:45, Paola Volonghi wrote: > > Hi all, > we developed a python program on ubuntu 13.10 using vtk library ver. 5.8.0 and itk library ver. 3.20.1. In our program we used also these command lines: > itk.VTKImageToImageFilter.IF3.New() > itk.ImageToVTKImageFilter[image_type].New() > itk.PyBuffer[image_type].GetArrayFromImage( ?. ) > but we discovered that they don't work on itk ver. 4.x. > Is there another way to convert images from itk to vtk and vice versa, using the newest versions of vtk and itk? > > Thanks! > > Paola > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From dae.wong at gmail.com Tue Oct 7 04:05:24 2014 From: dae.wong at gmail.com (Fabian Torres) Date: Tue, 7 Oct 2014 16:05:24 +0800 Subject: [ITK] [ITK-users] region inside points In-Reply-To: References: Message-ID: Hi Gib. Thanks for the quick response. The problem of using dilation and skeletonization is that some times the gap between pixels is big, and I will have to work with different and big structural elements to be sure that all the gaps were eliminated. I was hoping to find a class that works similar to a convex hull (it does not have to be convex) algorithm and then find the region surrounded by the hull. Thanks On Tue, Oct 7, 2014 at 3:46 PM, Gib Bogle wrote: > Sorry, I misread your post Fabian - I read it as you wanting the region > _surrounding_ the white pixels. But dilate might be usable to fill the > gaps, followed by skeletonization. > ------------------------------ > *From:* Insight-users [insight-users-bounces at itk.org] on behalf of Gib > Bogle [g.bogle at auckland.ac.nz] > *Sent:* Tuesday, 7 October 2014 8:40 p.m. > *To:* Fabian Torres; insight-users > *Subject:* Re: [ITK-users] region inside points > > Maybe you could do something with BinaryImageDilateFilter. > ------------------------------ > *From:* Insight-users [insight-users-bounces at itk.org] on behalf of Fabian > Torres [dae.wong at gmail.com] > *Sent:* Tuesday, 7 October 2014 8:38 p.m. > *To:* insight-users > *Subject:* [ITK-users] region inside points > > Hi all. > > I have an image that represents some pixels over the surface of an > object. Pixels in the surface have value of 1 while any other pixel has > value of 0. > The pixels are not a continuous line, there are some gaps between pixels. > I want to know the region surrounded by the white pixels in my image. > > I will be working with 2D and 3D data. Is there any class implemented in > ITK that I can use? > > Thanks > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.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 g.bogle at auckland.ac.nz Tue Oct 7 04:08:23 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 7 Oct 2014 08:08:23 +0000 Subject: [ITK] [ITK-users] region inside points In-Reply-To: References: , Message-ID: Maybe there is a way to use a rolling ball. Richard Beare has some morphological filters that might be applicable, but I think it will always be a bit complicated. ________________________________ From: Fabian Torres [dae.wong at gmail.com] Sent: Tuesday, 7 October 2014 9:05 p.m. To: Gib Bogle Cc: insight-users Subject: Re: [ITK-users] region inside points Hi Gib. Thanks for the quick response. The problem of using dilation and skeletonization is that some times the gap between pixels is big, and I will have to work with different and big structural elements to be sure that all the gaps were eliminated. I was hoping to find a class that works similar to a convex hull (it does not have to be convex) algorithm and then find the region surrounded by the hull. Thanks On Tue, Oct 7, 2014 at 3:46 PM, Gib Bogle > wrote: Sorry, I misread your post Fabian - I read it as you wanting the region _surrounding_ the white pixels. But dilate might be usable to fill the gaps, followed by skeletonization. ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Tuesday, 7 October 2014 8:40 p.m. To: Fabian Torres; insight-users Subject: Re: [ITK-users] region inside points Maybe you could do something with BinaryImageDilateFilter. ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian Torres [dae.wong at gmail.com] Sent: Tuesday, 7 October 2014 8:38 p.m. To: insight-users Subject: [ITK-users] region inside points Hi all. I have an image that represents some pixels over the surface of an object. Pixels in the surface have value of 1 while any other pixel has value of 0. The pixels are not a continuous line, there are some gaps between pixels. I want to know the region surrounded by the white pixels in my image. I will be working with 2D and 3D data. Is there any class implemented in ITK that I can use? Thanks -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.com -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.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 rousseau at unistra.fr Tue Oct 7 04:11:03 2014 From: rousseau at unistra.fr (francois rousseau) Date: Tue, 7 Oct 2014 10:11:03 +0200 Subject: [ITK] [ITK-users] Segmentation fault when using BSplineScatteredDataPointSetToImageFilter for 3D image Message-ID: <44223E94-F14E-4CF5-A0D6-C667CD3DDE29@unistra.fr> Hi everyone, I?m trying to use the BSplineScatteredDataPointSetToImageFilter. No problem when applying it on 2D images (using itkBSplineScatteredDataPointSetToImageFilterTest.cxx). However, after setting const unsigned int ParametricDimension = 3; it crashes when I try to apply it on 3D image (segmentation fault). Can this code be used for 3D images? Thank you Fran?ois -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 2828 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From ggigi78 at gmail.com Tue Oct 7 09:12:21 2014 From: ggigi78 at gmail.com (Gianluigi Caddeo) Date: Tue, 7 Oct 2014 14:12:21 +0100 Subject: [ITK] [ITK-users] 8. help installing ITK (Gianluigi Caddeo) solved Message-ID: Hi all, I solved my problem, I gave the correct path to the DOXYGEN_EXECUTABLE variable. Gg On Tue, Oct 7, 2014 at 9:05 AM, wrote: > Send Insight-users mailing list submissions to > insight-users at itk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/insight-users > or, via email, send a message with subject or body 'help' to > insight-users-request at itk.org > > You can reach the person managing the list at > insight-users-owner at itk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Insight-users digest..." > > > Today's Topics: > > 1. [ANNOUNCE] ITK 4.6.1 has been released! (Matt McCormick) > 2. Re: [ANNOUNCE] ITK 4.6.1 has been released! (Matt McCormick) > 3. Proper chaining of filters (Jo?l Schaerer) > 4. Re: [ITK] Proper chaining of filters (Matt McCormick) > 5. Re: [ITK] Proper chaining of filters (Jo?l Schaerer) > 6. 3D generalized hough transform (Pedro Morais) > 7. vector image registration (Lianli Liu) > 8. help installing ITK (Gianluigi Caddeo) > 9. How to remove a tag from MetaDataDictionary? (Arnaud Gelas) > 10. Overlap_image registration metrics (Emma Saunders) > 11. Texture Features extraction (Marco Ulge) > 12. Re: Texture Features extraction (Dominique T?pfer) > 13. Re: Texture Features extraction (Marco Ulge) > 14. Speed of ITKv4 based Gradient Descent Optimizer (Jiahui Wang) > 15. Re: How to remove a tag from MetaDataDictionary? (Matt McCormick) > 16. Re: Overlap_image registration metrics (Matt McCormick) > 17. Re: [ITK] Speed of ITKv4 based Gradient Descent Optimizer > (Andras Lasso) > 18. Polygon inside point (Fabian Torres) > 19. region inside points (Fabian Torres) > 20. Re: region inside points (Gib Bogle) > 21. Re: region inside points (Gib Bogle) > 22. Re: region inside points (Fabian Torres) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 1 Oct 2014 15:40:44 -0400 > From: Matt McCormick > To: "community at itk.org" , "insight-users at itk.org" > , ITK > Subject: [ITK-users] [ANNOUNCE] ITK 4.6.1 has been released! > Message-ID: > < > CALzTN-TXyhZ2aDaA-UQoFgbg3fPPCPzYKKFpAmKvuquf1EXgrw at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > On behalf of the Insight Toolkit Community, we are happy to announce > the release of ITK 4.6.1! > > This is a patch release that addresses critical issues. The 4.6.1 > release fixes DICOM, MetaIO, TIFF, and PNG IO issues, 32-bit WrapITK > build errors, Python wrapping warnings, CMake configuration with > COMPONENTS, performance and memory consumption of the ITKv4 > implementation of the mutual information matching metric, and a many > other issues. > > Congratulations and thanks to everyone who contributed to this > release. We are particularly grateful for the collaborations with the > 3D Slicer, Debian, GDCM, and MINC communities to address these issues. > Questions and comments are welcome on the ITK mailing lists. > > The release files can be downloaded from: > > http://itk.org/ITK/resources/software.html > > > The next feature release of 4.6.0 is scheduled for June. > > > Enjoy ITK! > > > > Changes from v4.6.0 to v4.6.1: > > Arnaud Gelas (5): > BUG: fix gdcm version in GDCMImageIO. > COMP: missing cast when calling gdcm::DataElement::SetByteValue > BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is > false > BUG: split include directories into appropriate cmake variables HDF5 > BUG: missing gdcm libraries when using system GDCM > > Brad King (2): > COMP: Fix vxl_config_macros usage of CMake check macros > BUG: Fix itk_module_config for repeated calls > > Bradley Lowekamp (8): > ENH: Adding License file from upstream MetaIO > ENH: Adding script to update MetaIO from upstream > ENH: Remove ITK MetaIO to prepare for upstream import > COMP: Fix variable type for Set/Get macros > BUG: Use METER of sCAL scale unit > BUG: Use PNG_SCALE_METER for PNG sCAL unit > BUG: Fix overflows computing size of read tiff image > BUG: Use array delete operator for array new allocations > > Christopher Mullins (2): > COMP: Allows latex to compile for ITKSoftwareGuide > COMP: Wrap MeshBase templates > > David T. Chen (1): > DOC: Fixed HistogramThresholdImageFitler > > Gert Wollny (1): > COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) > > Girish Mallya (1): > BUG: Tests added for BinaryImageToLabelMapFilter for single-row > images. > > Hans Johnson (12): > COMP: Add tolerance for comparing floating point > PERF: Remove non-threadable algorithm components > PERF: Remove large foot print of PDF derivatives. > PERF: Revert Remove large foot print of PDF derivatives. > STYLE: Test against almost equal for floating point values > STYLE: Non-exact floating point testing > PERF: Distribute initialization per thread buffers > ENH: Remove unnecessary mutable qualifier. > STYLE: Remove comment with no meaning. > ENH: Moved accumlator logic to main MI class > ENH: Allow staggering of accumulations per thread. > PERF: Zero reset thread buffers during finalize > > Matthew McCormick (31): > BUG: ArchiveTestingData.py future imports must occur at the > beginning. > DOC: Remove Image2.cxx reference from Book 2. > DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. > DOC: Remove references to Book 1 sections from Book 2. > DOC: Make BinaryThresholdImageFilter not floating. > DOC: Fix Software Guide figure caption for FlipImageFilter. > DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. > DOC: Remove duplicate figure in > LaplacianRecursiveGaussianImageFilter2.cxx. > DOC: ImageRandomConstIteratorWithIndex table reference. > BUG: Bump GCCXML to 2014-08-06. > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > BUG: Call clear instead of empty on PatchBasedDenoising > EmptyCaches(). > BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. > BUG: Fix alpha assignment for RGBA TIFF. > BUG: Fix Nifti IO read with large images. > BUG: Improve thread-safety and performance of > PCAShapeSignedDistanceFunction. > DOC: itk::statistics -> itk::Statistics. > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > DOC: Fix Software Guide page overruns in > IterativeClosestPoint{1,2}.cxx. > BUG: TransformFileReader does not clear its TransformList. > BUG: Prevent dangling pointer in HDF5TransformIO. > COMP: Fix missing prefix in ITKv3ImageRegistration20Test. > BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform > STYLE: Improve style in BinaryImageToLabelMapFilter. > BUG: Fix BinaryImageToLabelMapFilter on 1D image. > ENH: Improve precision of the joint PDF sum > BUG: Fix BinShrinkImageFilter for different input/output image types. > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > COMP: Add missing wrapping for TransformIOBaseTemplate. > BUG: gdcm::StringFilter recognizes backslash delimiter. > ENH: Bump ITK version to 4.6.1. > > MetaIO Maintainers (1): > MetaIO (reduced) > > Michka Popoff (4): > BUG: Improve SWIG version check > BUG: Add VTK_VERSION for older VTK versions > BUG: Update VTK minimum version (for release) > BUG: Fix memory leak in MetaImageIO after exception > > Vladimir S. FONOV (1): > BUG: Fixing incorrect MINC style inverse transform > > > ------------------------------ > > Message: 2 > Date: Wed, 1 Oct 2014 15:50:33 -0400 > From: Matt McCormick > To: "community at itk.org" , "insight-users at itk.org" > , ITK > Subject: Re: [ITK-users] [ANNOUNCE] ITK 4.6.1 has been released! > Message-ID: > < > CALzTN-S9DU8K8ACbgVP6L0ozXQGvcbnfXC7nz8iu_xqLTVtHsw at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Minor correction: > > > > > The next feature release of 4.6.0 is scheduled for June. > > > > The next feature release of 4.7.0 is scheduled for December. > > > ------------------------------ > > Message: 3 > Date: Thu, 02 Oct 2014 11:33:06 +0200 > From: Jo?l Schaerer > To: itk > Subject: [ITK-users] Proper chaining of filters > Message-ID: <542D1BD2.40801 at laposte.net> > Content-Type: text/plain; charset=utf-8; format=flowed > > Hi all, > > I've noticed a couple times that when building a pipeline with ITK, you > need to keep a reference to all filters before the pipeline is updated. > This seems a little counter-intuitive to me, so I would like to better > understand the issue and see if there is a way around it. > > As an example, the following code doesn't work: > > DilateType::Pointer dilate = DilateType::New(); > dilate->SetInput(thresh->GetOutput()); > dilate->SetKernel(kernel); > > dilate_filters.push_back(dilate); > for (int i=0; i<14; ++i) { > DilateType::Pointer temp = DilateType::New(); > temp->SetInput(dilate->GetOutput()); > temp->SetKernel(kernel); > dilate = temp; > } > dilate->Update(); > > Regions don't get propagated properly and I get the following exception > when writing the output: > > C++ exception with description > > "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: > itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not > fully contain requested paste IO regionPaste IO region: ImageIORegion > (0x7fff9bb72cc0) > Dimension: 3 > Index: 0 0 0 > Size: 0 0 0 > Largest possible region: ImageRegion (0x7fff9bb72bc0) > Dimension: 3 > Index: [0, 0, 0] > Size: [0, 0, 0] > " thrown in the test body. > > My guess is that the filters get destroyed before they get a chance to > be executed. If I explicitely keep references to each filter, it works: > > DilateType::Pointer dilate = DilateType::New(); > dilate->SetInput(thresh->GetOutput()); > dilate->SetKernel(kernel); > // We need to keep a reference to each filter in the pipeline before > it is updated > std::vector dilate_filters; > dilate_filters.push_back(dilate); > for (int i=0; i<14; ++i) { > DilateType::Pointer temp = DilateType::New(); > temp->SetInput(dilate_filters.back()->GetOutput()); > temp->SetKernel(kernel); > dilate = temp; > dilate_filters.push_back(temp); > } > dilate_filters.back()->Update(); > > My question is, why doesn't a filter keep a reference to the previous > filter in the pipeline? Is there a way around this? > > Thanks! > > Jo?l > > > ------------------------------ > > Message: 4 > Date: Thu, 2 Oct 2014 10:16:08 -0400 > From: Matt McCormick > To: Jo?l Schaerer > Cc: itk > Subject: Re: [ITK-users] [ITK] Proper chaining of filters > Message-ID: > v6XSg at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Jo?l, > > Calling > > temp->SetInput(dilate->GetOutput()); > > Connects the DataObject generated by dilate to the temp filter. temp > does not increment dilate's reference count, and it would be difficult > to do since the SetInput input is the DataObject, not the > ProcessObject. > > As a consequence, at least one SmartPointer needs to be kept in scope > as with your second example. > > HTH, > Matt > > On Thu, Oct 2, 2014 at 5:33 AM, Jo?l Schaerer > wrote: > > Hi all, > > > > I've noticed a couple times that when building a pipeline with ITK, you > need > > to keep a reference to all filters before the pipeline is updated. This > > seems a little counter-intuitive to me, so I would like to better > understand > > the issue and see if there is a way around it. > > > > As an example, the following code doesn't work: > > > > DilateType::Pointer dilate = DilateType::New(); > > dilate->SetInput(thresh->GetOutput()); > > dilate->SetKernel(kernel); > > > > dilate_filters.push_back(dilate); > > for (int i=0; i<14; ++i) { > > DilateType::Pointer temp = DilateType::New(); > > temp->SetInput(dilate->GetOutput()); > > temp->SetKernel(kernel); > > dilate = temp; > > } > > dilate->Update(); > > > > Regions don't get propagated properly and I get the following exception > when > > writing the output: > > > > C++ exception with description > > > "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: > > itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not > > fully contain requested paste IO regionPaste IO region: ImageIORegion > > (0x7fff9bb72cc0) > > Dimension: 3 > > Index: 0 0 0 > > Size: 0 0 0 > > Largest possible region: ImageRegion (0x7fff9bb72bc0) > > Dimension: 3 > > Index: [0, 0, 0] > > Size: [0, 0, 0] > > " thrown in the test body. > > > > My guess is that the filters get destroyed before they get a chance to be > > executed. If I explicitely keep references to each filter, it works: > > > > DilateType::Pointer dilate = DilateType::New(); > > dilate->SetInput(thresh->GetOutput()); > > dilate->SetKernel(kernel); > > // We need to keep a reference to each filter in the pipeline before > it is > > updated > > std::vector dilate_filters; > > dilate_filters.push_back(dilate); > > for (int i=0; i<14; ++i) { > > DilateType::Pointer temp = DilateType::New(); > > temp->SetInput(dilate_filters.back()->GetOutput()); > > temp->SetKernel(kernel); > > dilate = temp; > > dilate_filters.push_back(temp); > > } > > dilate_filters.back()->Update(); > > > > My question is, why doesn't a filter keep a reference to the previous > filter > > in the pipeline? Is there a way around this? > > > > Thanks! > > > > Jo?l > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the 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 > > > ------------------------------ > > Message: 5 > Date: Thu, 02 Oct 2014 16:22:24 +0200 > From: Jo?l Schaerer > To: Matt McCormick > Cc: itk > Subject: Re: [ITK-users] [ITK] Proper chaining of filters > Message-ID: <542D5FA0.8070903 at laposte.net> > Content-Type: text/plain; charset=utf-8; format=flowed > > Hi Matt, > > Thanks for the confirmation. I was thinking there might be another > mechanism I wasn't aware of. > > Jo?l > > On 10/02/2014 04:16 PM, Matt McCormick wrote: > > Hi Jo?l, > > > > Calling > > > > temp->SetInput(dilate->GetOutput()); > > > > Connects the DataObject generated by dilate to the temp filter. temp > > does not increment dilate's reference count, and it would be difficult > > to do since the SetInput input is the DataObject, not the > > ProcessObject. > > > > As a consequence, at least one SmartPointer needs to be kept in scope > > as with your second example. > > > > HTH, > > Matt > > > > On Thu, Oct 2, 2014 at 5:33 AM, Jo?l Schaerer > wrote: > >> Hi all, > >> > >> I've noticed a couple times that when building a pipeline with ITK, you > need > >> to keep a reference to all filters before the pipeline is updated. This > >> seems a little counter-intuitive to me, so I would like to better > understand > >> the issue and see if there is a way around it. > >> > >> As an example, the following code doesn't work: > >> > >> DilateType::Pointer dilate = DilateType::New(); > >> dilate->SetInput(thresh->GetOutput()); > >> dilate->SetKernel(kernel); > >> > >> dilate_filters.push_back(dilate); > >> for (int i=0; i<14; ++i) { > >> DilateType::Pointer temp = DilateType::New(); > >> temp->SetInput(dilate->GetOutput()); > >> temp->SetKernel(kernel); > >> dilate = temp; > >> } > >> dilate->Update(); > >> > >> Regions don't get propagated properly and I get the following exception > when > >> writing the output: > >> > >> C++ exception with description > >> > "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: > >> itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not > >> fully contain requested paste IO regionPaste IO region: ImageIORegion > >> (0x7fff9bb72cc0) > >> Dimension: 3 > >> Index: 0 0 0 > >> Size: 0 0 0 > >> Largest possible region: ImageRegion (0x7fff9bb72bc0) > >> Dimension: 3 > >> Index: [0, 0, 0] > >> Size: [0, 0, 0] > >> " thrown in the test body. > >> > >> My guess is that the filters get destroyed before they get a chance to > be > >> executed. If I explicitely keep references to each filter, it works: > >> > >> DilateType::Pointer dilate = DilateType::New(); > >> dilate->SetInput(thresh->GetOutput()); > >> dilate->SetKernel(kernel); > >> // We need to keep a reference to each filter in the pipeline before > it is > >> updated > >> std::vector dilate_filters; > >> dilate_filters.push_back(dilate); > >> for (int i=0; i<14; ++i) { > >> DilateType::Pointer temp = DilateType::New(); > >> temp->SetInput(dilate_filters.back()->GetOutput()); > >> temp->SetKernel(kernel); > >> dilate = temp; > >> dilate_filters.push_back(temp); > >> } > >> dilate_filters.back()->Update(); > >> > >> My question is, why doesn't a filter keep a reference to the previous > filter > >> in the pipeline? Is there a way around this? > >> > >> Thanks! > >> > >> Jo?l > >> _____________________________________ > >> Powered by www.kitware.com > >> > >> Visit other Kitware open-source projects at > >> http://www.kitware.com/opensource/opensource.html > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> http://www.kitware.com/products/protraining.php > >> > >> Please keep messages on-topic and check the 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 > > > > ------------------------------ > > Message: 6 > Date: Thu, 2 Oct 2014 09:24:31 -0700 (PDT) > From: Pedro Morais > To: insight-users at itk.org > Subject: [ITK-users] 3D generalized hough transform > Message-ID: <1412267071841-7586297.post at n2.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Hi all, > > I'm wonder if ITK has an implementation of a 3D generalized hough > transform. > Do you have any idea? > > Regards, > Pedro > > > > -- > View this message in context: > http://itk-insight-users.2283740.n2.nabble.com/3D-generalized-hough-transform-tp7586297.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > > > ------------------------------ > > Message: 7 > Date: Thu, 2 Oct 2014 20:40:16 -0400 > From: Lianli Liu > To: "insight-users at itk.org" > Subject: [ITK-users] vector image registration > Message-ID: > < > CAGKqDmfV89qpnVG5tq4bvZrc6FDHhNRHrkvWg7qEXjh_pObKsQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I wonder if ITK is supporting vector image registration now? If not, any > suggestions to achieve this goal? > > Thanks! > Lianli > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141002/87f15593/attachment-0001.html > > > > ------------------------------ > > Message: 8 > Date: Fri, 3 Oct 2014 10:05:29 +0100 > From: Gianluigi Caddeo > To: insight-users at itk.org > Subject: [ITK-users] help installing ITK > Message-ID: > < > CADeTECOS-PqOswWC4H2Wo_f8eKjd24eN+eSDfRG+YK8LKF7+CA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > during my installation on an ubuntu machine I had this problem: > > > > > > > *[100%] Built target ITKv3ThinPlateSplineWarp/bin/sh: 1: > DOXYGEN_EXECUTABLE-NOTFOUND: not foundmake[2]: *** > [Utilities/Doxygen/CMakeFiles/Documentation] Errore 127make[1]: *** > [Utilities/Doxygen/CMakeFiles/Documentation.dir/all] Errore 2make: *** > [all] Errore* > But doxygen exist and stay in my */usr/bin* directory > > How can I to force ITK to search doxygen in that directory? > > thanks a lot > > Gg > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141003/ec1ddfe8/attachment-0001.html > > > > ------------------------------ > > Message: 9 > Date: Mon, 6 Oct 2014 09:58:09 +0200 > From: Arnaud Gelas > To: insight-users > Cc: Mathieu Malaterre > Subject: [ITK-users] How to remove a tag from MetaDataDictionary? > Message-ID: > < > CAK3qF+8e1kg7bN4EcM2FUYy_e3AYz-M3ZrGGwkssWz0Kvz4y2Q at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I am trying to write a DICOM file in which, the orientation (among others) > has changed in my pipeline... > > 1- After having a look > > https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919 > > It appears to me that if the orientation is in the MetaDataDictionary, it > is saved anyway into the DICOM image, there is no way to force the ImageIO > to recompute it from the image and save it ??? > If there is, can anyone give me a pointer? > > 2- Since I can't find a way to update the image orientation in > itk::GDCMImageIO, I have been looking at removing the corresponding tag > from the MetaDataDictionary. I could not find any method or any way to do > it??? > If there is, can anyone give me a pointer? > > I wish I would not have to copy the dictionary and add if statement to > avoid copying the direction... > > Thanks in advance, > Arnaud > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141006/51ca077c/attachment-0001.html > > > > ------------------------------ > > Message: 10 > Date: Mon, 6 Oct 2014 12:31:03 +0100 > From: Emma Saunders > To: "insight-users at itk.org Users" > Subject: [ITK-users] Overlap_image registration metrics > Message-ID: > 1as4oZLo5UXQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello all, > > When computing metrics for image registration, does ITK calculated the > metric for only the regions in the image that overlap? > > If so is this performed on just the initial regions that overlap or will > this region of overlap increase during registration and thus require the > region in which the metric is calculated to alter? > > Thanks for any help > > Emma > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141006/639045b5/attachment-0001.html > > > > ------------------------------ > > Message: 11 > Date: Mon, 6 Oct 2014 06:20:27 -0700 (MST) > From: Marco Ulge > To: insight-users at itk.org > Subject: [ITK-users] Texture Features extraction > Message-ID: <1412601627242-34642.post at n7.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Hello, > > i'm currently working on texture feature extraction and I'm following this > examle: > http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures > > > It works fine and basically it's all i need. The only problem is that i > need > to able to specify an arbitrary window size (which is 3 in this example) > but > as soon as i try to assign it a different value this won't work anymore and > i can't figure out why. > > Can anyone help me with this please? > > Thanks. > > Marco > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.html > Sent from the ITK - Users mailing list archive at Nabble.com. > > > ------------------------------ > > Message: 12 > Date: Mon, 06 Oct 2014 15:47:12 +0200 > From: Dominique T?pfer > To: Marco Ulge , insight-users at itk.org > Subject: Re: [ITK-users] Texture Features extraction > Message-ID: <54329D60.9030004 at toepfer-web.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Marco, > > you probably forgot to adjust the range of the for-loops. They are > running from 1 to size-2 so that the window will not "leave" the image > at its boundaries. > > HTH > Dominique > > > On 06.10.2014 15:20, Marco Ulge wrote: > > Hello, > > > > i'm currently working on texture feature extraction and I'm following > this > > examle: > > http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures > > > > > > It works fine and basically it's all i need. The only problem is that i > need > > to able to specify an arbitrary window size (which is 3 in this example) > but > > as soon as i try to assign it a different value this won't work anymore > and > > i can't figure out why. > > > > Can anyone help me with this please? > > > > Thanks. > > > > Marco > > > > > > > > -- > > View this message in context: > http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.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 > > > > ------------------------------ > > Message: 13 > Date: Mon, 6 Oct 2014 07:18:26 -0700 (MST) > From: Marco Ulge > To: insight-users at itk.org > Subject: Re: [ITK-users] Texture Features extraction > Message-ID: <1412605106652-34644.post at n7.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Thanks for your reply, so if i wanted to specify a window size of 5 (for > example) i should iterate from 1 to size - 4? > > Thanks. > > Marco > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642p34644.html > Sent from the ITK - Users mailing list archive at Nabble.com. > > > ------------------------------ > > Message: 14 > Date: Mon, 6 Oct 2014 10:27:10 -0400 > From: Jiahui Wang > To: insight-users at itk.org > Subject: [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer > Message-ID: > UPK2wK-ksA6v1vKak75aE1f3ea-de7sLQSTrGiQwxEpQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear All, > > I modified ImageRegistration8.cxx to run my own rigid registration. > > However, I found that the processing time of ITKv4 based > RegularStepGradientDescentOptimizer is almost 10 times more than that of > ITKv3 based one. > > The program was run on the same machine. The only difference is the ITK > libraries. > > Could anyone give me some suggestions to solve this issue? > > Thanks, > > JW > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141006/40c2b5ce/attachment-0001.html > > > > ------------------------------ > > Message: 15 > Date: Mon, 6 Oct 2014 11:08:10 -0400 > From: Matt McCormick > To: Arnaud Gelas > Cc: insight-users , Mathieu Malaterre > > Subject: Re: [ITK-users] How to remove a tag from MetaDataDictionary? > Message-ID: > < > CALzTN-TjoXUpe16JNsViVH0srU_q1oTJpVYG94G3S6a0mUD3Eg at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Arnaud, > > > > I am trying to write a DICOM file in which, the orientation (among > others) > > has changed in my pipeline... > > > > 1- After having a look > > > https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919 > > > > It appears to me that if the orientation is in the MetaDataDictionary, > it is > > saved anyway into the DICOM image, there is no way to force the ImageIO > to > > recompute it from the image and save it ??? > > If there is, can anyone give me a pointer? > > If there is a Direction on the input image, it should use it [1]. But > the DICOM tag 0020|0037 cannot be present. > > > > 2- Since I can't find a way to update the image orientation in > > itk::GDCMImageIO, I have been looking at removing the corresponding tag > from > > the MetaDataDictionary. I could not find any method or any way to do > it??? > > If there is, can anyone give me a pointer? > > > > I wish I would not have to copy the dictionary and add if statement to > avoid > > copying the direction... > > This is the method I usually apply... > > Sorry for the lack of new tricks! > Matt > > [1] > https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L816-L828 > > > ------------------------------ > > Message: 16 > Date: Mon, 6 Oct 2014 11:12:52 -0400 > From: Matt McCormick > To: Emma Saunders > Cc: "insight-users at itk.org Users" > Subject: Re: [ITK-users] Overlap_image registration metrics > Message-ID: > < > CALzTN-SrbFWD0R7-GAPxxT0ssf2fzLN_bATjtHB+ZAyHYZjk+w at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Emma, > > > When computing metrics for image registration, does ITK calculated the > > metric for only the regions in the image that overlap? > > Yes. See, for example, [1]. > > > If so is this performed on just the initial regions that overlap or > will > > this region of overlap increase during registration and thus require the > > region in which the metric is calculated to alter? > > Yes. Ideally, as the registration progresses, the overlap increases, > and the registration becomes progressively better. > > HTH, > Matt > > [1] > http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.hxx;h=8a6069dde32309a214229968294a14911c701dd0;hb=HEAD#l312 > > > ------------------------------ > > Message: 17 > Date: Mon, 6 Oct 2014 15:44:08 +0000 > From: Andras Lasso > To: Jiahui Wang , "insight-users at itk.org" > > Subject: Re: [ITK-users] [ITK] Speed of ITKv4 based Gradient Descent > Optimizer > Message-ID: > < > B6FC5543F5C41E479B8B89158B0C58FF179374D9 at MP-DUP-MBX-02.AD.QUEENSU.CA> > Content-Type: text/plain; charset="utf-8" > > See this long thread about this issue: > > http://slicer-devel.65872.n3.nabble.com/BRAINS-rigid-registration-td4032229.html > > Short summary: There were some performance regressions in mutual > information metric computation, threading, etc. that have been recently > fixed, so use the latest ITK version. ITKv4 uses a slightly slower but more > accurate optimizer, but if you adjust the number of samples and stopping > condition then usually the registration time only increases by about 30-50% > (and you might get better quality results). > > You can see all the changes that have been done in 3D Slicer and BRAINS > repositories to go from a 10x-100x slowdown to an approximately equivalent > registration speed with ITKv4 compared to ITKv3. > > Andras > > From: Community [mailto:community-bounces at itk.org] On Behalf Of Jiahui > Wang > Sent: Monday, October 06, 2014 10:27 AM > To: insight-users at itk.org > Subject: [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer > > Dear All, > I modified ImageRegistration8.cxx to run my own rigid registration. > > However, I found that the processing time of ITKv4 based > RegularStepGradientDescentOptimizer is almost 10 times more than that of > ITKv3 based one. > > The program was run on the same machine. The only difference is the ITK > libraries. > > Could anyone give me some suggestions to solve this issue? > Thanks, > JW > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141006/230f318a/attachment-0001.html > > > > ------------------------------ > > Message: 18 > Date: Tue, 7 Oct 2014 15:13:06 +0800 > From: Fabian Torres > To: insight-users at itk.org > Subject: [ITK-users] Polygon inside point > Message-ID: > KP5XsjnYeFWGwWbifQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all. > > I have an image that represents some pixels over the surface of an object. > Pixels in the surface have value of 1 while any other pixel has value of 0. > The pixels are not a continuous line, there are some gaps between pixels. I > want to know the region surrounded by the white pixels in my image. > > I will be working with 2D and 3D data. Is there any class implemented in > ITK that I can use? > > Thanks > > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141007/152068ea/attachment-0001.html > > > > ------------------------------ > > Message: 19 > Date: Tue, 7 Oct 2014 15:38:49 +0800 > From: Fabian Torres > To: insight-users > Subject: [ITK-users] region inside points > Message-ID: > < > CALD_Ep+OEAE8Jik0hsy8PWYGBmxTHYWoRZOoFQaP2OqT1P_GyQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all. > > I have an image that represents some pixels over the surface of an object. > Pixels in the surface have value of 1 while any other pixel has value of 0. > The pixels are not a continuous line, there are some gaps between pixels. I > want to know the region surrounded by the white pixels in my image. > > I will be working with 2D and 3D data. Is there any class implemented in > ITK that I can use? > > Thanks > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141007/2f835b53/attachment-0001.html > > > > ------------------------------ > > Message: 20 > Date: Tue, 7 Oct 2014 07:40:40 +0000 > From: Gib Bogle > To: Fabian Torres , insight-users > > Subject: Re: [ITK-users] region inside points > Message-ID: > < > BD80F91C3E2E394894ED4780703D7F9E826C670A at uxcn10-tdc06.UoA.auckland.ac.nz> > > Content-Type: text/plain; charset="iso-8859-1" > > Maybe you could do something with BinaryImageDilateFilter. > ________________________________ > From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian > Torres [dae.wong at gmail.com] > Sent: Tuesday, 7 October 2014 8:38 p.m. > To: insight-users > Subject: [ITK-users] region inside points > > Hi all. > > I have an image that represents some pixels over the surface of an object. > Pixels in the surface have value of 1 while any other pixel has value of 0. > The pixels are not a continuous line, there are some gaps between pixels. > I want to know the region surrounded by the white pixels in my image. > > I will be working with 2D and 3D data. Is there any class implemented in > ITK that I can use? > > Thanks > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, > dae.wong at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141007/4f28baa5/attachment-0001.html > > > > ------------------------------ > > Message: 21 > Date: Tue, 7 Oct 2014 07:46:17 +0000 > From: Gib Bogle > To: Fabian Torres , insight-users > > Subject: Re: [ITK-users] region inside points > Message-ID: > < > BD80F91C3E2E394894ED4780703D7F9E826C671B at uxcn10-tdc06.UoA.auckland.ac.nz> > > Content-Type: text/plain; charset="iso-8859-1" > > Sorry, I misread your post Fabian - I read it as you wanting the region > _surrounding_ the white pixels. But dilate might be usable to fill the > gaps, followed by skeletonization. > ________________________________ > From: Insight-users [insight-users-bounces at itk.org] on behalf of Gib > Bogle [g.bogle at auckland.ac.nz] > Sent: Tuesday, 7 October 2014 8:40 p.m. > To: Fabian Torres; insight-users > Subject: Re: [ITK-users] region inside points > > Maybe you could do something with BinaryImageDilateFilter. > ________________________________ > From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian > Torres [dae.wong at gmail.com] > Sent: Tuesday, 7 October 2014 8:38 p.m. > To: insight-users > Subject: [ITK-users] region inside points > > Hi all. > > I have an image that represents some pixels over the surface of an object. > Pixels in the surface have value of 1 while any other pixel has value of 0. > The pixels are not a continuous line, there are some gaps between pixels. > I want to know the region surrounded by the white pixels in my image. > > I will be working with 2D and 3D data. Is there any class implemented in > ITK that I can use? > > Thanks > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, > dae.wong at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141007/4dee4e3f/attachment-0001.html > > > > ------------------------------ > > Message: 22 > Date: Tue, 7 Oct 2014 16:05:24 +0800 > From: Fabian Torres > To: Gib Bogle > Cc: insight-users > Subject: Re: [ITK-users] region inside points > Message-ID: > < > CALD_Ep+NkNKwMdz18XLQ3ygxBAdCwK0AGFBZcNPT3MfUpC_ARA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Gib. > > Thanks for the quick response. The problem of using dilation and > skeletonization is that some times the gap between pixels is big, and I > will have to work with different and big structural elements to be sure > that all the gaps were eliminated. > > I was hoping to find a class that works similar to a convex hull (it does > not have to be convex) algorithm and then find the region surrounded by the > hull. > > Thanks > > On Tue, Oct 7, 2014 at 3:46 PM, Gib Bogle wrote: > > > Sorry, I misread your post Fabian - I read it as you wanting the region > > _surrounding_ the white pixels. But dilate might be usable to fill the > > gaps, followed by skeletonization. > > ------------------------------ > > *From:* Insight-users [insight-users-bounces at itk.org] on behalf of Gib > > Bogle [g.bogle at auckland.ac.nz] > > *Sent:* Tuesday, 7 October 2014 8:40 p.m. > > *To:* Fabian Torres; insight-users > > *Subject:* Re: [ITK-users] region inside points > > > > Maybe you could do something with BinaryImageDilateFilter. > > ------------------------------ > > *From:* Insight-users [insight-users-bounces at itk.org] on behalf of > Fabian > > Torres [dae.wong at gmail.com] > > *Sent:* Tuesday, 7 October 2014 8:38 p.m. > > *To:* insight-users > > *Subject:* [ITK-users] region inside points > > > > Hi all. > > > > I have an image that represents some pixels over the surface of an > > object. Pixels in the surface have value of 1 while any other pixel has > > value of 0. > > The pixels are not a continuous line, there are some gaps between pixels. > > I want to know the region surrounded by the white pixels in my image. > > > > I will be working with 2D and 3D data. Is there any class implemented in > > ITK that I can use? > > > > Thanks > > -- > > Fabi?n Torres Robles > > Maestria en Ciencias en Ingenier?a Electr?nica > > Ingenier?a en Sistemas Electr?nicos > > tel. 58081280, 0445534661338 > > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > > > > > > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141007/6202b2cc/attachment.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Insight-users mailing list > Insight-users at itk.org > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > > End of Insight-users Digest, Vol 126, Issue 2 > ********************************************* > -------------- 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 65104355 at qq.com Tue Oct 7 10:06:17 2014 From: 65104355 at qq.com (=?ISO-8859-1?B?SmVycnk=?=) Date: Tue, 7 Oct 2014 22:06:17 +0800 Subject: [ITK] [ITK-users] Detect tube and ball typed objects in airway CT image. Message-ID: I am developing a segmentation algorithm that requires detect tube and ball typed airways in CT image. I tried canny, log, hessian etc. None of them looks promising. Any advice will be appreicated. Regards, Jerry -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: B3AB03A0 at 8E359815.59F33354.jpg Type: image/jpeg Size: 79219 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: tubecircle.jpg Type: application/octet-stream Size: 79219 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Tue Oct 7 10:18:10 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 7 Oct 2014 10:18:10 -0400 Subject: [ITK] [ITK-users] Detect tube and ball typed objects in airway CT image. In-Reply-To: References: Message-ID: <6FF244AB-597A-4CFB-8644-3E918F42F938@mail.nih.gov> Interesting. Have you considered looking at the ratio of a gaussian and a laplacian at certain scales to detect the feature you are interested in? Brad Brad On Oct 7, 2014, at 10:06 AM, Jerry <65104355 at qq.com> wrote: > I am developing a segmentation algorithm that requires detect tube and ball typed airways in CT image. I tried canny, log, hessian etc. None of them looks promising. Any advice will be appreicated. > > Regards, > > Jerry > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 matt.mccormick at kitware.com Tue Oct 7 10:28:40 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 7 Oct 2014 10:28:40 -0400 Subject: [ITK] [ITK-users] Segmentation fault when using BSplineScatteredDataPointSetToImageFilter for 3D image In-Reply-To: <44223E94-F14E-4CF5-A0D6-C667CD3DDE29@unistra.fr> References: <44223E94-F14E-4CF5-A0D6-C667CD3DDE29@unistra.fr> Message-ID: Hi Fran?ois, Yes, it should work on a 3D Image -- itkBSplineScatteredDataPointSetToImageFilterTest4.cxx is for ParametericDimension = 3. HTH, Matt On Tue, Oct 7, 2014 at 4:11 AM, francois rousseau wrote: > Hi everyone, > > I?m trying to use the BSplineScatteredDataPointSetToImageFilter. No problem > when applying it on 2D images (using > itkBSplineScatteredDataPointSetToImageFilterTest.cxx). > However, after setting const unsigned int ParametricDimension = 3; it > crashes when I try to apply it on 3D image (segmentation fault). Can this > code be used for 3D images? > > Thank you > Fran?ois > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 Tue Oct 7 10:43:55 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 7 Oct 2014 10:43:55 -0400 Subject: [ITK] [ITK-users] Detect tube and ball typed objects in airway CT image. In-Reply-To: References: Message-ID: Hi Jerry, The LesionSizingToolkit [1], and TubeTK [2], both based on ITK, may be helpful here. The LesionSizeToolkit is available as a Remote Module. It can be built by setting Module_LesionSizingToolkit=ON in your CMake configuration. HTH, Matt [1] http://public.kitware.com/LesionSizingKit/index.php/Main_Page [2] http://tubetk.org/ On Tue, Oct 7, 2014 at 10:06 AM, Jerry <65104355 at qq.com> wrote: > I am developing a segmentation algorithm that requires detect tube and > ball typed airways in CT image. I tried canny, log, hessian etc. None of > them looks promising. Any advice will be appreicated. > > Regards, > > Jerry > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 -------------- A non-text attachment was scrubbed... Name: B3AB03A0 at 8E359815.59F33354.jpg Type: image/jpeg Size: 79219 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Oct 7 11:52:56 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 7 Oct 2014 11:52:56 -0400 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/u/0/events/cs71fpcqpa7l9me2vq45mi61mq8 To get regular invites to these events, join the ITK Bar Camp G+ Community: https://plus.google.com/u/0/communities/111375098792764998322 All are welcome. Hope to talk to you then! From wjhzwy at gmail.com Tue Oct 7 13:44:47 2014 From: wjhzwy at gmail.com (Jiahui Wang) Date: Tue, 7 Oct 2014 13:44:47 -0400 Subject: [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer In-Reply-To: References: Message-ID: Thank you very much, Andras. Jiahui On Mon, Oct 6, 2014 at 11:44 AM, Andras Lasso wrote: > See this long thread about this issue: > > > http://slicer-devel.65872.n3.nabble.com/BRAINS-rigid-registration-td4032229.html > > > > Short summary: There were some performance regressions in mutual > information metric computation, threading, etc. that have been recently > fixed, so use the latest ITK version. ITKv4 uses a slightly slower but more > accurate optimizer, but if you adjust the number of samples and stopping > condition then usually the registration time only increases by about 30-50% > (and you might get better quality results). > > > > You can see all the changes that have been done in 3D Slicer and BRAINS > repositories to go from a 10x-100x slowdown to an approximately equivalent > registration speed with ITKv4 compared to ITKv3. > > > > Andras > > > > *From:* Community [mailto:community-bounces at itk.org] *On Behalf Of *Jiahui > Wang > *Sent:* Monday, October 06, 2014 10:27 AM > *To:* insight-users at itk.org > *Subject:* [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent > Optimizer > > > > Dear All, > > I modified ImageRegistration8.cxx to run my own rigid registration. > > > However, I found that the processing time of ITKv4 based > RegularStepGradientDescentOptimizer is almost 10 times more than that of > ITKv3 based one. > > > The program was run on the same machine. The only difference is the ITK > libraries. > > Could anyone give me some suggestions to solve this issue? > > Thanks, > > JW > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Oct 7 17:00:32 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 7 Oct 2014 17:00:32 -0400 Subject: [ITK] Network Resources Down Thursday, 5:30 PM Message-ID: Hi, A note that there will be a scheduled downtime for ITK network resources such as CDash Git Wiki Homepage Gerrit on Thursday, October 9th, 5:30 PM lasting approximately 10-20 minutes. Thanks, Matt From dae.wong at gmail.com Wed Oct 8 06:51:51 2014 From: dae.wong at gmail.com (Fabian Torres) Date: Wed, 8 Oct 2014 18:51:51 +0800 Subject: [ITK] [ITK-users] region inside points In-Reply-To: References: Message-ID: Hi all. Just wanted to let you know I solved the problem for 2D by doing the next: Arrange the white pixels in clockwise order 1. Calculate the centroid of the region define by the white pixels 2. Calculate the angle between the white pixels and the centroid using atan2( ) 3. Sort the white pixels in clockwise order. Draw a line between the pixels to fill the gap between points to obtain a closed contour 1. Using LineIterator to draw lines between the clockwise ordered points Fill the region inside the close contour. 1. Using GrayScaleFillholeImageFilter. I don?t know if this is a nice solution but it works for now. I will try to use this approach for 3D images, processing them slice by slice. I think I can use the itkSliceBySliceImageFilter, since I create an itk filter that outputs the closed contour image, but I don?t know if this is going to work. If any one have any advice on this matter it would be appreciated. Greetings On Tue, Oct 7, 2014 at 4:08 PM, Gib Bogle wrote: > Maybe there is a way to use a rolling ball. Richard Beare has some > morphological filters that might be applicable, but I think it will always > be a bit complicated. > ------------------------------ > *From:* Fabian Torres [dae.wong at gmail.com] > *Sent:* Tuesday, 7 October 2014 9:05 p.m. > *To:* Gib Bogle > *Cc:* insight-users > > *Subject:* Re: [ITK-users] region inside points > > Hi Gib. > > Thanks for the quick response. The problem of using dilation and > skeletonization is that some times the gap between pixels is big, and I > will have to work with different and big structural elements to be sure > that all the gaps were eliminated. > > I was hoping to find a class that works similar to a convex hull (it > does not have to be convex) algorithm and then find the region surrounded > by the hull. > > Thanks > > On Tue, Oct 7, 2014 at 3:46 PM, Gib Bogle wrote: > >> Sorry, I misread your post Fabian - I read it as you wanting the region >> _surrounding_ the white pixels. But dilate might be usable to fill the >> gaps, followed by skeletonization. >> ------------------------------ >> *From:* Insight-users [insight-users-bounces at itk.org] on behalf of Gib >> Bogle [g.bogle at auckland.ac.nz] >> *Sent:* Tuesday, 7 October 2014 8:40 p.m. >> *To:* Fabian Torres; insight-users >> *Subject:* Re: [ITK-users] region inside points >> >> Maybe you could do something with BinaryImageDilateFilter. >> ------------------------------ >> *From:* Insight-users [insight-users-bounces at itk.org] on behalf of >> Fabian Torres [dae.wong at gmail.com] >> *Sent:* Tuesday, 7 October 2014 8:38 p.m. >> *To:* insight-users >> *Subject:* [ITK-users] region inside points >> >> Hi all. >> >> I have an image that represents some pixels over the surface of an >> object. Pixels in the surface have value of 1 while any other pixel has >> value of 0. >> The pixels are not a continuous line, there are some gaps between pixels. >> I want to know the region surrounded by the white pixels in my image. >> >> I will be working with 2D and 3D data. Is there any class implemented >> in ITK that I can use? >> >> Thanks >> -- >> Fabi?n Torres Robles >> Maestria en Ciencias en Ingenier?a Electr?nica >> Ingenier?a en Sistemas Electr?nicos >> tel. 58081280, 0445534661338 >> e-mail fabian.trobles at gmail.com, dae.wong at gmail.com >> > > > > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.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 alfonso.castro at udc.es Wed Oct 8 14:13:43 2014 From: alfonso.castro at udc.es (Alfonso Castro) Date: Wed, 08 Oct 2014 20:13:43 +0200 Subject: [ITK] [ITK-users] Problem compiling ITK 4.6.1 Message-ID: <2757769.bt995I62FB@hinata> Hi. I'm trying to compile ITK 4.6.1 on OpenSuSE 13.1 with CUDA 6.5 from NVIDIA. Whwn I turn on the option of Module_SmoothingRecursiveYvvGaussianFilter and Module_VariationalRegistration with ITK_USE_GPU option. Make gives the follow errors: Building CXX object Modules/Remote/SmoothingRecursiveYvvGaussianFilter/src/CMakeFiles/SmoothingRecursiveYvvGaussianFilter.dir/GPUSmoothingRecursiveYvvGaussianImageFilterKernel.cxx.o In file included from /usr/local/cuda-6.5/include/CL/opencl.h:44:0, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkOpenCLUtil.h:36, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/SmoothingRecursiveYvvGaussianFilter/include/itkGPUSmoothingRecursiveYvvGaussianImageFilter.h:29, from /opt/mia/itk/Modules/Remote/SmoothingRecursiveYvvGaussianFilter/src/GPUSmoothingRecursiveYvvGaussianImageFilterKernel.cxx:1: /usr/local/cuda-6.5/include/CL/cl_gl_ext.h:44:4: warning: "/*" within comment [-Wcomment] * /* cl_VEN_extname extension */ ^ In file included from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkGPUImage.h:284:0, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkGPUKernelManager.h:30, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkGPUImageToImageFilter.h:22, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/SmoothingRecursiveYvvGaussianFilter/include/itkGPUSmoothingRecursiveYvvGaussianImageFilter.h:30, from /opt/mia/itk/Modules/Remote/SmoothingRecursiveYvvGaussianFilter/src/GPUSmoothingRecursiveYvvGaussianImageFilterKernel.cxx:1: /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkGPUImage.hxx: In member function ?virtual void itk::GPUImage::Graft(const itk::DataObject*)?: /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkGPUImage.hxx:188:56: warning: typedef ?GPUImageDataSuperclassPointer? locally defined but not used [-Wunused-local-typedefs] typedef typename GPUImageDataSuperclass::Pointer GPUImageDataSuperclassPointer; ^ Linking CXX static library ../../../../lib/libSmoothingRecursiveYvvGaussianFilter.a [100%] Built target SmoothingRecursiveYvvGaussianFilter Scanning dependencies of target SplitComponents-all [100%] Built target SplitComponents-all Scanning dependencies of target VariationalRegistration-all [100%] Built target VariationalRegistration-all Scanning dependencies of target VariationalRegistration [100%] Building CXX object Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/VariationalRegistrationMain.cxx.o In file included from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationFilter.h:24:0, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationMultiResolutionFilter.h:24, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/src/VariationalRegistrationMain.cxx:60: /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationFunction.h:156:11: error: duplicate ?virtual? virtual virtual void InitializeIteration(); ^ make[2]: *** [Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/VariationalRegistrationMain.cxx.o] Erro 1 make[1]: *** [Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/all] Erro 2 make: *** [all] Erro 2 If I deactivated the GPU option only, I obtained: [ 18%] Building CXX object Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/VariationalRegistrationMain.cxx.o In file included from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationFilter.h:24:0, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationMultiResolutionFilter.h:24, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/src/VariationalRegistrationMain.cxx:60: /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationFunction.h:156:11: error: duplicate ?virtual? virtual virtual void InitializeIteration(); ^ make[2]: *** [Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/VariationalRegistrationMain.cxx.o] Erro 1 make[1]: *** [Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/all] Erro 2 make: *** [all] Erro 2 If I deactivated GPU and Module_VariationalRegistration, ITK compile without problem. Is there some solution or walk around for those errors? Thanks. Alfonso Faculty of Computer Science University of A Coruna _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 curiale at gmail.com Thu Oct 9 10:43:03 2014 From: curiale at gmail.com (=?iso-8859-1?Q?Ariel_Hern=E1n_Curiale?=) Date: Thu, 9 Oct 2014 16:43:03 +0200 Subject: [ITK] [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members In-Reply-To: References: Message-ID: <2A6589EB-D292-4362-8863-D4804ADE41EC@gmail.com> Hi Matt, Is there any chance to see the video of the meeting on you tube, for example ? Cheers __________________________________ | Ariel Hern?n Curiale Ph.D Candidate | ETSI Telecomunicaci?n | Universidad de Valladolid | Campus Miguel Delibes | 47011 Valladolid, Spain | Phone: 983-423000 ext. 5590 | Web: www.curiale.com.ar |_________________________________ On 07/10/2014, at 17:52, Matt McCormick wrote: > On Friday, 11:00 AM Eastern USA time, an ITK development conference, > > https://plus.google.com/u/0/events/cs71fpcqpa7l9me2vq45mi61mq8 > > > To get regular invites to these events, join the ITK Bar Camp G+ Community: > > https://plus.google.com/u/0/communities/111375098792764998322 > > > All are welcome. Hope to talk to you then! > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From handongfeng at gmail.com Thu Oct 9 15:54:20 2014 From: handongfeng at gmail.com (Dongfeng Han) Date: Thu, 9 Oct 2014 15:54:20 -0400 Subject: [ITK] [ITK-users] TransformMatrix order in MHD file Message-ID: Dear ITK users, Now I have a 3x3 TransformMatrix , when I write to mhd file, it just one line. I should write as row order or column order? thanks dongfeng - -------------- 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 fbudin at email.unc.edu Fri Oct 10 08:35:04 2014 From: fbudin at email.unc.edu (Budin, Francois) Date: Fri, 10 Oct 2014 12:35:04 +0000 Subject: [ITK] [ITK-users] itkTransformFileReaderTemplate In-Reply-To: <4FAFFD37-9479-4FF9-ACB7-27C50195B685@unc.edu> References: <4FAFFD37-9479-4FF9-ACB7-27C50195B685@unc.edu> Message-ID: Hello, I use to read transform files with itkTransformFileReader, but I discovered the new class in itk4.5 and above called itkTransformFileReaderTemplate. This class seems very convenient as it converts my transforms from let?s say float to double automatically if my transform file is a float transform, but if my reader is instantiated as double. However, I was wondering if there is a way to know the original type in which the transform in the file is encoded. I would like to be able to know if my file contains a float or a double transform (without manually reading the transform file myself). Sincerely, Francois _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From hans-johnson at uiowa.edu Fri Oct 10 08:37:26 2014 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Fri, 10 Oct 2014 12:37:26 +0000 Subject: [ITK] [ITK-users] itkTransformFileReaderTemplate Message-ID: Ali Ghayoor in my lab did this work. I?ll allow him to respond appropriately today. Hans On 10/10/14, 7:35 AM, "Budin, Francois" wrote: >Hello, > >I use to read transform files with itkTransformFileReader, but I >discovered the new class in itk4.5 and above called >itkTransformFileReaderTemplate. This class seems very convenient as it >converts my transforms from let?s say float to double automatically if my >transform file is a float transform, but if my reader is instantiated as >double. However, I was wondering if there is a way to know the original >type in which the transform in the file is encoded. I would like to be >able to know if my file contains a float or a double transform (without >manually reading the transform file myself). >Sincerely, > >Francois >_____________________________________ >Powered by www.kitware.com > >Visit other Kitware open-source projects at >http://www.kitware.com/opensource/opensource.html > >Kitware offers ITK Training Courses, for more information visit: >http://www.kitware.com/products/protraining.php > >Please keep messages on-topic and check the ITK FAQ at: >http://www.itk.org/Wiki/ITK_FAQ > >Follow this link to subscribe/unsubscribe: >http://public.kitware.com/mailman/listinfo/insight-users ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 alii.ghayoor at gmail.com Fri Oct 10 14:40:55 2014 From: alii.ghayoor at gmail.com (Ali Ghayoor) Date: Fri, 10 Oct 2014 13:40:55 -0500 Subject: [ITK] [ITK-users] itkTransformFileReaderTemplate In-Reply-To: References: Message-ID: Well, I am not sure whether there is a way to know about the original precision type of transform parameters before reading them in ITK. Based on the reader class implementation, the parameters precision types are casted to the request type (float or double) instantly while reading the parameters from the transform buffer, so we don?t need any knowledge about their current type. Ali On 10/10/14, 7:37 AM, "Johnson, Hans J" wrote: >Ali Ghayoor in my lab did this work. I?ll allow him to respond >appropriately today. > >Hans > > >On 10/10/14, 7:35 AM, "Budin, Francois" wrote: > >>Hello, >> >>I use to read transform files with itkTransformFileReader, but I >>discovered the new class in itk4.5 and above called >>itkTransformFileReaderTemplate. This class seems very convenient as it >>converts my transforms from let?s say float to double automatically if my >>transform file is a float transform, but if my reader is instantiated as >>double. However, I was wondering if there is a way to know the original >>type in which the transform in the file is encoded. I would like to be >>able to know if my file contains a float or a double transform (without >>manually reading the transform file myself). >>Sincerely, >> >>Francois >>_____________________________________ >>Powered by www.kitware.com >> >>Visit other Kitware open-source projects at >>http://www.kitware.com/opensource/opensource.html >> >>Kitware offers ITK Training Courses, for more information visit: >>http://www.kitware.com/products/protraining.php >> >>Please keep messages on-topic and check the ITK FAQ at: >>http://www.itk.org/Wiki/ITK_FAQ >> >>Follow this link to subscribe/unsubscribe: >>http://public.kitware.com/mailman/listinfo/insight-users > > > >________________________________ >Notice: This UI Health Care e-mail (including attachments) is covered by >the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is >confidential and may be legally privileged. If you are not the intended >recipient, you are hereby notified that any retention, dissemination, >distribution, or copying of this communication is strictly prohibited. >Please reply to the sender that you have received the message in error, >then delete it. Thank you. >________________________________ >_____________________________________ >Powered by www.kitware.com > >Visit other Kitware open-source projects at >http://www.kitware.com/opensource/opensource.html > >Kitware offers ITK Training Courses, for more information visit: >http://www.kitware.com/products/protraining.php > >Please keep messages on-topic and check the 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 bschaffer at superstem.org Sat Oct 11 14:59:03 2014 From: bschaffer at superstem.org (Dr Bernhard Schaffer) Date: Sat, 11 Oct 2014 20:59:03 +0200 Subject: [ITK] Hello & beginners question Message-ID: <004c01cfe585$6e5fb1d0$4b1f1570$@superstem.org> Hi to all, I've just signed up to this list, so please be patient with me and presumably dumb questions. Potentially a lot of questions. I'm still trying to get a grip on ITK in general. I'm using it as an extension in another application, where I already have images & visualization, so I'm mainly interest in utilizing some of the more advanced image-computation algorithms. So far I've been to the usual suspects of information (ITK webpage, itkWiki, InsightSoftwarGuide-Book, Doxygen documentation) and I've been able to get ITK compiled and incorporated in my project (on a basic level). However, quite a lot of itk-concepts are strange/new to me and the syntax is not always clear to me neither. Upfront question: Is it generally better to ask (itk) coding-related questions in this group, or on a more general platform like StackOverlow with the [itk] tag ? (First) coding question: Right now, I'm looking for simple code/syntax example for the use of EvaluatePosition(). I've seen the method in the Doxygen documentation, but so far I've not found a good example code anywhere and the parameters are a bit obscure to me. What I'm trying to do is the following: 1. Load a set of vertices (2D) into the VoronoiDiagram2DGenerator 2. Generate the diagram (using the size of an existing image as outer boundary) 3. Test points of the image ( a subset ) against the generated VoronoiDiagram to label them with the VoronoiCellIndex 4. Eventually label all of the points of my image to create a simple Voronoi label map from my image. Steps 1 & 2 are pretty clear to me, as they are in the VoronoiDiagram WikiExample (http://www.itk.org/Wiki/ITK/Examples/Segmentation/WishList/VoronoiDiagram2D Generator) Step 3 is where I would need some example code. (Maybe as an extension to the example above?) Step 4 would follow, but if there is a smarter/faster way of creating such a "pixelated" VoronoiDiagram, I would love to see some example code as well. Thanks in advance, Bernhard -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Sun Oct 12 22:49:24 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 12 Oct 2014 22:49:24 -0400 Subject: [ITK] [ITK-users] vector image registration In-Reply-To: References: Message-ID: Hi Lianli, No, ITK does not have any vector image registration methods yet. There could be many approaches here that are often problem specific. Extracting a scalar pixel value from the vectors for application in the metric is a workable approach. Hope this helps, Matt On Thu, Oct 2, 2014 at 8:40 PM, Lianli Liu wrote: > Hi all, > > I wonder if ITK is supporting vector image registration now? If not, any > suggestions to achieve this goal? > > Thanks! > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 stnava at gmail.com Sun Oct 12 22:59:29 2014 From: stnava at gmail.com (brian avants) Date: Sun, 12 Oct 2014 22:59:29 -0400 Subject: [ITK] [ITK-users] vector image registration In-Reply-To: References: Message-ID: Both: itkMultiGradientImageToImageMetricv4RegistrationTest.cxx and itkMeanSquaresImageToImageMetricv4VectorRegistrationTest.cxx can achieve some form of vector image registration. but it depends on what you mean by *vector*. brian On Sun, Oct 12, 2014 at 10:49 PM, Matt McCormick wrote: > Hi Lianli, > > No, ITK does not have any vector image registration methods yet. > There could be many approaches here that are often problem specific. > Extracting a scalar pixel value from the vectors for application in > the metric is a workable approach. > > Hope this helps, > Matt > > On Thu, Oct 2, 2014 at 8:40 PM, Lianli Liu wrote: > > Hi all, > > > > I wonder if ITK is supporting vector image registration now? If not, any > > suggestions to achieve this goal? > > > > Thanks! > > Lianli > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Mon Oct 13 11:11:20 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 13 Oct 2014 11:11:20 -0400 Subject: [ITK] [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members In-Reply-To: <2A6589EB-D292-4362-8863-D4804ADE41EC@gmail.com> References: <2A6589EB-D292-4362-8863-D4804ADE41EC@gmail.com> Message-ID: Hi Ariel, I'll see if we can record and upload the audio next time. Thanks, Matt On Thu, Oct 9, 2014 at 10:43 AM, Ariel Hern?n Curiale wrote: > Hi Matt, > Is there any chance to see the video of the meeting on you tube, for example > ? > > Cheers > __________________________________ > | Ariel Hern?n Curiale Ph.D Candidate > | ETSI Telecomunicaci?n > | Universidad de Valladolid > | Campus Miguel Delibes > | 47011 Valladolid, Spain > | Phone: 983-423000 ext. 5590 > | Web: www.curiale.com.ar > |_________________________________ > > On 07/10/2014, at 17:52, Matt McCormick wrote: > > On Friday, 11:00 AM Eastern USA time, an ITK development conference, > > https://plus.google.com/u/0/events/cs71fpcqpa7l9me2vq45mi61mq8 > > > To get regular invites to these events, join the ITK Bar Camp G+ Community: > > https://plus.google.com/u/0/communities/111375098792764998322 > > > All are welcome. Hope to talk to you then! > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > From matt.mccormick at kitware.com Mon Oct 13 11:20:13 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 13 Oct 2014 11:20:13 -0400 Subject: [ITK] [ITK-users] TransformMatrix order in MHD file In-Reply-To: References: Message-ID: Hi Dongfeng, Column order. See itkImageIODirection3DTest [1] [2] for reference. HTH, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/IO/ImageBase/test/itkImageIODirection3DTest.cxx;h=dc0f351944bc9dc293d95cf6ffb01bb832059bf8;hb=HEAD [2] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/IO/ImageBase/test/CMakeLists.txt;h=1f8c20ec0ade96b860d000e3a777ee0d613cc467;hb=HEAD#l217 On Thu, Oct 9, 2014 at 3:54 PM, Dongfeng Han wrote: > Dear ITK users, > > Now I have a 3x3 TransformMatrix , when I write to mhd file, it just one > line. > I should write as row order or column order? > > thanks > > dongfeng > - > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 noreply at insightsoftwareconsortium.org Mon Oct 13 14:29:18 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 14:29:18 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Challenge on Endocardial Three-dimensional Ultrasound Segmentation (CETUS) Message-ID: <20141013182918.87F7E3D6C171@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Challenge on Endocardial Three-dimensional Ultrasound Segmentation (CETUS) Authors: Bernard O., Heyde B., Alessandrini M., Barbosa D., Camarasu-Pop S., Cervenansky F., Valette S., Mirea O., Galli E., Geleijnse M., Papachristidis A., Bosch J.G., D'hooge J. Abstract: Real-time 3D echocardiography has already been shown to be an accurate tool for left ventricular (LV) volume assessment. However, LV border identification remains a challenging task, mainly because of the low contrast of the images combined with drop-out artifacts. Many (semi-)automatic algorithms have been proposed to segment the LV border, but a systematic and fair comparison between such methods has so far been impossible due to a lack of publicly available common database. The aim of this MICCAI challenge was to gather researchers around the field of LV segmentation in 3D cardiac ultrasound by providing a common database to compare algorithms directly. The proposed platform will allow a consistent evaluation and ranking of the current state-of-the-art segmentation solutions and will contribute to a faster clinical translation of groundbreaking technical advances. The purpose of this paper is to describe the technical aspects of the generation of the database, give an ov erview of the ranking strategy and the outline of the challenge itself. Download and review this publication at: http://hdl.handle.net/10380/3479 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 15:20:14 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 15:20:14 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Clinical Expert Delineation of 3D Left Ventricular Echocardiograms for the CETUS Segmentation Challenge Message-ID: <20141013192014.688FB3D6C4F4@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Clinical Expert Delineation of 3D Left Ventricular Echocardiograms for the CETUS Segmentation Challenge Authors: Papachristidis A., Geleijnse M.L., Galli E., Heyde B., Alessandrini M., Barbosa D., Monaghan M.J., Bernard O., D'hooge J., Bosch J.G. Abstract: Within the framework of the CETUS challenge, forty-five 3D echocardiographic datasets have been acquired and segmented independently by three clinical experts from different hospitals. The goal was to generate a well-established ground truth of validated expert contours on this broad range of images from different ultrasound vendors, for a number of common pathologies. Image data were acquired and segmented according to a specifically designed protocol. Since there is no clear standard or guideline for segmentation for 3DUS, we defined a tracing consensus which results in clinically acceptable and reproducible contours. Tracing was performed in four longitudinal and five transversal 3D-derived 2D planes in ED and ES. 3D contours were constructed from these tracings. If the contours or their clinical parameters differed by more than a predefined level, the tracings were compared and the experts would reach a consensus interpretation on the best segmentation. One or more experts would then adapt their tracings. Final distance differences in contours were 0.77??0.18mm for the training set and 0.82??0.27mmfor the testing set. For the training set, 69% of contours were retraced. For the testing set, 76% of contours were retraced. The used protocol resulted in well-established ground truth contours. Download and review this publication at: http://hdl.handle.net/10380/3480 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 15:40:38 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 15:40:38 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Fast Tracking of the Left Ventricle Using Global Anatomical Affine Optical Flow and Local Recursive Block Matching Message-ID: <20141013194038.520803D6C2EB@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Fast Tracking of the Left Ventricle Using Global Anatomical Affine Optical Flow and Local Recursive Block Matching Authors: Barbosa D., Friboulet D., D'hooge J., Bernard O. Abstract: We present a novel method for segmentation and tracking of the left ventricle (LV) in 4D ultrasound sequences using a combination of automatic segmentation at the end-diastolic frame and tracking using both a global optical flow-based tracker and local block matching. The core novelty of the proposed algorithm relies on the recursive formulation of the block-matching problem, which introduces temporal consistency on the patterns being tracked. The proposed method offers a competitive solution, with average segmentation errors of 2.29 and 2.26mm in the training (#=15) and testing (#=15) datasets respectively. Download and review this publication at: http://hdl.handle.net/10380/3481 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 15:47:08 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 15:47:08 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Automatized Evaluation of the Left Ventricular Ejection Fraction from Echocardiographic Images Using Graph Cut Message-ID: <20141013194708.C4BD63D6C4EC@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Automatized Evaluation of the Left Ventricular Ejection Fraction from Echocardiographic Images Using Graph Cut Authors: Bernier M., Jodoin P., Lalande A. Abstract: In this paper, we present a fast and interactive graph cut method for 3D segmentation of the endocardial wall of the left ventricle (LV) given 3D echocardiographic images. This is a challenging task due to the poor contrast and the low signal-to-noise ratio typical of echocardiographic images. The method is carried out in 3 steps. First, 3D sampling of the LV cavity is made in a spherical-cylindrical coordinate system. Then, a gradient-based energy term is assigned to each voxel, some of which being given an infinite energy to make sure the resulting volume passes through key anatomical points. Then, a graph-cut procedure provides delineation of the endocardial surface. Results obtained on 30 exams from the 2014 CETUS MICCAI challenge dataset reveal that our method takes between 5 and 10 seconds to segment a 3D volume with an overall mean surface distance lower than 2.3 mm and an ejection fraction error of less than 5% compared to a manual tracing by an expert. Download and review this publication at: http://hdl.handle.net/10380/3482 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 15:56:17 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 15:56:17 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Endocardial Segmentation using Structured Random Forests in 3D Echocardiography Message-ID: <20141013195617.B23403D6C4DA@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Endocardial Segmentation using Structured Random Forests in 3D Echocardiography Authors: Domingos J.S., Stebbing R.V., Noble A.J. Abstract: Segmentation of the left ventricle endocardium in 3D echocardiography is a critical step for the diagnosis of heart disease. Although recent work has shown effective endocardial edge detection, these techniques still preserve spurious anatomical edge responses that undermine overall ventricle segmentation. In this paper we propose a robust semiautomatic framework based on 2D structured learning that facilitates full 3D model-based endocardial segmentation. This method is evaluated on 30 publicly available datasets from different brands of ultrasound machines. Results show that the proposed method accurately finds the endocardium and effectively converges an explicit and continuous surface model to it. Download and review this publication at: http://hdl.handle.net/10380/3483 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 16:25:11 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:25:11 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Endocardial 3D Ultrasound Segmentation using Autocontext Random Forests Message-ID: <20141013202511.6AA1B3D6C291@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Endocardial 3D Ultrasound Segmentation using Autocontext Random Forests Authors: Keraudren K., Oktay O., Shi W., Hajnal J.V., Rueckert D. Abstract: In this paper, we present the use of a generic image segmentation method, namely a succession of Random Forest classifiers in an autocontext framework, for the MICCAI 2014 Challenge on Endocardial 3D Ultrasound Segmentation (CETUS). The proposed method segments each frame independently in 90 sec, without requiring temporal information such as end-diastolic or end-systolic time points nor any registration. For better segmentation accuracy, non-local means denoising can be applied to the images at the cost of an increased run-time. The mean Dice score on the testing dataset was 84.4% without denoising and 86.4% with denoising. The originality of our approach lies in the introduction of two classes, the myocardium and the mitral valve, in addition to the left ventricle and the background classes, in order to gain contextual information for the segmentation task. Download and review this publication at: http://hdl.handle.net/10380/3484 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 16:30:11 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:30:11 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Left Ventricle Segmentation in Cardiac Ultrasound Using Hough-Forests With Implicit Shape and Appearance Priors Message-ID: <20141013203011.25A3E3D6C3C2@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Left Ventricle Segmentation in Cardiac Ultrasound Using Hough-Forests With Implicit Shape and Appearance Priors Authors: Milletari F., Yigitsoy M., Navab N., Ahmadi S. Abstract: We propose a learning based approach to perform automatic segmentation of the left ventricle in 3D cardiac ultrasound images. The segmentation contour is estimated through the use of a variant of Hough forests whose object localization capabilities are coupled with a patch-wise, appearance driven, contour estimation strategy. The performance of the proposed method is evaluated on a dataset of 30 images acquired from 15 patients using different equipment and settings. Download and review this publication at: http://hdl.handle.net/10380/3485 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 16:34:43 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:34:43 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Learning Shape Representations for Multi-Atlas Endocardium Segmentation in 3D Echo Images Message-ID: <20141013203443.D24FA3D6C55B@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Learning Shape Representations for Multi-Atlas Endocardium Segmentation in 3D Echo Images Authors: Oktay O., Shi W., Keraudren K., Caballero J., Rueckert D. Abstract: As part of the CETUS challenge, we present a multi-atlas segmentation framework to delineate the left-ventricle endocardium in echocardiographic images. To increase the robustness of the registration step, we introduce a speckle reduction step and a new shape representation based on sparse coding and manifold approximation in dictionary space. The shape representation, unlike intensity values, provides consistent shape information across different images. The validation results on the test set show that registration based on our shape representation significantly improves the performance of multi-atlas segmentation compared to intensity based registration. To our knowledge it is the first time that multi-atlas segmentation achieves state-of-the-art results for echocardiographic images. Download and review this publication at: http://hdl.handle.net/10380/3486 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 16:38:35 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:38:35 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Real-time Tracking of the Left Ventricle in 3D Ultrasound Using Kalman Filter and Mean Value Coordinates Message-ID: <20141013203835.114943D6C407@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Real-time Tracking of the Left Ventricle in 3D Ultrasound Using Kalman Filter and Mean Value Coordinates Authors: Smistad E., Lindseth F. Abstract: A method for real-time automatic tracking of the left ventricle (LV) in 3D ultrasound is presented. A mesh model of the LV is deformed using mean value coordinates enabling large variations. Kalman filtering and edge detection is used to track the mesh in each frame. The method is evaluated using the framework of the Challenge on Endocardial Three-dimensional Ultrasound Segmentation (CETUS). The results show that the method is able to robustly track the LV in all sequences with a mean mesh difference of about 2.5 mm Download and review this publication at: http://hdl.handle.net/10380/3487 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 16:45:33 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:45:33 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Segmentation of Multi-Center 3D Left Ventricular Echocardiograms by Active Appearance Models Message-ID: <20141013204533.E60203D6C46C@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Segmentation of Multi-Center 3D Left Ventricular Echocardiograms by Active Appearance Models Authors: Van Stralen M., Haak A., Leung E.K., Van Burken G., Bosch J.G. Abstract: Segmentation of 3D echocardiograms (3DEs) is still a challenging task due to the low signal-to-noise ratio, the limited field of view, and typical ultrasound artifacts. We propose to segment the left ventricular endocardial surface by using Active Appearance Models (AAMs). Separate end-diastolic (ED) and end-systolic (ES) AAMs were built from presegmented 3DEs of the CETUS training data and 25 previously acquired 3DEs, imaged using various 3DE equipment. The AAMs fully automatically segmented the 15 training sets in a leave-one-out cross validation, comparing two training populations and various initialization strategies. All segmentations took about 15 seconds per patient. The comparison on the CETUS training data shows that the AAM benefits from additional training data and more accurate initialization. The results on the CETUS training and testing data confirm good ED and ES segmentation accuracy on multi-center, multi-vendor, multi-pathology data, and corresponding EF e stimation. Selection from different initialization strategies, based on the minimal residual error, and propagation of detected ED contours to initialize ES detection, contributed to more accurate segmentations in this heterogeneous population. Download and review this publication at: http://hdl.handle.net/10380/3488 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 16:51:08 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:51:08 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Model-based left ventricle segmentation in 3D ultrasound using phase image Message-ID: <20141013205108.426C23D6C7AE@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Model-based left ventricle segmentation in 3D ultrasound using phase image Authors: Wang C., Smedby O. Abstract: In this paper, we propose a semi-automatic method for left ventricle segmentation. The proposed method utilizes a multi-scale quadrature filter method to enhance the 3D volume, followed by a model-based level set method to segment the endocardial surface of the left ventricle. The phase map from the quadrature filters is also used to weight the influence of contour points when updating the statistical model. Download and review this publication at: http://hdl.handle.net/10380/3489 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Mon Oct 13 17:39:15 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 13 Oct 2014 17:39:15 -0400 Subject: [ITK] Gerrit Down Time Message-ID: Hi, Gerrit will be down tonight for a few hours starting at 7:00 PM Eastern USA time for infrastructure upgrades. Sorry for any inconvenience. Matt From davis.vigneault at gmail.com Tue Oct 14 11:31:09 2014 From: davis.vigneault at gmail.com (DVigneault) Date: Tue, 14 Oct 2014 08:31:09 -0700 (PDT) Subject: [ITK] [ITK-users] Operator overloading in ITK objects. Message-ID: <1413300669946-7586346.post@n2.nabble.com> All-- I've defined an ITK object inheriting from itk::DataObject (full header file copied below). The object has two properties: Index and Value. I've tried to overload the == and < operators (basing my syntax off of itk::Point) so that the two objects would be equal if they have the same index, and one would be less than the other if one's value is less than the other's: bool operator==(const Self & pt) const { return this->GetIndex() == pt->GetIndex(); } bool operator<(const Self & pt) const { return this->GetValue() < pt->GetValue(); } However, the less than operator isn't functioning as intended: typedef IndexValuePair< IndexType, PixelType > PairType; typename PairType::Pointer pair1 = PairType::New(); IndexType index1; pair1->SetIndex( index1.Fill( 0 ) ); pair1->SetValue( 1 ); typename PairType::Pointer pair2 = PairType::New(); IndexType index2; pair2->SetIndex( index2.Fill( 1 ) ); pair2->SetValue( 0 ); std::cout << (pair1 == pair2) << std::endl; // 0 std::cout << (pair1 == pair1) << std::endl; // 1 std::cout << (pair1 < pair2) << std::endl; // 1 Interestingly, the results do not change if I comment out the overloading operators in the header file, or if I change the values of the pairs, suggesting that the program is comparing the objects based on some other criteria. Any ideas what I'm doing wrong? Apologies in advance if this is more of a c++ question and less of an ITK question--I'm sometimes not sure whether my problem is due to my misunderstanding the language or the library. Best, --Davis Best, and thanks, --Davis *** Header ** #ifndef __itkIndexValuePair_h #define __itkIndexValuePair_h #include "itkDataObject.h" namespace itk { template < typename IndexType, typename ValueType > class IndexValuePair:public DataObject { public: /** Standard class typedefs. */ typedef IndexValuePair Self; typedef DataObject Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; /** Method for creation through the object factory. */ itkNewMacro(Self); /** Standard part of every itk Object. */ itkTypeMacro(IndexValuePair, DataObject); itkSetMacro( Index, IndexType ); itkGetMacro( Index, IndexType ); itkSetMacro( Value, ValueType ); itkGetMacro( Value, ValueType ); /** Compare two points for equality. */ bool operator==(const Self & pt) const { return this->GetIndex() == pt->GetIndex(); } /** Less than. */ bool operator<(const Self & pt) const { return this->GetValue() < pt->GetValue(); } protected: /** Constructor for use by New() method. */ IndexValuePair() {} ~IndexValuePair() {} // virtual void PrintSelf(std::ostream & os, Indent indent) const; IndexType m_Index; ValueType m_Value; private: IndexValuePair(const Self &); //purposely not implemented void operator=(const Self &); //purposely not implemented }; } #endif -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Operator-overloading-in-ITK-objects-tp7586346.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 blowekamp at mail.nih.gov Tue Oct 14 11:38:49 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 14 Oct 2014 11:38:49 -0400 Subject: [ITK] [ITK-users] Operator overloading in ITK objects. In-Reply-To: <1413300669946-7586346.post@n2.nabble.com> References: <1413300669946-7586346.post@n2.nabble.com> Message-ID: <47CDDE20-C688-4DA0-A28B-AAEE0BBAC93A@mail.nih.gov> Hello, I think the issue is that the variables pair1 and pair2 are SmartPointers not the derived data object type, so your operators are working on a different object type than you expected. ITK was not designed for use with overloaded operators with it's data objects and process objects. You could likely hack it by doing (*pair1) == (*pair2), if you really want to use overloaded operators. Otherwise a conventional member function could just as easily be used. Brad On Oct 14, 2014, at 11:31 AM, DVigneault wrote: > All-- > > I've defined an ITK object inheriting from itk::DataObject (full header file > copied below). The object has two properties: Index and Value. I've tried > to overload the == and < operators (basing my syntax off of itk::Point) so > that the two objects would be equal if they have the same index, and one > would be less than the other if one's value is less than the other's: > > bool operator==(const Self & pt) const { > return this->GetIndex() == pt->GetIndex(); } > > bool operator<(const Self & pt) const { > return this->GetValue() < pt->GetValue(); } > > However, the less than operator isn't functioning as intended: > > typedef IndexValuePair< IndexType, PixelType > PairType; > typename PairType::Pointer pair1 = PairType::New(); > IndexType index1; > pair1->SetIndex( index1.Fill( 0 ) ); > pair1->SetValue( 1 ); > > typename PairType::Pointer pair2 = PairType::New(); > IndexType index2; > pair2->SetIndex( index2.Fill( 1 ) ); > pair2->SetValue( 0 ); > > std::cout << (pair1 == pair2) << std::endl; // 0 > std::cout << (pair1 == pair1) << std::endl; // 1 > std::cout << (pair1 < pair2) << std::endl; // 1 > > Interestingly, the results do not change if I comment out the overloading > operators in the header file, or if I change the values of the pairs, > suggesting that the program is comparing the objects based on some other > criteria. Any ideas what I'm doing wrong? Apologies in advance if this is > more of a c++ question and less of an ITK question--I'm sometimes not sure > whether my problem is due to my misunderstanding the language or the > library. > > Best, > > --Davis > > Best, and thanks, > > --Davis > > *** Header ** > > #ifndef __itkIndexValuePair_h > #define __itkIndexValuePair_h > > #include "itkDataObject.h" > > namespace itk > { > > template < typename IndexType, typename ValueType > > class IndexValuePair:public DataObject > { > > public: > > /** Standard class typedefs. */ > typedef IndexValuePair Self; > typedef DataObject Superclass; > typedef SmartPointer< Self > Pointer; > typedef SmartPointer< const Self > ConstPointer; > > /** Method for creation through the object factory. */ > itkNewMacro(Self); > > /** Standard part of every itk Object. */ > itkTypeMacro(IndexValuePair, DataObject); > > itkSetMacro( Index, IndexType ); > itkGetMacro( Index, IndexType ); > > itkSetMacro( Value, ValueType ); > itkGetMacro( Value, ValueType ); > > > /** Compare two points for equality. */ > bool > operator==(const Self & pt) const > { > return this->GetIndex() == pt->GetIndex(); > } > > /** Less than. */ > bool > operator<(const Self & pt) const > { > return this->GetValue() < pt->GetValue(); > } > > protected: > /** Constructor for use by New() method. */ > IndexValuePair() {} > ~IndexValuePair() {} > // virtual void PrintSelf(std::ostream & os, Indent indent) const; > > IndexType m_Index; > ValueType m_Value; > > private: > IndexValuePair(const Self &); //purposely not implemented > void operator=(const Self &); //purposely not implemented > > }; > > } > > #endif > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Operator-overloading-in-ITK-objects-tp7586346.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 gaetano.esposito at outlook.com Tue Oct 14 18:23:07 2014 From: gaetano.esposito at outlook.com (Gaetano Esposito) Date: Tue, 14 Oct 2014 22:23:07 +0000 Subject: [ITK] ITK -- Transform an image with a change of coordinates Message-ID: Hello, I apologize in advance for using a vague language, but I just started to play with image processing and segmentation. Given an image, I would like to define an arbitrary origin, get the coordinates of every pixel from Cartesian (x,y) to polar(rho, theta), and then create a new image whose x axis is "rho" and whose y axis is "theta". In other words, I would like to map a circular image in Cartesian Coordinates to a periodic line in polar coordinates. I am a little confused about how I would achieve this in ITK. I believe that I can take advantage of a couple of Transform based Polar-Cartesian algorithms out there, some of them published on the Insight Journal. The transform typically seems to act on a single point. Is using a transform the right approach? If yes, once I have the correct transform from Cartesian to Polar, how do I create the "polar" image that I am seeking? Thanks for your feedback, Gaetano -------------- next part -------------- An HTML attachment was scrubbed... URL: From gabrielgimenez85 at gmail.com Tue Oct 14 19:51:39 2014 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Tue, 14 Oct 2014 16:51:39 -0700 (PDT) Subject: [ITK] [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform Message-ID: <1413330699438-7586348.post@n2.nabble.com> Hello everyone, I modified the example 8 for use OnePlusOneEvolutionaryOptimizer and itkMattesMutualInformationImageToImageMetric, this worked for me. Now, i try to use itkRegistrationParameterScalesFromPhysicalShift for to estimate the parameters of scale. I adapted my code to use the ITKv4, but, but I have this error: *Optimizer stop condition: OnePlusOneEvolutionaryOptimizerv4: Fnorm (0.000777958) is less than Epsilon (1 at iteration #0* I found almost no documentation of ITK version 4, why ?In Manuals not found anything. This is the part of code to configure the estimation scale (based on examples found in the DoxyGen): typedef itk::RegistrationParameterScalesFromPhysicalShift ScalesEstimatorType; ScalesEstimatorType::Pointer scalesEstimator = ScalesEstimatorType::New(); scalesEstimator->SetMetric( metric ); scalesEstimator->SetTransformForward( true ); scalesEstimator->SetSmallParameterVariation( 1.0 ); optimizer->SetScalesEstimator( scalesEstimator ); optimizer->SetDoEstimateScales(true); Hopefully someone can help me with something, thanks. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348.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 j.plumat at auckland.ac.nz Tue Oct 14 21:42:19 2014 From: j.plumat at auckland.ac.nz (Jerome Plumat) Date: Wed, 15 Oct 2014 14:42:19 +1300 Subject: [ITK] [ITK-users] how to visualise deformed volume along registration process Message-ID: <543DD0FB.1040609@auckland.ac.nz> Hello everyone, I'm facing to a problem and I hope some may have ideas to help me. I'm using Multi Resolution Symmetric Log-Domain Diffeomorphic Demons Algorithm (http://www.insight-journal.org/browse/publication/644) to register volumes. The current results are not very good and I would like to observe them along the registration process. My current solution uses object to display metrics and information along pyramid levels: template class ShowProgressObject { public: ShowProgressLevelObject(TRegistration* o) { m_Process = o; } void ShowProgress() { std::cout << "Level: " << m_Process->GetCurrentLevel() << " "; std::cout << "Progress: " << m_Process->GetProgress() << " "; std::cout << "Starting Metric: " << m_Process->GetRegistrationFilter()->GetMetric() << " "; std::cout << std::endl; } typename TRegistration::Pointer m_Process; }; .... typedef ShowProgressObject ProgressType; ProgressType progressWatch(registrator); itk::SimpleMemberCommand::Pointer command; command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(&progressWatch, &ProgressType::ShowProgress); I would like to use this object to display the current deformed image at each level of the pyramid. My current (not so good) idea is to use fixed and moving images and current deformation field. I'm using warper to deform the moving image in the ShowProgressObject::ShowProgress function: warper->SetInput( m_originalMoving ); warper->SetInterpolator( interpolator ); warper->SetOutputSpacing( m_fixed->GetSpacing() ); warper->SetOutputOrigin( m_fixed->GetOrigin() ); warper->SetOutputDirection( m_fixed->GetDirection() ); warper->SetDisplacementField( m_Process->GetRegistrationFilter()->GetDeformationField() ); warper->Update(); Then the result would be display with QuickView. But ... it appears that using fixed and moving images in this process makes them unavailable for the registration. I can make copies of them but this seems very inefficient. Any recommendations or advices to achieve to display deformed image along process? Thanks a lot. -- Jerome ------- School of Medical Sciences University of Auckland If I am not for myself, who will be for me? And if I am only for myself, then what an I? And if not now when? ? Hillel HaZaken _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 shinya.onogi at live.jp Wed Oct 15 05:45:39 2014 From: shinya.onogi at live.jp (Shinya Onogi) Date: Wed, 15 Oct 2014 02:45:39 -0700 (MST) Subject: [ITK] [ITK-users] ITK build failed in using ITK_USE_FLOAT_SPACE_PRECISION Message-ID: <1413366339221-34689.post@n7.nabble.com> Hi, When ITK_USE_FLOAT_SPACE_PRECISION is TRUE, Compilation error occurs in itkTransformFactoryBase.cxx at L274 and L275. I could not find the issue in Google; therefore, I will note it here for anyone. L274: TransformFactory< GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform >::RegisterTransform (); L275 TransformFactory< GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform >::RegisterTransform (); My env is followings. OS: Windows 8.1 Platform: Visual Studio 2013 ITK: ITK-4.6.1 -- View this message in context: http://itk-users.7.n7.nabble.com/ITK-build-failed-in-using-ITK-USE-FLOAT-SPACE-PRECISION-tp34689.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 Wed Oct 15 08:32:47 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 15 Oct 2014 08:32:47 -0400 Subject: [ITK] [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: <1413330699438-7586348.post@n2.nabble.com> References: <1413330699438-7586348.post@n2.nabble.com> Message-ID: <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> Hello, > > *Optimizer stop condition: OnePlusOneEvolutionaryOptimizerv4: Fnorm > (0.000777958) is less than Epsilon (1 at iteration #0* This message may mean that the scales are not correctly set, and the the initial search area failed to yield a significant change. Things that can impact the scales include the metric used and the spacing of your image. This can some times be a difficult thing to track down. Would the spacing of you image happen to be very large or very small? Also keep in mind that the Versor transforms are not Euclidean spaces and a best suited for use with the regular step gradient descent optimizers as only that optimizer takes into consideration the correct normalization of the versor space. In short I think you have picked three challenging components that may just now work well together. Brad > > I found almost no documentation of ITK version 4, why ?In Manuals not found > anything. > > This is the part of code to configure the estimation scale (based on > examples found in the DoxyGen): > > typedef itk::RegistrationParameterScalesFromPhysicalShift > ScalesEstimatorType; > ScalesEstimatorType::Pointer scalesEstimator = > ScalesEstimatorType::New(); > scalesEstimator->SetMetric( metric ); > scalesEstimator->SetTransformForward( true ); > scalesEstimator->SetSmallParameterVariation( 1.0 ); > > optimizer->SetScalesEstimator( scalesEstimator ); > optimizer->SetDoEstimateScales(true); > > Hopefully someone can help me with something, thanks. > > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348.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 emmasaunders123 at gmail.com Wed Oct 15 08:56:33 2014 From: emmasaunders123 at gmail.com (Emma Saunders) Date: Wed, 15 Oct 2014 13:56:33 +0100 Subject: [ITK] [ITK-users] Metric Distance on Manifold Message-ID: Hello all, ITK offers numerous diffeomorphic registration algorithms, is there a mechanism within ITK to calculate the distance each transformation has moved along the diffeomorphic manifold? If not is it possible to perform such a calculation on the displacement fields themselves. Thanks for any help Emma -------------- 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 Wed Oct 15 09:14:25 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 15 Oct 2014 09:14:25 -0400 Subject: [ITK] [ITK-users] ITK build failed in using ITK_USE_FLOAT_SPACE_PRECISION In-Reply-To: <1413366339221-34689.post@n7.nabble.com> References: <1413366339221-34689.post@n7.nabble.com> Message-ID: Hello, I tried compiling with this options with gcc 4.8.2 on Linux and I am getting a large number of compilation errors too. Looks like it would requite a bit of work to get this working again. Perhaps This option worked with the ITK 4.5 release? Brad On Oct 15, 2014, at 5:45 AM, Shinya Onogi wrote: > Hi, > > When ITK_USE_FLOAT_SPACE_PRECISION is TRUE, Compilation error occurs in > itkTransformFactoryBase.cxx at L274 and L275. I could not find the issue in > Google; therefore, I will note it here for anyone. > > L274: > TransformFactory< > GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform >> ::RegisterTransform (); > > L275 > TransformFactory< > GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform >> ::RegisterTransform (); > > > My env is followings. > OS: Windows 8.1 > Platform: Visual Studio 2013 > ITK: ITK-4.6.1 > > > > > -- > View this message in context: http://itk-users.7.n7.nabble.com/ITK-build-failed-in-using-ITK-USE-FLOAT-SPACE-PRECISION-tp34689.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 gabrielgimenez85 at gmail.com Wed Oct 15 10:26:00 2014 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Wed, 15 Oct 2014 07:26:00 -0700 (PDT) Subject: [ITK] [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> References: <1413330699438-7586348.post@n2.nabble.com> <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> Message-ID: <1413383160042-7586354.post@n2.nabble.com> Hello Brad ,thanks for answering, I need the definition of scales Optimizer (translation and rotation) to be dynamic, not hard, so I use the RegistrationParameterScalesFromPhysicalShift class. Any other alternatives for my problem?. Nor do I find much information about how to define these scales and even less dynamically. Theoretically ITK architecture is fully modular and low-coupling, then, should be no problem to combine different types of optimizers, transformations, etc, or am I wrong? -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348p7586354.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 blowekamp at mail.nih.gov Wed Oct 15 10:43:45 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 15 Oct 2014 10:43:45 -0400 Subject: [ITK] [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: <1413383160042-7586354.post@n2.nabble.com> References: <1413330699438-7586348.post@n2.nabble.com> <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> <1413383160042-7586354.post@n2.nabble.com> Message-ID: <7F36D103-169A-415A-8FB4-0585E40876EB@mail.nih.gov> Hello, The scales are going to be for the serializable optimization parameters for the Transform defined in the doxygen[1]. You may wish to try the other scales estimators: RegistrationPatameterScalesFromIndexShift, RegistrationParameterScalesFromJacobian Also the other parameters for your optimizer may need to be adjusted such as InitialRadius, ShrinkFactor and the GrowthFactor. I have not investigated if these optimizer parameters are correctly scales into the parameter space when applied, but they should be. As you are doing you can theoretically plug any combination of components together. However the results may not be robust or stable. Again I will urge caution with using the Versor transforms with an optimizer other than the RegularStepGradientDescent as there is some coupling of these two to do the correct normalization in the versor space. Brad [1] http://www.itk.org/Doxygen/html/classitk_1_1VersorRigid3DTransform.html On Oct 15, 2014, at 10:26 AM, Gabriel A. Gim?nez wrote: > Hello Brad ,thanks for answering, > > I need the definition of scales Optimizer (translation and rotation) to be > dynamic, not hard, so I use the RegistrationParameterScalesFromPhysicalShift > class. Any other alternatives for my problem?. Nor do I find much > information about how to define these scales and even less dynamically. > > > Theoretically ITK architecture is fully modular and low-coupling, then, > should be no problem to combine different types of optimizers, > transformations, etc, or am I wrong? > > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348p7586354.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 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Wed Oct 15 15:34:19 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 15 Oct 2014 19:34:19 +0000 Subject: [ITK] Stitching Message-ID: Hi all, This is not really an ITK question, but it's on a topic that will be familiar to many here. There are several algorithms and programs for stitching together image pieces to create a whole image. As far as I can tell, these tend to assume that the pieces overlap. We are exploring a course of action in which a fluorescently-labelled biological sample is cut into slices (e.g. 100 microns thick) in order to image with confocal microscopy. I have been asked about the feasibility of joining the thick image slices together to reconstitute the whole sample. The problem, of course, is matching the non-overlapping cut surfaces, since there will be inevitable distortion and loss of information. I'd like to know of any publications on this kind of stitching. Thanks Gib -------------- next part -------------- An HTML attachment was scrubbed... URL: From llliu at umich.edu Wed Oct 15 18:13:19 2014 From: llliu at umich.edu (Lianli Liu) Date: Wed, 15 Oct 2014 18:13:19 -0400 Subject: [ITK] [ITK-users] get B spline coefficients Message-ID: Hi all, I have a deformation field (m*n*k*3 vector image) obtained from B spline registration and I want to get the B spline coefficient from the deformation field. Here are my questions: Shall I use the itkBSplineDecompositionImageFilter to do this? If so, do I need to decompose it along each dimension all just input the entire vector image? Do I need to down sample the image first before decomposition? How should I save my decomposition results? Thanks! Lianli -------------- 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 gabrielgimenez85 at gmail.com Wed Oct 15 21:40:06 2014 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Wed, 15 Oct 2014 18:40:06 -0700 (PDT) Subject: [ITK] [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: <7F36D103-169A-415A-8FB4-0585E40876EB@mail.nih.gov> References: <1413330699438-7586348.post@n2.nabble.com> <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> <1413383160042-7586354.post@n2.nabble.com> <7F36D103-169A-415A-8FB4-0585E40876EB@mail.nih.gov> Message-ID: <1413423606327-7586357.post@n2.nabble.com> thank you very much Brad! Some documentation on how to configure these scales (translation and rotation) manually? -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348p7586357.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 Thu Oct 16 00:05:07 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 16 Oct 2014 00:05:07 -0400 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: There are a couple of upcoming opportunities to share, discuss, design, and learn with your fellow ITK community members. On Thursday (tomorrow), 1:00 PM Eastern USA time, there will be a Google+ Hangout where we will be doing code reviews: https://plus.google.com/events/cg7hf091i0k638gm43n3ktkfic0 On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/events/c3fr7aeqa06lhp2j1r601586o1s For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 To get regular invites to these events, join the ITK Bar Camp G+ Community: https://plus.google.com/u/0/communities/111375098792764998322 All are welcome. Hope to talk to you then! From matt.mccormick at kitware.com Thu Oct 16 00:14:17 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 16 Oct 2014 00:14:17 -0400 Subject: [ITK] ITK -- Transform an image with a change of coordinates In-Reply-To: References: Message-ID: Hi Gaetano, Yes, using a Transform is one way to go. See this Insight Journal article [1] and this class [2]. Hope this helps, Matt [1] http://insight-journal.org/browse/publication/722 [2] http://www.itk.org/Doxygen/html/classitk_1_1AzimuthElevationToCartesianTransform.html On Tue, Oct 14, 2014 at 6:23 PM, Gaetano Esposito wrote: > Hello, > > I apologize in advance for using a vague language, but I just started to > play with image processing and segmentation. > > Given an image, I would like to define an arbitrary origin, get the > coordinates of every pixel from Cartesian (x,y) to polar(rho, theta), and > then create a new image whose x axis is "rho" and whose y axis is "theta". > In other words, I would like to map a circular image in Cartesian > Coordinates to a periodic line in polar coordinates. > > I am a little confused about how I would achieve this in ITK. > I believe that I can take advantage of a couple of Transform based > Polar-Cartesian algorithms out there, some of them published on the Insight > Journal. The transform typically seems to act on a single point. > > Is using a transform the right approach? If yes, once I have the correct > transform from Cartesian to Polar, how do I create the "polar" image that I > am seeking? > > Thanks for your feedback, > > Gaetano > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From matt.mccormick at kitware.com Thu Oct 16 00:25:03 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 16 Oct 2014 00:25:03 -0400 Subject: [ITK] [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: <1413423606327-7586357.post@n2.nabble.com> References: <1413330699438-7586348.post@n2.nabble.com> <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> <1413383160042-7586354.post@n2.nabble.com> <7F36D103-169A-415A-8FB4-0585E40876EB@mail.nih.gov> <1413423606327-7586357.post@n2.nabble.com> Message-ID: Hi Gabriel, Documentation on the ITKv4 registration scale estimation can be found in the Nightly build of the ITK Software Guide. There is is usually a link to the Nightly PDF builds of the ITK Software Guide on the dashboard [1], but it is currently not available due to some build issues. The code for the examples in the software guide can be found in the Examples/Registrationv4/ direction of ITK Git master [2]. Hope this helps, Matt [1] http://open.cdash.org/index.php?project=Insight [2] http://www.itk.org/Wiki/ITK/Git On Wed, Oct 15, 2014 at 9:40 PM, Gabriel A. Gim?nez wrote: > thank you very much Brad! > Some documentation on how to configure these scales (translation and > rotation) manually? > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348p7586357.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 matt.mccormick at kitware.com Thu Oct 16 00:34:11 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 16 Oct 2014 00:34:11 -0400 Subject: [ITK] [ITK-users] how to visualise deformed volume along registration process In-Reply-To: <543DD0FB.1040609@auckland.ac.nz> References: <543DD0FB.1040609@auckland.ac.nz> Message-ID: Hi Jerome, Writing out the Transform as the program progresses may work. Then, use a separate program to generate the resampled images from the input images and the transform. Also, the Transform Visualizer [1] available in the current Slicer Nightly build [2] (soon to be 4.4.0), is a great tool. Hope this helps, Matt [1] http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/TransformVisualizer [2] http://download.slicer.org/ On Tue, Oct 14, 2014 at 9:42 PM, Jerome Plumat wrote: > Hello everyone, > I'm facing to a problem and I hope some may have ideas to help me. > > I'm using Multi Resolution Symmetric Log-Domain Diffeomorphic Demons > Algorithm (http://www.insight-journal.org/browse/publication/644) to > register volumes. The current results are not very good and I would like to > observe them along the registration process. > > My current solution uses object to display metrics and information along > pyramid levels: > > template > class ShowProgressObject > { > public: > ShowProgressLevelObject(TRegistration* o) > { > m_Process = o; > } > > void ShowProgress() > { > std::cout << "Level: " << m_Process->GetCurrentLevel() << " "; > std::cout << "Progress: " << m_Process->GetProgress() << " "; > std::cout << "Starting Metric: " << > m_Process->GetRegistrationFilter()->GetMetric() << " "; > std::cout << std::endl; > > } > > typename TRegistration::Pointer m_Process; > }; > > .... > > typedef ShowProgressObject ProgressType; > ProgressType progressWatch(registrator); > > itk::SimpleMemberCommand::Pointer command; > command = itk::SimpleMemberCommand::New(); > command->SetCallbackFunction(&progressWatch, &ProgressType::ShowProgress); > > > I would like to use this object to display the current deformed image at > each level of the pyramid. My current (not so good) idea is to use fixed and > moving images and current deformation field. I'm using warper to deform the > moving image in the ShowProgressObject::ShowProgress function: > warper->SetInput( m_originalMoving ); > warper->SetInterpolator( interpolator ); > warper->SetOutputSpacing( m_fixed->GetSpacing() ); > warper->SetOutputOrigin( m_fixed->GetOrigin() ); > warper->SetOutputDirection( m_fixed->GetDirection() ); > warper->SetDisplacementField( > m_Process->GetRegistrationFilter()->GetDeformationField() ); > warper->Update(); > > Then the result would be display with QuickView. > > But ... it appears that using fixed and moving images in this process makes > them unavailable for the registration. I can make copies of them but this > seems very inefficient. > > Any recommendations or advices to achieve to display deformed image along > process? > > Thanks a lot. > > -- > > Jerome > ------- > > School of Medical Sciences > University of Auckland > > If I am not for myself, who will be for me? And if I am only for myself, > then what an I? And if not now when? ? Hillel HaZaken > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 Thu Oct 16 15:30:10 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 16 Oct 2014 15:30:10 -0400 Subject: [ITK] [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members In-Reply-To: References: <2A6589EB-D292-4362-8863-D4804ADE41EC@gmail.com> Message-ID: Based on feedback at the Code Review Hangout today, to respect the privacy of participants, we are not going to record the audio tomorrow. Matt On Mon, Oct 13, 2014 at 11:11 AM, Matt McCormick wrote: > Hi Ariel, > > I'll see if we can record and upload the audio next time. > > Thanks, > Matt > > On Thu, Oct 9, 2014 at 10:43 AM, Ariel Hern?n Curiale wrote: >> Hi Matt, >> Is there any chance to see the video of the meeting on you tube, for example >> ? >> >> Cheers >> __________________________________ >> | Ariel Hern?n Curiale Ph.D Candidate >> | ETSI Telecomunicaci?n >> | Universidad de Valladolid >> | Campus Miguel Delibes >> | 47011 Valladolid, Spain >> | Phone: 983-423000 ext. 5590 >> | Web: www.curiale.com.ar >> |_________________________________ >> >> On 07/10/2014, at 17:52, Matt McCormick wrote: >> >> On Friday, 11:00 AM Eastern USA time, an ITK development conference, >> >> https://plus.google.com/u/0/events/cs71fpcqpa7l9me2vq45mi61mq8 >> >> >> To get regular invites to these events, join the ITK Bar Camp G+ Community: >> >> https://plus.google.com/u/0/communities/111375098792764998322 >> >> >> All are welcome. Hope to talk to you then! >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 boll0107 at umn.edu Thu Oct 16 16:00:17 2014 From: boll0107 at umn.edu (Evan Bollig PhD) Date: Thu, 16 Oct 2014 15:00:17 -0500 Subject: [ITK] [ITK-users] SimpleITK python3.4 OSX egg/homebrew Message-ID: Can someone generate a SimpleITK egg for python3.4 on OSX? easy_install SimpleITK comes back with 0 hits for me, and I'd rather not try to figure out how to reproduce your builds. By the way, you should also consider writing a Homebrew recipe to build and install the library as well. I can provide an example recipe for another CMake project that provides Python (SWIG wrapped) libraries if you're interested. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan at msi.umn.edu boll0107 at umn.edu _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 gabrielgimenez85 at gmail.com Thu Oct 16 20:36:42 2014 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Thu, 16 Oct 2014 17:36:42 -0700 (PDT) Subject: [ITK] [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: References: <1413330699438-7586348.post@n2.nabble.com> <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> <1413383160042-7586354.post@n2.nabble.com> <7F36D103-169A-415A-8FB4-0585E40876EB@mail.nih.gov> <1413423606327-7586357.post@n2.nabble.com> Message-ID: <1413506202830-7586363.post@n2.nabble.com> Thanks Matt, I sure will be very useful! I'm working on my thesis, I would like to implement a GA optimizer for ITK. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348p7586363.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 blowekamp at mail.nih.gov Fri Oct 17 08:12:16 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 17 Oct 2014 08:12:16 -0400 Subject: [ITK] [ITK-users] SimpleITK python3.4 OSX egg/homebrew In-Reply-To: References: Message-ID: Hello, There are quite a large number of different binary distributions of Python and not all of them can be supported. Currently the the binaries are compatible with OSX's system python. It is not too hard to build SimpleITK itself for you custom installation. Information on how to do that can be found here [1]. If you are familiar with Homebrew then it should not be too hard to write a recipe for that packaging system. Contributing this to the community would be very welcomed and appreciated by many. There is a recipe for the anaconda python distribution that may be a good basis for Homebrew[2]. Brad [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself [2] https://github.com/conda/conda-recipes/blob/master/simpleitk/build.sh On Oct 16, 2014, at 4:00 PM, Evan Bollig PhD wrote: > Can someone generate a SimpleITK egg for python3.4 on OSX? > easy_install SimpleITK comes back with 0 hits for me, and I'd rather > not try to figure out how to reproduce your builds. > > By the way, you should also consider writing a Homebrew recipe to > build and install the library as well. I can provide an example recipe > for another CMake project that provides Python (SWIG wrapped) > libraries if you're interested. > > Cheers, > -Evan Bollig > Research Associate | Application Developer | User Support Consultant > Minnesota Supercomputing Institute > 599 Walter Library > 612 624 1447 > evan at msi.umn.edu > boll0107 at umn.edu > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 gaetano.esposito at outlook.com Fri Oct 17 08:38:23 2014 From: gaetano.esposito at outlook.com (Gaetano Esposito) Date: Fri, 17 Oct 2014 12:38:23 +0000 Subject: [ITK] ITK -- Transform an image with a change of coordinates In-Reply-To: References: , Message-ID: Thank you for the pointer. I will update this thread as I go. > Date: Thu, 16 Oct 2014 00:14:17 -0400 > Subject: Re: [ITK] ITK -- Transform an image with a change of coordinates > From: matt.mccormick at kitware.com > To: gaetano.esposito at outlook.com > CC: community at itk.org > > Hi Gaetano, > > Yes, using a Transform is one way to go. See this Insight Journal > article [1] and this class [2]. > > Hope this helps, > Matt > > [1] http://insight-journal.org/browse/publication/722 > > [2] http://www.itk.org/Doxygen/html/classitk_1_1AzimuthElevationToCartesianTransform.html > > On Tue, Oct 14, 2014 at 6:23 PM, Gaetano Esposito > wrote: > > Hello, > > > > I apologize in advance for using a vague language, but I just started to > > play with image processing and segmentation. > > > > Given an image, I would like to define an arbitrary origin, get the > > coordinates of every pixel from Cartesian (x,y) to polar(rho, theta), and > > then create a new image whose x axis is "rho" and whose y axis is "theta". > > In other words, I would like to map a circular image in Cartesian > > Coordinates to a periodic line in polar coordinates. > > > > I am a little confused about how I would achieve this in ITK. > > I believe that I can take advantage of a couple of Transform based > > Polar-Cartesian algorithms out there, some of them published on the Insight > > Journal. The transform typically seems to act on a single point. > > > > Is using a transform the right approach? If yes, once I have the correct > > transform from Cartesian to Polar, how do I create the "polar" image that I > > am seeking? > > > > Thanks for your feedback, > > > > Gaetano > > > > _______________________________________________ > > Community mailing list > > Community at itk.org > > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joel.schaerer at laposte.net Fri Oct 17 12:03:49 2014 From: joel.schaerer at laposte.net (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=) Date: Fri, 17 Oct 2014 18:03:49 +0200 Subject: [ITK] [ITK-users] Possible missing method in itkImageSource Message-ID: <54413DE5.1050108@laposte.net> Hi all, I've run into a problem with named outputs, which I believe could be a bug in ITK. When using named outputs, one is supposed to create the output data objects in the constructor using the MakeOutput method (see http://www.itk.org/Wiki/ITK/Examples/Developer/ImageFilterMultipleOutputs for an example). The MakeOutput method exists for both indexed and named outputs. . These methods are declared and defined first in itkProcessObject: .h: * ... * ProcessObject::MakeOutput. Note that MakeOutput always returns a * itkSmartPointer to a DataObject. ImageSource and MeshSource override * this method to create the correct type of image and mesh respectively. * If a filter has multiple outputs of different types, then that * filter must provide an implementation of MakeOutput(). */ virtual DataObjectPointer MakeOutput( const DataObjectIdentifierType & ); virtual DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx); .cxx DataObject::Pointer ProcessObject ::MakeOutput( const DataObjectIdentifierType & name ) { itkDebugMacro("MakeOutput(" << name << ")"); if( this->IsIndexedOutputName(name) ) { return this->MakeOutput( this->MakeIndexFromOutputName(name) ); } return static_cast(DataObject::New().GetPointer()); } DataObject::Pointer ProcessObject ::MakeOutput(DataObjectPointerArraySizeType) { return static_cast(DataObject::New().GetPointer()); } For indexed outputs, it is redefined in ImageSource in order to create an image object of the correct type. template< typename TOutputImage > ProcessObject::DataObjectPointer ImageSource< TOutputImage > ::MakeOutput(ProcessObject::DataObjectPointerArraySizeType) { return TOutputImage::New().GetPointer(); } So far, so good. However, the named output version of MakeOutput is not redefined in ImageSource, contrary to what the comment in itkProcessObject.h says. And so if someone tries to use it in an ImageToImageFilter, it will crash. Any reason for this behavior? Is this an oversight? Thanks, Jo?l _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From millerjv at gmail.com Fri Oct 17 17:01:57 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 17 Oct 2014 17:01:57 -0400 Subject: [ITK] [ITK-users] Possible missing method in itkImageSource In-Reply-To: <54413DE5.1050108@laposte.net> References: <54413DE5.1050108@laposte.net> Message-ID: <3271CF4A-5DCC-47A5-8456-05BB9325FC4C@gmail.com> At first glance it looks like an oversight. I would expect, however, that we should be seeing warnings about the named version of MakeOutput in ProcessObject being hidden. Jim > On Oct 17, 2014, at 12:03 PM, Jo?l Schaerer wrote: > > Hi all, > > I've run into a problem with named outputs, which I believe could be a bug in ITK. > > When using named outputs, one is supposed to create the output data objects in the constructor using the MakeOutput method (see http://www.itk.org/Wiki/ITK/Examples/Developer/ImageFilterMultipleOutputs for an example). The MakeOutput method exists for both indexed and named outputs. > . > These methods are declared and defined first in itkProcessObject: > > .h: > * ... > * ProcessObject::MakeOutput. Note that MakeOutput always returns a > * itkSmartPointer to a DataObject. ImageSource and MeshSource override > * this method to create the correct type of image and mesh respectively. > * If a filter has multiple outputs of different types, then that > * filter must provide an implementation of MakeOutput(). */ > virtual DataObjectPointer MakeOutput( const DataObjectIdentifierType & ); > virtual DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx); > > .cxx > DataObject::Pointer > ProcessObject > ::MakeOutput( const DataObjectIdentifierType & name ) > { > itkDebugMacro("MakeOutput(" << name << ")"); > if( this->IsIndexedOutputName(name) ) > { > return this->MakeOutput( this->MakeIndexFromOutputName(name) ); > } > return static_cast(DataObject::New().GetPointer()); > } > > DataObject::Pointer > ProcessObject > ::MakeOutput(DataObjectPointerArraySizeType) > { > return static_cast(DataObject::New().GetPointer()); > } > > > For indexed outputs, it is redefined in ImageSource in order to create an image object of the correct type. > > template< typename TOutputImage > > ProcessObject::DataObjectPointer > ImageSource< TOutputImage > > ::MakeOutput(ProcessObject::DataObjectPointerArraySizeType) > { > return TOutputImage::New().GetPointer(); > } > > So far, so good. However, the named output version of MakeOutput is not redefined in ImageSource, contrary to what the comment in itkProcessObject.h says. And so if someone tries to use it in an ImageToImageFilter, it will crash. > > Any reason for this behavior? Is this an oversight? > > Thanks, > > Jo?l > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 gralewskik at email.chop.edu Sun Oct 19 20:13:09 2014 From: gralewskik at email.chop.edu (Kevin) Date: Sun, 19 Oct 2014 17:13:09 -0700 (MST) Subject: [ITK] [ITK-users] Error running Exmaple code -- ICP2.cxx Message-ID: <1413763989914-34707.post@n7.nabble.com> Hello, Just started working with ITK and could use help from this nice community getting up to speed. As the subject reads, I'm currently trying to run iterativeclosestpoint2.cxx from the example source code to register 2 volume meshes. Below is the copied error message I keep getting (ClosestPoint3D is the executable name, obviously): /ClosestPoint3D(15746,0x7fff79138310) malloc: *** error for object 0x7f818d00e328: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Abort trap: 6/ I haven't coded in about 10 years and was never great at debugging so I'm at a bit of a loss. I'm running the official release 4.6.1 on OS X 10.9.5 with clang, Apple LLVM 6.0 (based on 3.5). Here are a few more details/curious notes: when I would pass it the mesh files in either .STL or .vtk format the code would get stuck in the indexing function (I just dropped and returned an counter in the while loop). It never kicked out even after running for iterations orders of magnitude more than the points (and edges for that matter). I then passed it a point cloud file as both a .txt and .xyz (a 3D point plot from MeshLab 1.3.3). This is when I get the checksum error. The code indexed and returned the points tally fine, and initiated a matrix transform, but would the abort. Even more oddly, when I run the executable again (with the same files) to make sure I got the error message right it returned a solution with the .txt, along with the checksum error, but not the .xyz point cloud. Lastly, I lowered the convergence criterion, epsilon, to .001 thinking maybe it wasn't converging before the number of iterations was hit, but that didn't alleviate the issue. In fact, it wouldn't return the initial identity matrix. -- View this message in context: http://itk-users.7.n7.nabble.com/Error-running-Exmaple-code-ICP2-cxx-tp34707.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 matt.mccormick at kitware.com Sun Oct 19 23:47:47 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 19 Oct 2014 23:47:47 -0400 Subject: [ITK] [ITK-users] Error running Exmaple code -- ICP2.cxx In-Reply-To: <1413763989914-34707.post@n7.nabble.com> References: <1413763989914-34707.post@n7.nabble.com> Message-ID: Hi Kevin, Welcome to ITK! Please send your CMakeLists.txt, code, data, and the command that you run so that others may understand the problem. Thanks, Matt On Sun, Oct 19, 2014 at 8:13 PM, Kevin wrote: > Hello, > > Just started working with ITK and could use help from this nice community > getting up to speed. > > As the subject reads, I'm currently trying to run iterativeclosestpoint2.cxx > from the example source code to register 2 volume meshes. Below is the > copied error message I keep getting (ClosestPoint3D is the executable name, > obviously): > > /ClosestPoint3D(15746,0x7fff79138310) malloc: *** error for object > 0x7f818d00e328: incorrect checksum for freed object - object was probably > modified after being freed. > *** set a breakpoint in malloc_error_break to debug > Abort trap: 6/ > > I haven't coded in about 10 years and was never great at debugging so I'm > at a bit of a loss. I'm running the official release 4.6.1 on OS X 10.9.5 > with clang, Apple LLVM 6.0 (based on 3.5). > > Here are a few more details/curious notes: when I would pass it the mesh > files in either .STL or .vtk format the code would get stuck in the indexing > function (I just dropped and returned an counter in the while loop). It > never kicked out even after running for iterations orders of magnitude more > than the points (and edges for that matter). > > I then passed it a point cloud file as both a .txt and .xyz (a 3D point plot > from MeshLab 1.3.3). This is when I get the checksum error. The code indexed > and returned the points tally fine, and initiated a matrix transform, but > would the abort. Even more oddly, when I run the executable again (with the > same files) to make sure I got the error message right it returned a > solution with the .txt, along with the checksum error, but not the .xyz > point cloud. > > Lastly, I lowered the convergence criterion, epsilon, to .001 thinking maybe > it wasn't converging before the number of iterations was hit, but that > didn't alleviate the issue. In fact, it wouldn't return the initial identity > matrix. > > > > > -- > View this message in context: http://itk-users.7.n7.nabble.com/Error-running-Exmaple-code-ICP2-cxx-tp34707.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 gralewskik at email.chop.edu Mon Oct 20 21:43:38 2014 From: gralewskik at email.chop.edu (Kevin) Date: Mon, 20 Oct 2014 18:43:38 -0700 (MST) Subject: [ITK] [ITK-users] Error running Exmaple code -- ICP2.cxx In-Reply-To: References: <1413763989914-34707.post@n7.nabble.com> Message-ID: <1413855818662-34709.post@n7.nabble.com> Thanks, Matt. And thanks for the quick reply. Attached are the requested files: CMakeLists.txt IterativeClosestPoint2.cxx (directly from source package) Data_1.txt Data_2.txt Again, I'm running OS x and follow the method outlined in the manual to configure, compile and run. The line commands are: ccmake ../(directory containing CMakelists.txt and code) make ./(executable name) (file 1) (file 2) -- View this message in context: http://itk-users.7.n7.nabble.com/Error-running-Exmaple-code-ICP2-cxx-tp34707p34709.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 lefebvre at imnc.in2p3.fr Tue Oct 21 12:18:02 2014 From: lefebvre at imnc.in2p3.fr (=?ISO-8859-1?Q?Fran=E7oise_Lefebvre?=) Date: Tue, 21 Oct 2014 18:18:02 +0200 Subject: [ITK] [ITK-users] Error compiling msvc2010 + ITK4.6 + Qt Message-ID: <5446873A.7070500@imnc.in2p3.fr> Hi, ITK 4.6 was succesfully build using cmake2.8.10.2, the default parameters and the Module_ITKReview on. I am now trying to compile a program developed in C++ using Qt5.1.1 and Microsoft Visual C++ express 2010 on Windows 7. I get the following link error : 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: static class itksys::Encoding::CommandLineArguments __cdecl itksys::Encoding::CommandLineArguments::Main(int,char const * const *)" (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) I didn't get this error when compiling with itk4.3 . Any hint ? Thank you for your help, F. Lefebvre _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 Oct 21 13:18:05 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 21 Oct 2014 13:18:05 -0400 Subject: [ITK] [ITK-users] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: <5446873A.7070500@imnc.in2p3.fr> References: <5446873A.7070500@imnc.in2p3.fr> Message-ID: <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> Did you try the latest 4.6.1 release? Brad On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre wrote: > > Hi, > > ITK 4.6 was succesfully build using cmake2.8.10.2, the default parameters and the Module_ITKReview on. > > I am now trying to compile a program developed in C++ using Qt5.1.1 and Microsoft Visual C++ express 2010 on Windows 7. > > I get the following link error : > > 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: static class itksys::Encoding::CommandLineArguments __cdecl itksys::Encoding::CommandLineArguments::Main(int,char const * const *)" (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) > > I didn't get this error when compiling with itk4.3 . > > Any hint ? > > Thank you for your help, > > F. Lefebvre > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 marina.bendersky at gmail.com Tue Oct 21 18:05:00 2014 From: marina.bendersky at gmail.com (Marina Bendersky) Date: Tue, 21 Oct 2014 15:05:00 -0700 Subject: [ITK] [ITK-users] Find corresponding slices in two different volumes Message-ID: Hi all, I need to find corresponding slices in 2 different volumes. I used the ImageRegistration20.cxx example to register "volumeSource" and "volumeTarget". My question is, then, to which slice in "volumeTarget" does ?slice 10? in "volumeSource" correspond? Is there an ITK example/hints that could guide me in the right direction? I?ve just started using ITK and would be grateful for any help. Thank you very much! Marina -------------- 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 rsvpitt at gmail.com Tue Oct 21 18:06:54 2014 From: rsvpitt at gmail.com (Vikas) Date: Tue, 21 Oct 2014 18:06:54 -0400 Subject: [ITK] [ITK-users] Problem applying landmarks in FEM registration Message-ID: Hi, I am having issues applying landmarks to FEM registration and would appreciate any help to resolve it. I am following the example in RegistrationITKv4/DeformableRegistration11 with the following modification: //Add landmartks RegistrationType::PointType SourceLandmark; RegistrationType::PointType TargetLandmark; SourceLandmark[0] = 23;SourceLandmark[1] = 12;SourceLandmark[2] = 41; TargetLandmark[0] = 26;TargetLandmark[1] = 16;TargetLandmark[2] = 45; registrationFilter->AddLandmark(SourceLandmark,TargetLandmark); registrationFilter->SetUseLandmarks(true); I get a run time error: "Vector subscript out of range". The call stack is as follows: > msvcp90d.dll!std::_Debug_message(const wchar_t * message=0x000000013fa48fc8, const wchar_t * file=0x000000013fa49010, unsigned int line=779) Line 24 C++ HybridRegistration.exe!std::vector >::operator[](unsigned __int64 _Pos=0) Line 780 C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::ApplyLoads(itk::Size<3> ImgSz={...}, double * scaling=0x0000000000000000) Line 410 + 0x35 bytes C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::MultiResSolve() Line 1173 C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::RunRegistration() Line 169 C++ HybridRegistration.exe!main(int argc=1, char * * argv=0x0000000002546b40) Line 225 C++ HybridRegistration.exe!__tmainCRTStartup() Line 586 + 0x19 bytes C HybridRegistration.exe!mainCRTStartup() Line 403 C Thanks Vikas -------------- 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 lefebvre at imnc.in2p3.fr Wed Oct 22 03:23:48 2014 From: lefebvre at imnc.in2p3.fr (=?ISO-8859-1?Q?Fran=E7oise_Lefebvre?=) Date: Wed, 22 Oct 2014 09:23:48 +0200 Subject: [ITK] [ITK-users] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> Message-ID: <54475B84.5020906@imnc.in2p3.fr> Yes I did. Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : > Did you try the latest 4.6.1 release? > > Brad > > On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre wrote: > >> Hi, >> >> ITK 4.6 was succesfully build using cmake2.8.10.2, the default parameters and the Module_ITKReview on. >> >> I am now trying to compile a program developed in C++ using Qt5.1.1 and Microsoft Visual C++ express 2010 on Windows 7. >> >> I get the following link error : >> >> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: static class itksys::Encoding::CommandLineArguments __cdecl itksys::Encoding::CommandLineArguments::Main(int,char const * const *)" (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) >> >> I didn't get this error when compiling with itk4.3 . >> >> Any hint ? >> >> Thank you for your help, >> >> F. Lefebvre >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 -- Fran?oise LEFEBVRE IMNC (Imagerie et Mod?lisation en Neurobiologie et Canc?rologie) Campus d'Orsay - B?t 440 91405 ORSAY Cedex 01 69 15 51 87 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 Wed Oct 22 09:44:15 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 22 Oct 2014 09:44:15 -0400 Subject: [ITK] [ITK-users] Possible missing method in itkImageSource In-Reply-To: <3271CF4A-5DCC-47A5-8456-05BB9325FC4C@gmail.com> References: <54413DE5.1050108@laposte.net> <3271CF4A-5DCC-47A5-8456-05BB9325FC4C@gmail.com> Message-ID: <0023FC88-13F9-4ED2-9767-FB324A2EE0CB@mail.nih.gov> Hello, I'm going to take a look at this issue. Brad On Oct 17, 2014, at 5:01 PM, Jim Miller wrote: > At first glance it looks like an oversight. I would expect, however, that we should be seeing warnings about the named version of MakeOutput in ProcessObject being hidden. > > Jim > >> On Oct 17, 2014, at 12:03 PM, Jo?l Schaerer wrote: >> >> Hi all, >> >> I've run into a problem with named outputs, which I believe could be a bug in ITK. >> >> When using named outputs, one is supposed to create the output data objects in the constructor using the MakeOutput method (see http://www.itk.org/Wiki/ITK/Examples/Developer/ImageFilterMultipleOutputs for an example). The MakeOutput method exists for both indexed and named outputs. >> . >> These methods are declared and defined first in itkProcessObject: >> >> .h: >> * ... >> * ProcessObject::MakeOutput. Note that MakeOutput always returns a >> * itkSmartPointer to a DataObject. ImageSource and MeshSource override >> * this method to create the correct type of image and mesh respectively. >> * If a filter has multiple outputs of different types, then that >> * filter must provide an implementation of MakeOutput(). */ >> virtual DataObjectPointer MakeOutput( const DataObjectIdentifierType & ); >> virtual DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx); >> >> .cxx >> DataObject::Pointer >> ProcessObject >> ::MakeOutput( const DataObjectIdentifierType & name ) >> { >> itkDebugMacro("MakeOutput(" << name << ")"); >> if( this->IsIndexedOutputName(name) ) >> { >> return this->MakeOutput( this->MakeIndexFromOutputName(name) ); >> } >> return static_cast(DataObject::New().GetPointer()); >> } >> >> DataObject::Pointer >> ProcessObject >> ::MakeOutput(DataObjectPointerArraySizeType) >> { >> return static_cast(DataObject::New().GetPointer()); >> } >> >> >> For indexed outputs, it is redefined in ImageSource in order to create an image object of the correct type. >> >> template< typename TOutputImage > >> ProcessObject::DataObjectPointer >> ImageSource< TOutputImage > >> ::MakeOutput(ProcessObject::DataObjectPointerArraySizeType) >> { >> return TOutputImage::New().GetPointer(); >> } >> >> So far, so good. However, the named output version of MakeOutput is not redefined in ImageSource, contrary to what the comment in itkProcessObject.h says. And so if someone tries to use it in an ImageToImageFilter, it will crash. >> >> Any reason for this behavior? Is this an oversight? >> >> Thanks, >> >> Jo?l >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 norman-k-williams at uiowa.edu Wed Oct 22 14:35:12 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Wed, 22 Oct 2014 18:35:12 +0000 Subject: [ITK] [ITK-dev] Can I get permission to upload a file to http://midas3.kitware.com? Message-ID: I have an account, I can upload my own public & private files, but I don?t have permission to add new test Data. Can I be added to the permitted uploaders? Thanks! ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Wed Oct 22 14:41:19 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 22 Oct 2014 14:41:19 -0400 Subject: [ITK] [ITK-dev] Can I get permission to upload a file to http://midas3.kitware.com? In-Reply-To: References: Message-ID: Hi Kent, You have been added to the Community Moderator group. Please try to upload again and let use know if you have any difficulties. Thanks, Matt On Wed, Oct 22, 2014 at 2:35 PM, Williams, Norman K wrote: > I have an account, I can upload my own public & private files, but I don?t > have permission to add new test Data. Can I be added to the permitted > uploaders? > > Thanks! > > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the > Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential > and may be legally privileged. If you are not the intended recipient, you > are hereby notified that any retention, dissemination, distribution, or > copying of this communication is strictly prohibited. Please reply to the > sender that you have received the message in error, then delete it. Thank > you. > ________________________________ > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From nikita at iitj.ac.in Wed Oct 22 18:33:23 2014 From: nikita at iitj.ac.in (Nikita Chopra) Date: Wed, 22 Oct 2014 18:33:23 -0400 Subject: [ITK] [ITK-users] Data Structure to save Vectors obtained from Demons Registration. Message-ID: Hello All I'm using itk:DemonsRegistrationFilter to apply registration on each successive frame that I obtain from Video .Please tell me how can I save the vector obtained from registration, what is the data structure I should use for saving the vector field. If it is saved automatically let me know how can I retrieve it . Also ,Please suggest me how to visualize these vectors as well. Thanks for the help in advance. Regards Nikita -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From lasso at queensu.ca Wed Oct 22 18:56:44 2014 From: lasso at queensu.ca (Andras Lasso) Date: Wed, 22 Oct 2014 22:56:44 +0000 Subject: [ITK] [ITK-users] Data Structure to save Vectors obtained from Demons Registration. In-Reply-To: References: Message-ID: If you save the transform as a displacement field (in a nrrd or mha file) then you can load it into 3D Slicer as a transform and visualize it in 2D and 3D (as glyphs, deformed grid, or contour lines) overlaid with your images, segmentation results, landmarks, etc. See more info and some examples here: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms Andras ________________________________ From: Nikita Chopra Sent: ?2014-?10-?22 18:33 To: insight-users at itk.org Subject: [ITK] [ITK-users] Data Structure to save Vectors obtained from Demons Registration. Hello All I'm using itk:DemonsRegistrationFilter to apply registration on each successive frame that I obtain from Video .Please tell me how can I save the vector obtained from registration, what is the data structure I should use for saving the vector field. If it is saved automatically let me know how can I retrieve it . Also ,Please suggest me how to visualize these vectors as well. Thanks for the help in advance. Regards Nikita -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Oct 23 00:54:06 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 23 Oct 2014 00:54:06 -0400 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: There are a couple of upcoming opportunities to share, discuss, design, and learn with your fellow ITK community members. On Thursday (tomorrow), 1:00 PM Eastern USA time, there will be a Google+ Hangout where we will be doing code reviews: https://plus.google.com/events/cn4gsqfr90k9ssa0jogal8vobco On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/events/c2qo0onsh06h3adslvkcj66nr7k? For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 To get regular invites to these events, join the ITK Bar Camp G+ Community: https://plus.google.com/u/0/communities/111375098792764998322 All are welcome. Hope to talk to you then! From g.lemaitre58 at gmail.com Thu Oct 23 04:43:23 2014 From: g.lemaitre58 at gmail.com (=?UTF-8?Q?Guillaume_Lema=C3=AEtre?=) Date: Thu, 23 Oct 2014 10:43:23 +0200 Subject: [ITK] [ITK-users] Issue installing SimpleITK via conda-recipe Message-ID: Hi all, First, I am a newbie in Python and anaconda and sorry in advance if things seems trivial I tried to install SimpleITK through conda-recipe. The installation by itself seems to be fined but the test is failling: ==== testing package: simpleitk-0.8.0.post29-py27_0 ===== import: u'SimpleITK' Traceback (most recent call last): File "/home/lemaitre/anaconda/conda-bld/test-tmp_dir/run_test.py", line 25, in import SimpleITK File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/__init__.py", line 1, in from .SimpleITK import * File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 28, in _SimpleITK = swig_import_helper() File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 24, in swig_import_helper _mod = imp.load_module('_SimpleITK', fp, pathname, description) ImportError: /home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: symbol TIFFFieldDataType, version LIBTIFF_4.0 not defined in file libtiff.so.5 with link time reference TESTS FAILED: simpleitk-0.8.0.post29-py27_0 I got that the issue is linked with the libtiff but I believed that anaconda would manage the installation of the dependencies needed. My system is: Ubuntu 14.04 Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 Cheers, -- *LEMA?TRE GuillaumePhD CandiateMSc Erasmus Mundus ViBOT (Vision-roBOTic)MSc Business Innovation and Technology Management* g.lemaitre58 at gmail.com *ViCOROB - Computer Vision and Robotic Team* Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 http://vicorob.udg.es/ *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 http://le2i.cnrs.fr https://sites.google.com/site/glemaitre58/ Vice - Chairman of A.S.C. Fours UFOLEP Chairman of A.S.C. Fours FFC Webmaster of http://ascfours.free.fr -------------- 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 rsvpitt at gmail.com Thu Oct 23 07:04:10 2014 From: rsvpitt at gmail.com (Vikas) Date: Thu, 23 Oct 2014 07:04:10 -0400 Subject: [ITK] [ITK-users] Problem applying landmarks in FEM registration Message-ID: Hi, I am having issues applying landmarks to FEM registration and would appreciate any help to resolve it. I am following the example in RegistrationITKv4/DeformableRegistration11 with the following modification: //Add landmartks RegistrationType::PointType SourceLandmark; RegistrationType::PointType TargetLandmark; SourceLandmark[0] = 23;SourceLandmark[1] = 12;SourceLandmark[2] = 41; TargetLandmark[0] = 26;TargetLandmark[1] = 16;TargetLandmark[2] = 45; registrationFilter->AddLandmark(SourceLandmark,TargetLandmark); registrationFilter->SetUseLandmarks(true); I get a run time error: "Vector subscript out of range". The call stack is as follows: > msvcp90d.dll!std::_Debug_message(const wchar_t * message=0x000000013fa48fc8, const wchar_t * file=0x000000013fa49010, unsigned int line=779) Line 24 C++ HybridRegistration.exe!std::vector >::operator[](unsigned __int64 _Pos=0) Line 780 C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::ApplyLoads(itk::Size<3> ImgSz={...}, double * scaling=0x0000000000000000) Line 410 + 0x35 bytes C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::MultiResSolve() Line 1173 C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::RunRegistration() Line 169 C++ HybridRegistration.exe!main(int argc=1, char * * argv=0x0000000002546b40) Line 225 C++ HybridRegistration.exe!__tmainCRTStartup() Line 586 + 0x19 bytes C HybridRegistration.exe!mainCRTStartup() Line 403 C Thanks Vikas -------------- 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 Oct 23 08:52:07 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 23 Oct 2014 08:52:07 -0400 Subject: [ITK] [ITK-users] Issue installing SimpleITK via conda-recipe In-Reply-To: References: Message-ID: <4129C8F3-7952-4104-94E4-A4407A40D41C@mail.nih.gov> Hello, Can you please send me you CMakeCache.txt file from the build directory. The simplest thing to do may be to remote using the anaconda "system" tiff library and just use the one ITK has. This can be done by modifying the conda recipe build script here [1]. Most likely there is some confusion which occurs during the CMake configuration about which tiff library to use. Brad [1] https://github.com/conda/conda-recipes/blob/master/simpleitk/build.sh#L35 On Oct 23, 2014, at 4:43 AM, Guillaume Lema?tre wrote: > Hi all, > > First, I am a newbie in Python and anaconda and sorry in advance if things seems trivial > I tried to install SimpleITK through conda-recipe. The installation by itself seems to be fined but the test is failling: > > ==== testing package: simpleitk-0.8.0.post29-py27_0 ===== > import: u'SimpleITK' > Traceback (most recent call last): > File "/home/lemaitre/anaconda/conda-bld/test-tmp_dir/run_test.py", line 25, in > import SimpleITK > File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/__init__.py", line 1, in > from .SimpleITK import * > File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 28, in > _SimpleITK = swig_import_helper() > File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 24, in swig_import_helper > _mod = imp.load_module('_SimpleITK', fp, pathname, description) > ImportError: /home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: symbol TIFFFieldDataType, version LIBTIFF_4.0 not defined in file libtiff.so.5 with link time reference > TESTS FAILED: simpleitk-0.8.0.post29-py27_0 > > I got that the issue is linked with the libtiff but I believed that anaconda would manage the installation of the dependencies needed. > > My system is: > Ubuntu 14.04 > Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21) > [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 > > Cheers, > > -- > LEMA?TRE Guillaume > PhD Candiate > MSc Erasmus Mundus ViBOT (Vision-roBOTic) > MSc Business Innovation and Technology Management > > g.lemaitre58 at gmail.com > > > ViCOROB - Computer Vision and Robotic Team > Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona > Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 > http://vicorob.udg.es/ > LE2I - Le Creusot > IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot > Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 > http://le2i.cnrs.fr > > https://sites.google.com/site/glemaitre58/ > Vice - Chairman of A.S.C. Fours UFOLEP > Chairman of A.S.C. Fours FFC > Webmaster of http://ascfours.free.fr > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.lemaitre58 at gmail.com Thu Oct 23 09:00:13 2014 From: g.lemaitre58 at gmail.com (=?UTF-8?Q?Guillaume_Lema=C3=AEtre?=) Date: Thu, 23 Oct 2014 15:00:13 +0200 Subject: [ITK] [ITK-users] Issue installing SimpleITK via conda-recipe In-Reply-To: <4129C8F3-7952-4104-94E4-A4407A40D41C@mail.nih.gov> References: <4129C8F3-7952-4104-94E4-A4407A40D41C@mail.nih.gov> Message-ID: Hi Brad, Find attached the CMakeCache.txt from ./anaconda/conda-bld/work/build In this file it seems that, ITK_USE_SYSTEM_TIFF:BOOL=ON Does it mean that the TIFF used is from the anaconda "system"? I assume that I have to try to put the boolean to OFF to use the one of ITK. Thanks, On 23 October 2014 14:52, Bradley Lowekamp wrote: > Hello, > > Can you please send me you CMakeCache.txt file from the build directory. > > The simplest thing to do may be to remote using the anaconda "system" tiff > library and just use the one ITK has. This can be done by modifying the > conda recipe build script here [1]. > > Most likely there is some confusion which occurs during the CMake > configuration about which tiff library to use. > > Brad > > [1] > https://github.com/conda/conda-recipes/blob/master/simpleitk/build.sh#L35 > > On Oct 23, 2014, at 4:43 AM, Guillaume Lema?tre > wrote: > > Hi all, > > First, I am a newbie in Python and anaconda and sorry in advance if things > seems trivial > I tried to install SimpleITK through conda-recipe. The installation by > itself seems to be fined but the test is failling: > > ==== testing package: simpleitk-0.8.0.post29-py27_0 ===== > import: u'SimpleITK' > Traceback (most recent call last): > File "/home/lemaitre/anaconda/conda-bld/test-tmp_dir/run_test.py", line > 25, in > import SimpleITK > File > "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/__init__.py", > line 1, in > from .SimpleITK import * > File > "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", > line 28, in > _SimpleITK = swig_import_helper() > File > "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", > line 24, in swig_import_helper > _mod = imp.load_module('_SimpleITK', fp, pathname, description) > ImportError: > /home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: > symbol TIFFFieldDataType, version LIBTIFF_4.0 not defined in file > libtiff.so.5 with link time reference > TESTS FAILED: simpleitk-0.8.0.post29-py27_0 > > I got that the issue is linked with the libtiff but I believed that > anaconda would manage the installation of the dependencies needed. > > My system is: > Ubuntu 14.04 > Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21) > [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 > > Cheers, > > -- > > > > > *LEMA?TRE GuillaumePhD CandiateMSc Erasmus Mundus ViBOT > (Vision-roBOTic)MSc Business Innovation and Technology Management* > g.lemaitre58 at gmail.com > > > *ViCOROB - Computer Vision and Robotic Team* > Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona > Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 > http://vicorob.udg.es/ > > *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la > Fonderie, 71200 Le Creusot > Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 > http://le2i.cnrs.fr > > https://sites.google.com/site/glemaitre58/ > Vice - Chairman of A.S.C. Fours UFOLEP > Chairman of A.S.C. Fours FFC > Webmaster of http://ascfours.free.fr > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > -- *LEMA?TRE GuillaumePhD CandiateMSc Erasmus Mundus ViBOT (Vision-roBOTic)MSc Business Innovation and Technology Management* g.lemaitre58 at gmail.com *ViCOROB - Computer Vision and Robotic Team* Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 http://vicorob.udg.es/ *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 http://le2i.cnrs.fr https://sites.google.com/site/glemaitre58/ Vice - Chairman of A.S.C. Fours UFOLEP Chairman of A.S.C. Fours FFC Webmaster of http://ascfours.free.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- # This is the CMakeCache file. # For build in directory: /home/lemaitre/anaconda/conda-bld/work/build # It was generated by CMake: /home/lemaitre/anaconda/envs/_build/bin/cmake # You can edit this file to change values found and used by cmake. # If you do not want to change any of the values, simply exit the editor. # If you do want to change a value, simply edit, save, and exit the editor. # The syntax for the file is as follows: # KEY:TYPE=VALUE # KEY is the name of a variable in the cache. # TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!. # VALUE is the current value for the KEY. ######################## # EXTERNAL cache entries ######################## //path to the bison executable BISON_EXECUTABLE:FILEPATH=/usr/bin/bison //Flags used by bison BISON_FLAGS:STRING= //Enable Building of the SimpleITK Examples as a separate project. BUILD_EXAMPLES:BOOL=ON //Build SimpleITK ITK with shared libraries. This does not effect // wrapped languages. BUILD_SHARED_LIBS:BOOL=OFF //Turn on Testing for SimpleITK BUILD_TESTING:BOOL=OFF //Path to a program. CMAKE_AR:FILEPATH=/usr/bin/ar //No help, variable specified on the command line. CMAKE_BUILD_TYPE:STRING=RELEASE //Enable/Disable color output during build. CMAKE_COLOR_MAKEFILE:BOOL=ON //CXX compiler. CMAKE_CXX_COMPILER:FILEPATH=/usr/bin/c++ //No help, variable specified on the command line. CMAKE_CXX_FLAGS:STRING=-fvisibility=hidden -fvisibility-inlines-hidden //Flags used by the compiler during debug builds. CMAKE_CXX_FLAGS_DEBUG:STRING=-g //Flags used by the compiler during release builds for minimum // size. CMAKE_CXX_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG //Flags used by the compiler during release builds. CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -DNDEBUG //Flags used by the compiler during release builds with debug info. CMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG //C compiler. CMAKE_C_COMPILER:FILEPATH=/usr/bin/cc //No help, variable specified on the command line. CMAKE_C_FLAGS:STRING=-fvisibility=hidden //Flags used by the compiler during debug builds. CMAKE_C_FLAGS_DEBUG:STRING=-g //Flags used by the compiler during release builds for minimum // size. CMAKE_C_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG //Flags used by the compiler during release builds. CMAKE_C_FLAGS_RELEASE:STRING=-O3 -DNDEBUG //Flags used by the compiler during release builds with debug info. CMAKE_C_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG //Flags used by the linker. CMAKE_EXE_LINKER_FLAGS:STRING=' ' //Flags used by the linker during debug builds. CMAKE_EXE_LINKER_FLAGS_DEBUG:STRING= //Flags used by the linker during release minsize builds. CMAKE_EXE_LINKER_FLAGS_MINSIZEREL:STRING= //Flags used by the linker during release builds. CMAKE_EXE_LINKER_FLAGS_RELEASE:STRING= //Flags used by the linker during Release with Debug Info builds. CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO:STRING= //Enable/Disable output of compile commands during generation. CMAKE_EXPORT_COMPILE_COMMANDS:BOOL=OFF //Where all the prerequisite libraries go CMAKE_INSTALL_PREFIX:PATH=/home/lemaitre/anaconda/conda-bld/work/build //No help, variable specified on the command line. CMAKE_INSTALL_PREFIX=:PATH=/home/lemaitre/anaconda/envs/_build //Path to a program. CMAKE_LINKER:FILEPATH=/usr/bin/ld //Path to a program. CMAKE_MAKE_PROGRAM:FILEPATH=/usr/bin/make //Flags used by the linker during the creation of modules. CMAKE_MODULE_LINKER_FLAGS:STRING=' ' //Flags used by the linker during debug builds. CMAKE_MODULE_LINKER_FLAGS_DEBUG:STRING= //Flags used by the linker during release minsize builds. CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL:STRING= //Flags used by the linker during release builds. CMAKE_MODULE_LINKER_FLAGS_RELEASE:STRING= //Flags used by the linker during Release with Debug Info builds. CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO:STRING= //Path to a program. CMAKE_NM:FILEPATH=/usr/bin/nm //Path to a program. CMAKE_OBJCOPY:FILEPATH=/usr/bin/objcopy //Path to a program. CMAKE_OBJDUMP:FILEPATH=/usr/bin/objdump //No help, variable specified on the command line. CMAKE_OSX_DEPLOYMENT_TARGET:STRING= //Value Computed by CMake CMAKE_PROJECT_NAME:STATIC=SuperBuildSimpleITK //Path to a program. CMAKE_RANLIB:FILEPATH=/usr/bin/ranlib //Flags used by the linker during the creation of dll's. CMAKE_SHARED_LINKER_FLAGS:STRING=' ' //Flags used by the linker during debug builds. CMAKE_SHARED_LINKER_FLAGS_DEBUG:STRING= //Flags used by the linker during release minsize builds. CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL:STRING= //Flags used by the linker during release builds. CMAKE_SHARED_LINKER_FLAGS_RELEASE:STRING= //Flags used by the linker during Release with Debug Info builds. CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO:STRING= //If set, runtime paths are not added when installing shared libraries, // but are added when building. CMAKE_SKIP_INSTALL_RPATH:BOOL=NO //If set, runtime paths are not added when using shared libraries. CMAKE_SKIP_RPATH:BOOL=NO //Flags used by the linker during the creation of static libraries. CMAKE_STATIC_LINKER_FLAGS:STRING= //Flags used by the linker during debug builds. CMAKE_STATIC_LINKER_FLAGS_DEBUG:STRING= //Flags used by the linker during release minsize builds. CMAKE_STATIC_LINKER_FLAGS_MINSIZEREL:STRING= //Flags used by the linker during release builds. CMAKE_STATIC_LINKER_FLAGS_RELEASE:STRING= //Flags used by the linker during Release with Debug Info builds. CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO:STRING= //Path to a program. CMAKE_STRIP:FILEPATH=/usr/bin/strip //If true, cmake will use relative paths in makefiles and projects. CMAKE_USE_RELATIVE_PATHS:BOOL=OFF //If this value is on, makefiles will be generated without the // .SILENT directive, and all commands will be echoed to the console // during the make. This is useful for debugging only. With Visual // Studio IDE projects all commands are done without /nologo. CMAKE_VERBOSE_MAKEFILE:BOOL=FALSE //C# target platform: x86, x64, anycpu, or itanium CSHARP_PLATFORM:STRING=anycpu //git command line client GIT_EXECUTABLE:FILEPATH=/usr/bin/git //No help, variable specified on the command line. ITK_USE_SYSTEM_JPEG:BOOL=ON //No help, variable specified on the command line. ITK_USE_SYSTEM_PNG:BOOL=ON //No help, variable specified on the command line. ITK_USE_SYSTEM_TIFF:BOOL=ON //No help, variable specified on the command line. ITK_USE_SYSTEM_ZLIB:BOOL=ON //Turn OFF wrapping ITK with WrapITK ITK_WRAPPING:BOOL=OFF //Path to a file. JAVA_AWT_INCLUDE_PATH:PATH=/usr/lib/jvm/default-java/include //Path to a library. 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PYTHON_INCLUDE_PATH:PATH=/home/lemaitre/anaconda/envs/_build/include/python2.7 //No help, variable specified on the command line. PYTHON_LIBRARY:FILEPATH=/home/lemaitre/anaconda/envs/_build/lib/libpython2.7.so //Path to a library. PYTHON_LIBRARY_DEBUG:FILEPATH=PYTHON_LIBRARY_DEBUG-NOTFOUND //Rscript executable. RSCRIPT_EXECUTABLE:FILEPATH=RSCRIPT_EXECUTABLE-NOTFOUND //The Ruby arch header dir (2.0+) RUBY_ARCHHDR_DIR:PATH= //The Ruby arch dir RUBY_ARCH_DIR:PATH=/usr/lib/ruby/1.9.1/x86_64-linux //Path to a file. RUBY_CONFIG_INCLUDE_DIR:PATH=RUBY_CONFIG_INCLUDE_DIR-NOTFOUND //Path to a program. RUBY_EXECUTABLE:FILEPATH=/usr/bin/ruby //Vendor Ruby is available RUBY_HAS_VENDOR_RUBY:BOOL= //The Ruby header dir (1.9+) RUBY_HDR_DIR:PATH=/usr/include/ruby-1.9.1 //Path to a file. RUBY_INCLUDE_DIR:PATH=RUBY_INCLUDE_DIR-NOTFOUND //Path to a library. 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TCL_INCLUDE_PATH-ADVANCED:INTERNAL=1 //ADVANCED property for variable: TCL_LIBRARY TCL_LIBRARY-ADVANCED:INTERNAL=1 //ADVANCED property for variable: TCL_TCLSH TCL_TCLSH-ADVANCED:INTERNAL=1 //ADVANCED property for variable: TK_INCLUDE_PATH TK_INCLUDE_PATH-ADVANCED:INTERNAL=1 //ADVANCED property for variable: TK_LIBRARY TK_LIBRARY-ADVANCED:INTERNAL=1 //ADVANCED property for variable: TK_WISH TK_WISH-ADVANCED:INTERNAL=1 //ADVANCED property for variable: USE_SYSTEM_ITK USE_SYSTEM_ITK-ADVANCED:INTERNAL=1 //ADVANCED property for variable: USE_SYSTEM_SWIG USE_SYSTEM_SWIG-ADVANCED:INTERNAL=1 -------------- 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 Oct 23 09:21:31 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 23 Oct 2014 09:21:31 -0400 Subject: [ITK] [ITK-users] Issue installing SimpleITK via conda-recipe In-Reply-To: References: <4129C8F3-7952-4104-94E4-A4407A40D41C@mail.nih.gov> Message-ID: Hello, Yes, Changing the problematic USE_SYSTEM cmake options to OFF should fix this issue. Unfortunately, the variables I was looking for were not in that CMakeCache.txt file. They would be in the CMakeCache.txt file in the ITK-buiild subdirectory. Could you please e-mail that one off list? Thanks, Brad On Oct 23, 2014, at 9:00 AM, Guillaume Lema?tre wrote: > Hi Brad, > > Find attached the CMakeCache.txt from ./anaconda/conda-bld/work/build > In this file it seems that, > ITK_USE_SYSTEM_TIFF:BOOL=ON > > Does it mean that the TIFF used is from the anaconda "system"? I assume that I have to try to put the boolean to OFF to use the one of ITK. > > Thanks, > > On 23 October 2014 14:52, Bradley Lowekamp wrote: > Hello, > > Can you please send me you CMakeCache.txt file from the build directory. > > The simplest thing to do may be to remote using the anaconda "system" tiff library and just use the one ITK has. This can be done by modifying the conda recipe build script here [1]. > > Most likely there is some confusion which occurs during the CMake configuration about which tiff library to use. > > Brad > > [1] https://github.com/conda/conda-recipes/blob/master/simpleitk/build.sh#L35 > > On Oct 23, 2014, at 4:43 AM, Guillaume Lema?tre wrote: > >> Hi all, >> >> First, I am a newbie in Python and anaconda and sorry in advance if things seems trivial >> I tried to install SimpleITK through conda-recipe. The installation by itself seems to be fined but the test is failling: >> >> ==== testing package: simpleitk-0.8.0.post29-py27_0 ===== >> import: u'SimpleITK' >> Traceback (most recent call last): >> File "/home/lemaitre/anaconda/conda-bld/test-tmp_dir/run_test.py", line 25, in >> import SimpleITK >> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/__init__.py", line 1, in >> from .SimpleITK import * >> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 28, in >> _SimpleITK = swig_import_helper() >> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 24, in swig_import_helper >> _mod = imp.load_module('_SimpleITK', fp, pathname, description) >> ImportError: /home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: symbol TIFFFieldDataType, version LIBTIFF_4.0 not defined in file libtiff.so.5 with link time reference >> TESTS FAILED: simpleitk-0.8.0.post29-py27_0 >> >> I got that the issue is linked with the libtiff but I believed that anaconda would manage the installation of the dependencies needed. >> >> My system is: >> Ubuntu 14.04 >> Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21) >> [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 >> >> Cheers, >> >> -- >> LEMA?TRE Guillaume >> PhD Candiate >> MSc Erasmus Mundus ViBOT (Vision-roBOTic) >> MSc Business Innovation and Technology Management >> >> g.lemaitre58 at gmail.com >> >> >> ViCOROB - Computer Vision and Robotic Team >> Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona >> Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 >> http://vicorob.udg.es/ >> LE2I - Le Creusot >> IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot >> Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 >> http://le2i.cnrs.fr >> >> https://sites.google.com/site/glemaitre58/ >> Vice - Chairman of A.S.C. Fours UFOLEP >> Chairman of A.S.C. Fours FFC >> Webmaster of http://ascfours.free.fr >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > > > > > -- > LEMA?TRE Guillaume > PhD Candiate > MSc Erasmus Mundus ViBOT (Vision-roBOTic) > MSc Business Innovation and Technology Management > > g.lemaitre58 at gmail.com > > > ViCOROB - Computer Vision and Robotic Team > Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona > Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 > http://vicorob.udg.es/ > LE2I - Le Creusot > IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot > Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 > http://le2i.cnrs.fr > > https://sites.google.com/site/glemaitre58/ > Vice - Chairman of A.S.C. Fours UFOLEP > Chairman of A.S.C. Fours FFC > Webmaster of http://ascfours.free.fr > -------------- 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 Oct 23 09:57:01 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 23 Oct 2014 09:57:01 -0400 Subject: [ITK] [ITK-users] Issue installing SimpleITK via conda-recipe In-Reply-To: References: <4129C8F3-7952-4104-94E4-A4407A40D41C@mail.nih.gov> Message-ID: <3CA52435-26B7-46DA-B0CD-3ADF369F23F6@mail.nih.gov> Hello, Thank you for sending me the file off list. I asked that just because of the potential size of the file. It's best to keep the conversation on the list so that all can benefit. It does appear that there is a problem with the SimpleITK using system libraries not picking up the anaconda dependencies but instead the system ones. For example here in the ITK CMakeCache.txt file we have: TIFF_INCLUDE_DIR:PATH=/usr/include/x86_64-linux-gnu TIFF_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libtiff.so PNG_PNG_INCLUDE_DIR:PATH=/usr/include and simular things for jpeg and zlib. I'd recommend turning them all off until a better solution is found. I have a pull request for this change here: https://github.com/conda/conda-recipes/pull/201 Thanks, Brad On Oct 23, 2014, at 9:21 AM, Bradley Lowekamp wrote: > Hello, > > Yes, Changing the problematic USE_SYSTEM cmake options to OFF should fix this issue. > > Unfortunately, the variables I was looking for were not in that CMakeCache.txt file. They would be in the CMakeCache.txt file in the ITK-buiild subdirectory. Could you please e-mail that one off list? > > Thanks, > Brad > > On Oct 23, 2014, at 9:00 AM, Guillaume Lema?tre wrote: > >> Hi Brad, >> >> Find attached the CMakeCache.txt from ./anaconda/conda-bld/work/build >> In this file it seems that, >> ITK_USE_SYSTEM_TIFF:BOOL=ON >> >> Does it mean that the TIFF used is from the anaconda "system"? I assume that I have to try to put the boolean to OFF to use the one of ITK. >> >> Thanks, >> >> On 23 October 2014 14:52, Bradley Lowekamp wrote: >> Hello, >> >> Can you please send me you CMakeCache.txt file from the build directory. >> >> The simplest thing to do may be to remote using the anaconda "system" tiff library and just use the one ITK has. This can be done by modifying the conda recipe build script here [1]. >> >> Most likely there is some confusion which occurs during the CMake configuration about which tiff library to use. >> >> Brad >> >> [1] https://github.com/conda/conda-recipes/blob/master/simpleitk/build.sh#L35 >> >> On Oct 23, 2014, at 4:43 AM, Guillaume Lema?tre wrote: >> >>> Hi all, >>> >>> First, I am a newbie in Python and anaconda and sorry in advance if things seems trivial >>> I tried to install SimpleITK through conda-recipe. The installation by itself seems to be fined but the test is failling: >>> >>> ==== testing package: simpleitk-0.8.0.post29-py27_0 ===== >>> import: u'SimpleITK' >>> Traceback (most recent call last): >>> File "/home/lemaitre/anaconda/conda-bld/test-tmp_dir/run_test.py", line 25, in >>> import SimpleITK >>> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/__init__.py", line 1, in >>> from .SimpleITK import * >>> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 28, in >>> _SimpleITK = swig_import_helper() >>> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 24, in swig_import_helper >>> _mod = imp.load_module('_SimpleITK', fp, pathname, description) >>> ImportError: /home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: symbol TIFFFieldDataType, version LIBTIFF_4.0 not defined in file libtiff.so.5 with link time reference >>> TESTS FAILED: simpleitk-0.8.0.post29-py27_0 >>> >>> I got that the issue is linked with the libtiff but I believed that anaconda would manage the installation of the dependencies needed. >>> >>> My system is: >>> Ubuntu 14.04 >>> Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21) >>> [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 >>> >>> Cheers, >>> >>> -- >>> LEMA?TRE Guillaume >>> PhD Candiate >>> MSc Erasmus Mundus ViBOT (Vision-roBOTic) >>> MSc Business Innovation and Technology Management >>> >>> g.lemaitre58 at gmail.com >>> >>> >>> ViCOROB - Computer Vision and Robotic Team >>> Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona >>> Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 >>> http://vicorob.udg.es/ >>> LE2I - Le Creusot >>> IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot >>> Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 >>> http://le2i.cnrs.fr >>> >>> https://sites.google.com/site/glemaitre58/ >>> Vice - Chairman of A.S.C. Fours UFOLEP >>> Chairman of A.S.C. Fours FFC >>> Webmaster of http://ascfours.free.fr >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> >> >> -- >> LEMA?TRE Guillaume >> PhD Candiate >> MSc Erasmus Mundus ViBOT (Vision-roBOTic) >> MSc Business Innovation and Technology Management >> >> g.lemaitre58 at gmail.com >> >> >> ViCOROB - Computer Vision and Robotic Team >> Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona >> Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 >> http://vicorob.udg.es/ >> LE2I - Le Creusot >> IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot >> Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 >> http://le2i.cnrs.fr >> >> https://sites.google.com/site/glemaitre58/ >> Vice - Chairman of A.S.C. Fours UFOLEP >> Chairman of A.S.C. Fours FFC >> Webmaster of http://ascfours.free.fr >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 lefebvre at imnc.in2p3.fr Thu Oct 23 12:20:03 2014 From: lefebvre at imnc.in2p3.fr (=?ISO-8859-1?Q?Fran=E7oise_Lefebvre?=) Date: Thu, 23 Oct 2014 18:20:03 +0200 Subject: [ITK] [ITK-users] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: <54475B84.5020906@imnc.in2p3.fr> References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> <54475B84.5020906@imnc.in2p3.fr> Message-ID: <54492AB3.2030006@imnc.in2p3.fr> Hi, I also tried on Windows 8,msvc2012_opengl and Qt5.3. I get exactly the same link error. FL Le 22/10/2014 09:23, Fran?oise Lefebvre a ?crit : > Yes I did. > > Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : >> Did you try the latest 4.6.1 release? >> >> Brad >> >> On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre >> wrote: >> >>> Hi, >>> >>> ITK 4.6 was succesfully build using cmake2.8.10.2, the default >>> parameters and the Module_ITKReview on. >>> >>> I am now trying to compile a program developed in C++ using Qt5.1.1 >>> and Microsoft Visual C++ express 2010 on Windows 7. >>> >>> I get the following link error : >>> >>> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe >>> non r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction >>> "public: static class itksys::Encoding::CommandLineArguments __cdecl >>> itksys::Encoding::CommandLineArguments::Main(int,char const * const >>> *)" (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) >>> >>> I didn't get this error when compiling with itk4.3 . >>> >>> Any hint ? >>> >>> Thank you for your help, >>> >>> F. Lefebvre >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the 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 norman-k-williams at uiowa.edu Thu Oct 23 13:32:05 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Thu, 23 Oct 2014 17:32:05 +0000 Subject: [ITK] [ITK-dev] Can't build using NINJA with ITKDCMTK/ITKIODCMTK turned on. Message-ID: A couple of years ago, with massive help from Brad King, I managed to get an embedded ExternalProject build of DCMTK embedded into ITK/Modules/ThirdParty. This was workable, because the CMake dependencies were explicitly set up such that the DCMTK libraries depended on the ExternalProject DCMTK target, and the DCMTKImageIO module depended on the libraries. When using the CMake with the Makefile generator, this hangs together, because the sub-make in Modules/IO/DCMTK won?t happen until the ExternalProject build in Modules/ThirdParty/DCMTK is complete. Ninja, on the other hand, makes one flat megamake at the top level of ITK, and if you try and build with Module_ITKDCMTK/Module_ITKIODCMTK/Module_IOTransformDCMTK turned on, it fails immediately because the targets in Modules/IO/DCMTK depend on non-existent DCMTK libraries. It?s a problem if we support all CMake generators except Ninja. I like using Ninja because it shaves several seconds off build times, which is great when you?re in an edit/compile/test workflow. I have no idea how this could be resolved, except to remove the internal DCMTK build and require USE_SYSTEM_DCMTK=ON. Does anyone have a better idea. ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- 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 bill.hoffman at kitware.com Thu Oct 23 13:57:08 2014 From: bill.hoffman at kitware.com (Bill Hoffman) Date: Thu, 23 Oct 2014 13:57:08 -0400 Subject: [ITK] [ITK-dev] Can't build using NINJA with ITKDCMTK/ITKIODCMTK turned on. In-Reply-To: References: Message-ID: <54494174.1080602@kitware.com> On 10/23/2014 1:32 PM, Williams, Norman K wrote: > I have no idea how this could be resolved, except to remove the internal > DCMTK build and require USE_SYSTEM_DCMTK=ON. Does anyone have a better > idea. > The other option is to build this without external project and use add_subdirectory like we do with other 3rd party stuff (png, etc). Using ExternalProject does not work unless you build everything with external project as this case shows. How hard would that be to do? -Bill _______________________________________________ Powered by www.kitware.com 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 Oct 23 14:03:21 2014 From: brad.king at kitware.com (Brad King) Date: Thu, 23 Oct 2014 14:03:21 -0400 Subject: [ITK] [ITK-dev] Can't build using NINJA with ITKDCMTK/ITKIODCMTK turned on. In-Reply-To: References: Message-ID: <544942E9.40805@kitware.com> On 10/23/2014 01:32 PM, Williams, Norman K wrote: > it fails immediately because the targets in Modules/IO/DCMTK depend > on non-existent DCMTK libraries. This cannot be solved cleanly without addressing these issues: https://github.com/martine/ninja/issues/760#issuecomment-46540858 http://www.cmake.org/Bug/view.php?id=14963#c36130 Currently the only way to build an ExternalProject cleanly with Ninja is if the outer project contains nothing except custom commands/targets, i.e. a superbuild that does both DCMTK and ITK as external projects. -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 norman-k-williams at uiowa.edu Thu Oct 23 15:04:14 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Thu, 23 Oct 2014 19:04:14 +0000 Subject: [ITK] [ITK-dev] Can't build using NINJA with ITKDCMTK/ITKIODCMTK turned on. In-Reply-To: <544942E9.40805@kitware.com> References: <544942E9.40805@kitware.com> Message-ID: Yeah that?s the problem right there. I would have no problem with including DCMTK in the distro. On 10/23/14, 1:03 PM, "Brad King" wrote: >On 10/23/2014 01:32 PM, Williams, Norman K wrote: >> it fails immediately because the targets in Modules/IO/DCMTK depend >> on non-existent DCMTK libraries. > >This cannot be solved cleanly without addressing these issues: > > https://github.com/martine/ninja/issues/760#issuecomment-46540858 > http://www.cmake.org/Bug/view.php?id=14963#c36130 > >Currently the only way to build an ExternalProject cleanly >with Ninja is if the outer project contains nothing except >custom commands/targets, i.e. a superbuild that does both >DCMTK and ITK as external projects. > >-Brad > ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Thu Oct 23 17:37:02 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 23 Oct 2014 17:37:02 -0400 Subject: [ITK] [ITK-users] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: <54492AB3.2030006@imnc.in2p3.fr> References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> <54475B84.5020906@imnc.in2p3.fr> <54492AB3.2030006@imnc.in2p3.fr> Message-ID: Hi, Are you using CMake to configure your project? Matt On Thu, Oct 23, 2014 at 12:20 PM, Fran?oise Lefebvre wrote: > Hi, > > I also tried on Windows 8,msvc2012_opengl and Qt5.3. I get exactly the same > link error. > > FL > > > Le 22/10/2014 09:23, Fran?oise Lefebvre a ?crit : > >> Yes I did. >> >> Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : >>> >>> Did you try the latest 4.6.1 release? >>> >>> Brad >>> >>> On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre >>> wrote: >>> >>>> Hi, >>>> >>>> ITK 4.6 was succesfully build using cmake2.8.10.2, the default >>>> parameters and the Module_ITKReview on. >>>> >>>> I am now trying to compile a program developed in C++ using Qt5.1.1 and >>>> Microsoft Visual C++ express 2010 on Windows 7. >>>> >>>> I get the following link error : >>>> >>>> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non >>>> r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: >>>> static class itksys::Encoding::CommandLineArguments __cdecl >>>> itksys::Encoding::CommandLineArguments::Main(int,char const * const *)" >>>> (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) >>>> >>>> I didn't get this error when compiling with itk4.3 . >>>> >>>> Any hint ? >>>> >>>> Thank you for your help, >>>> >>>> F. Lefebvre >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the 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 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 JCerrola at childrensnational.org Thu Oct 23 17:53:24 2014 From: JCerrola at childrensnational.org (Cerrolaza, Juan) Date: Thu, 23 Oct 2014 21:53:24 +0000 Subject: [ITK] Question about the use of LevelSetsv4 Message-ID: <9560AC300206F04C862B7A34B9BC37A902DC69AA@PVTH-EXMBX2.cnmc.org> Dear ITK community, I recently started to use the new framework ITK provides for Level Sets (LevelSetsv4). It seems to be a pretty nice framework and an ideal way to combine different terms from Level Sets theory (advection terms, curvature-based terms, propagation terms, etc). However, I'm still a bit confused about how to use and configure it. I would really appreciate if anyone of you could help me to clarify any of these questions. i) Looking into the description of these terms, for instance the curvature term: 'LevelSetEquationCurvatureTerm' (though this is this is also valid for any other term such as the advection term 'LevelSetEquationAdvectionTerm', or the propagation term 'LevelSetEquationPropagationTerm'), it seems like the user has the option to define a specific curvature image (according to the literature, this terms is typically defined as an the result of using any edge detector to the image we are trying to segment. If no curvature image is set, it casts the input image and uses it in the term contribution calculation. My question is how does ITK calculate this term actually. Does it use any edge detector over the input image (such as 1/(1 + G(I)), where I is the input image, and G(.) is the Gaussian filter)? What happened if both, the input image and the curvature image are defined? Does ITK ignore the first one? ii) The second question is about how to control the propagation direction of the level set. In the example, the level set is initialized as a big square area that contains all the elements to segment. In this scenario, the evolution of the level set should be inward. What if we initialize the level set inside the target structure? In this case the evolution of the level set should be outward. How can we control it? My guess was that the sign of the coefficients that define the weight of each term would control it, but after making different test, I'm not completely sure about it. Thank you very much in advance. Juan Juan J. Cerrolaza PhD Sheikh Zayed Institute for Pediatric Surgical Innovation Children's National Health System 111 Michigan Avenue, NW Washington, DC 20010 E-mail: JCerrola at cnmc.org, jjcerromar at gmail.com Phone: +1 (202) 476-1272 We stand for children. www.ChildrensNational.org ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lefebvre at imnc.in2p3.fr Fri Oct 24 04:00:59 2014 From: lefebvre at imnc.in2p3.fr (=?UTF-8?B?RnJhbsOnb2lzZSBMZWZlYnZyZQ==?=) Date: Fri, 24 Oct 2014 10:00:59 +0200 Subject: [ITK] [ITK-users] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> <54475B84.5020906@imnc.in2p3.fr> <54492AB3.2030006@imnc.in2p3.fr> Message-ID: <544A073B.4080905@imnc.in2p3.fr> No, I'm not. I have always used a .pro file and qmake. Le 23/10/2014 23:37, Matt McCormick a ?crit : > Hi, > > Are you using CMake to configure your project? > > Matt > > On Thu, Oct 23, 2014 at 12:20 PM, Fran?oise Lefebvre > wrote: >> Hi, >> >> I also tried on Windows 8,msvc2012_opengl and Qt5.3. I get exactly the same >> link error. >> >> FL >> >> >> Le 22/10/2014 09:23, Fran?oise Lefebvre a ?crit : >> >>> Yes I did. >>> >>> Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : >>>> Did you try the latest 4.6.1 release? >>>> >>>> Brad >>>> >>>> On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre >>>> wrote: >>>> >>>>> Hi, >>>>> >>>>> ITK 4.6 was succesfully build using cmake2.8.10.2, the default >>>>> parameters and the Module_ITKReview on. >>>>> >>>>> I am now trying to compile a program developed in C++ using Qt5.1.1 and >>>>> Microsoft Visual C++ express 2010 on Windows 7. >>>>> >>>>> I get the following link error : >>>>> >>>>> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non >>>>> r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: >>>>> static class itksys::Encoding::CommandLineArguments __cdecl >>>>> itksys::Encoding::CommandLineArguments::Main(int,char const * const *)" >>>>> (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) >>>>> >>>>> I didn't get this error when compiling with itk4.3 . >>>>> >>>>> Any hint ? >>>>> >>>>> Thank you for your help, >>>>> >>>>> F. Lefebvre >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the 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 -- Fran?oise LEFEBVRE IMNC (Imagerie et Mod?lisation en Neurobiologie et Canc?rologie) Campus d'Orsay - B?t 440 91405 ORSAY Cedex 01 69 15 51 87 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 abdul.sw84 at gmail.com Fri Oct 24 04:30:29 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 10:30:29 +0200 Subject: [ITK] [ITK-users] ImageFileReader Update() Message-ID: Hello, I'm new to ITK, and just want to ask about what "Update()" means when used with ImageFileReader. For instance: typedef itk::ImageFileReader ReaderType; ReaderType::Pointer imageReader = ReaderType::New(); imageReader->SetFileName( argv[1] ); * imageReader->Update();* Thanks. -------------- 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 abdul.sw84 at gmail.com Fri Oct 24 04:32:33 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 10:32:33 +0200 Subject: [ITK] [ITK-users] Numeric traits Message-ID: Hello, I came across the following statement: PixelType label = itk::NumericTraits::One; It seems to be related to numric traits, which I have visited its documentation website, here , but, yet, didn't get the idea of the statement. Can you kindly just describe to me what the statement means? Thanks. -------------- 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 abdul.sw84 at gmail.com Fri Oct 24 05:00:42 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 11:00:42 +0200 Subject: [ITK] [ITK-users] ImageRegionIteratorWithIndex Message-ID: Hello, What is the purpose of ImageRegionIteratorWithIndex ? I didn't get the whole point from the documentation. Can you kindly just clarify it a bit? Thanks. -------------- 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 abdul.sw84 at gmail.com Fri Oct 24 05:04:01 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 11:04:01 +0200 Subject: [ITK] [ITK-users] ItI in itk Message-ID: Hello, I came across this code: itk::ImageRegionIteratorWithIndex *ItI*( imageReader->GetOutput(), imageReader->GetOutput()->GetLargestPossibleRegion() ); What does "ItI" mean? Thanks. -------------- 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 abdul.sw84 at gmail.com Fri Oct 24 05:11:02 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 11:11:02 +0200 Subject: [ITK] [ITK-users] Shouldn't they be swapped? Message-ID: Hello, I came across the following code: PixelType maxValue = itk::NumericTraits::NonpositiveMin(); PixelType minValue = itk::NumericTraits::max(); Shouldn't the above statements be swapped? That is, minValue for the first, and ,maxValue for the second? Thanks. -------------- 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 arnaudgelas at gmail.com Fri Oct 24 05:16:40 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Fri, 24 Oct 2014 11:16:40 +0200 Subject: [ITK] [ITK-users] ImageFileReader Update() In-Reply-To: References: Message-ID: Hi Abdul, A good starting point is the software guide: http://www.itk.org/ItkSoftwareGuide.pdf Best Arnaud On Oct 24, 2014, at 10:30 AM, Abdul Abdul wrote: > Hello, > > I'm new to ITK, and just want to ask about what "Update()" means when used with ImageFileReader. > > For instance: > > typedef itk::ImageFileReader ReaderType; > ReaderType::Pointer imageReader = ReaderType::New(); > imageReader->SetFileName( argv[1] ); > imageReader->Update(); > > Thanks. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 abdul.sw84 at gmail.com Fri Oct 24 05:54:53 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 11:54:53 +0200 Subject: [ITK] [ITK-users] Pointers and New() Message-ID: Hello, I noticed that when we want to use "New()" in itk with some type, we use "Pointer" with that type. Like for instance: SomeType::Pointer st = SomeType::New(); In "itk", is this always the case? Is it because in order to access the "functions" with a a type in itk, this can only be done through pointers? Thanks. -------------- 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 abdul.sw84 at gmail.com Fri Oct 24 06:10:45 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 12:10:45 +0200 Subject: [ITK] [ITK-users] ImageFileReader Update() In-Reply-To: References: Message-ID: Hi Arnaud, Thanks for your kind reply. That is very helpful. I got the following from the guide regarding "Update()": *The pipeline update mechanism ensures that the reader only executes when a data request is made to the reader and the reader has not read any data.* But, it is yet not very clear. Can you kindly describe it a bit? Thanks. On Fri, Oct 24, 2014 at 11:16 AM, Arnaud Gelas wrote: > Hi Abdul, > > A good starting point is the software guide: > > http://www.itk.org/ItkSoftwareGuide.pdf > > Best > Arnaud > > On Oct 24, 2014, at 10:30 AM, Abdul Abdul wrote: > > Hello, > > I'm new to ITK, and just want to ask about what "Update()" means when used > with ImageFileReader. > > For instance: > > typedef itk::ImageFileReader ReaderType; > ReaderType::Pointer imageReader = ReaderType::New(); > imageReader->SetFileName( argv[1] ); > * imageReader->Update();* > > Thanks. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 arnaudgelas at gmail.com Fri Oct 24 07:03:46 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Fri, 24 Oct 2014 13:03:46 +0200 Subject: [ITK] [ITK-users] ImageFileReader Update() In-Reply-To: References: Message-ID: <8261ECB7-BEFC-4841-9A95-E9F3BD9C612F@gmail.com> please read section 3.5 Data Processing Pipeline On Oct 24, 2014, at 12:10 PM, Abdul Abdul wrote: > Hi Arnaud, > > Thanks for your kind reply. That is very helpful. I got the following from the guide regarding "Update()": > > The pipeline update mechanism ensures that the reader only executes when a data request is made to the reader and the reader has not read any data. > > But, it is yet not very clear. > > Can you kindly describe it a bit? > > Thanks. > > On Fri, Oct 24, 2014 at 11:16 AM, Arnaud Gelas wrote: > Hi Abdul, > > A good starting point is the software guide: > > http://www.itk.org/ItkSoftwareGuide.pdf > > Best > Arnaud > > On Oct 24, 2014, at 10:30 AM, Abdul Abdul wrote: > >> Hello, >> >> I'm new to ITK, and just want to ask about what "Update()" means when used with ImageFileReader. >> >> For instance: >> >> typedef itk::ImageFileReader ReaderType; >> ReaderType::Pointer imageReader = ReaderType::New(); >> imageReader->SetFileName( argv[1] ); >> imageReader->Update(); >> >> Thanks. >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 millerjv at gmail.com Fri Oct 24 07:31:24 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 24 Oct 2014 07:31:24 -0400 Subject: [ITK] [ITK-users] Numeric traits In-Reply-To: References: Message-ID: This statement assigns the value of 1 to variable "label". The value of NumericTraits::One is specific to the datatype PixelType. For instance, For an integer type, NumericTraits::One will be 1. For a floating point type, it will be 1.0. Techniques like this are used in Generic Programming to initialize or assign a variable a value of the appropriate type (and avoid compiler warnings and performance associated with casting between types). On Fri, Oct 24, 2014 at 4:32 AM, Abdul Abdul wrote: > Hello, > > I came across the following statement: > > PixelType label = itk::NumericTraits::One; > > It seems to be related to numric traits, which I have visited its > documentation website, here > , but, > yet, didn't get the idea of the statement. > > Can you kindly just describe to me what the statement means? > > Thanks. > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 millerjv at gmail.com Fri Oct 24 07:33:26 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 24 Oct 2014 07:33:26 -0400 Subject: [ITK] [ITK-users] ImageRegionIteratorWithIndex In-Reply-To: References: Message-ID: Image Iterators allow you to visit every pixel in an image (or image region) with a prescribed pattern of access. We use Image Iterators to write generic code that can operate on 1D, 2D, 3D, and 4D images without requiring the algorithm code to understand the dimension of the image. The WithIndex variants of the Image Iterators are optimized to be able to report the pixel position (Index) of the iterator. On Fri, Oct 24, 2014 at 5:00 AM, Abdul Abdul wrote: > Hello, > > What is the purpose of ImageRegionIteratorWithIndex > ? > I didn't get the whole point from the documentation. Can you kindly just > clarify it a bit? > > Thanks. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 millerjv at gmail.com Fri Oct 24 07:34:54 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 24 Oct 2014 07:34:54 -0400 Subject: [ITK] [ITK-users] ItI in itk In-Reply-To: References: Message-ID: Itl is this case is a variable of type ImageRegionIteratorWithIndex. Its constructor is being called with the output of the ImageReader and the iterator will walk the LargestPossibleRegion of the ImageReader's output. On Fri, Oct 24, 2014 at 5:04 AM, Abdul Abdul wrote: > Hello, > > I came across this code: > > itk::ImageRegionIteratorWithIndex *ItI*( > imageReader->GetOutput(), > imageReader->GetOutput()->GetLargestPossibleRegion() ); > > What does "ItI" mean? > > Thanks. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 millerjv at gmail.com Fri Oct 24 07:36:52 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 24 Oct 2014 07:36:52 -0400 Subject: [ITK] [ITK-users] Shouldn't they be swapped? In-Reply-To: References: Message-ID: Most likely you are looking at code that is just before a loop that is searching to find the min and max values within an image. It is common practice to initialize the current values of min and max in this manner so that you can write code like if (value > maxValue) { value = maxValue; } On Fri, Oct 24, 2014 at 5:11 AM, Abdul Abdul wrote: > Hello, > > I came across the following code: > > PixelType maxValue = itk::NumericTraits::NonpositiveMin(); > PixelType minValue = itk::NumericTraits::max(); > > Shouldn't the above statements be swapped? That is, minValue for the > first, and ,maxValue for the second? > > Thanks. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 anton.delehony at gmail.com Fri Oct 24 09:56:56 2014 From: anton.delehony at gmail.com (Anton Delehony) Date: Fri, 24 Oct 2014 09:56:56 -0400 Subject: [ITK] [ITK-users] Liver lobes atlas Message-ID: Hi All, I'm looking for a liver atlas that I can use to segment the different lobes of the liver from MR images. Does something like this exist? Anton -------------- 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 norman-k-williams at uiowa.edu Fri Oct 24 10:06:41 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Fri, 24 Oct 2014 14:06:41 +0000 Subject: [ITK] [ITK-users] ImageRegionIteratorWithIndex In-Reply-To: References: Message-ID: Normally, to visit every pixel in an Image, you?d use an ImageRegionIterator, or ImageRegionConstIterator. The latter you?d use when you don?t want to or cannot modify the image. ImageRegionIteratorWithIndex (and ImageRegionConstIteratorWithIndex) are, as Jim Miller said, optimized for reporting the index of the voxel currently referenced by the iterator. A very common use would be to iterate through an image, but use the index to access another image?s voxels as well. Generally, you?d use an iterator for each image but there are cases ? like when you only occasionally use the index to access another image ? where it makes sense not to bother with the second iterator. From: Abdul Abdul > Date: Friday, October 24, 2014 at 4:00 AM To: Insight > Subject: [ITK-users] ImageRegionIteratorWithIndex Hello, What is the purpose of ImageRegionIteratorWithIndex? I didn't get the whole point from the documentation. Can you kindly just clarify it a bit? Thanks. ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- 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 sami.koho at gmail.com Fri Oct 24 10:36:01 2014 From: sami.koho at gmail.com (Sami Koho) Date: Fri, 24 Oct 2014 17:36:01 +0300 Subject: [ITK] [ITK-users] Example medical images for teaching Image Segmentation Message-ID: Hello, This is not directly related to ITK, but I will ask anyway, out of curiosity. This fall I have been teaching Digital Image Processing to Biomedical imaging students. The next subject will be Image Segmentation (Edge detection models, / thresholding). Would any of you have some favorite medical images to demonstrate these subjects? I can of course use any pictures, but having examples relevant to the students would be nice. I have my own libraries as well, but they are mostly of cells and their internals (microscopy lab). Feel free to send any links/files, if something comes to mind. Best, Sami -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Fri Oct 24 10:56:17 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 24 Oct 2014 10:56:17 -0400 Subject: [ITK] [ITK-users] Pointers and New() In-Reply-To: References: Message-ID: Hi Abdul, Welcome to ITK! Yes, we always want to use ::New(), which returns ITK SmartPointer's [1] since this is used by the reference count kept in all ITK Object's [2]. This is described in more detail in the ITK Software Guide [3]. Hope this helps, Matt [1] http://www.itk.org/Doxygen/html/classitk_1_1SmartPointer.html [2] http://www.itk.org/Doxygen/html/classitk_1_1Object.html [3] http://itk.org/ItkSoftwareGuide.pdf On Fri, Oct 24, 2014 at 5:54 AM, Abdul Abdul wrote: > Hello, > > I noticed that when we want to use "New()" in itk with some type, we use > "Pointer" with that type. Like for instance: > > SomeType::Pointer st = SomeType::New(); > > In "itk", is this always the case? Is it because in order to access the > "functions" with a a type in itk, this can only be done through pointers? > > Thanks. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 Fri Oct 24 10:57:29 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 24 Oct 2014 10:57:29 -0400 Subject: [ITK] [ITK-users] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: <544A073B.4080905@imnc.in2p3.fr> References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> <54475B84.5020906@imnc.in2p3.fr> <54492AB3.2030006@imnc.in2p3.fr> <544A073B.4080905@imnc.in2p3.fr> Message-ID: Hi Fran?oise, CMake is recommended -- it will avoid this problem and others. It works well with Qt. Thanks, Matt On Fri, Oct 24, 2014 at 4:00 AM, Fran?oise Lefebvre wrote: > > No, I'm not. I have always used a .pro file and qmake. > > Le 23/10/2014 23:37, Matt McCormick a ?crit : > >> Hi, >> >> Are you using CMake to configure your project? >> >> Matt >> >> On Thu, Oct 23, 2014 at 12:20 PM, Fran?oise Lefebvre >> wrote: >>> >>> Hi, >>> >>> I also tried on Windows 8,msvc2012_opengl and Qt5.3. I get exactly the >>> same >>> link error. >>> >>> FL >>> >>> >>> Le 22/10/2014 09:23, Fran?oise Lefebvre a ?crit : >>> >>>> Yes I did. >>>> >>>> Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : >>>>> >>>>> Did you try the latest 4.6.1 release? >>>>> >>>>> Brad >>>>> >>>>> On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre >>>>> >>>>> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> ITK 4.6 was succesfully build using cmake2.8.10.2, the default >>>>>> parameters and the Module_ITKReview on. >>>>>> >>>>>> I am now trying to compile a program developed in C++ using Qt5.1.1 >>>>>> and >>>>>> Microsoft Visual C++ express 2010 on Windows 7. >>>>>> >>>>>> I get the following link error : >>>>>> >>>>>> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non >>>>>> r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: >>>>>> static class itksys::Encoding::CommandLineArguments __cdecl >>>>>> itksys::Encoding::CommandLineArguments::Main(int,char const * const >>>>>> *)" >>>>>> (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) >>>>>> >>>>>> I didn't get this error when compiling with itk4.3 . >>>>>> >>>>>> Any hint ? >>>>>> >>>>>> Thank you for your help, >>>>>> >>>>>> F. Lefebvre >>>>>> >>>>>> _____________________________________ >>>>>> Powered by www.kitware.com >>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>> http://www.kitware.com/products/protraining.php >>>>>> >>>>>> Please keep messages on-topic and check the 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 > > > -- > Fran?oise LEFEBVRE > IMNC (Imagerie et Mod?lisation en Neurobiologie et Canc?rologie) > Campus d'Orsay - B?t 440 > 91405 ORSAY Cedex > 01 69 15 51 87 > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 grothausmann.roman at mh-hannover.de Wed Oct 1 11:27:57 2014 From: grothausmann.roman at mh-hannover.de (Dr. Roman Grothausmann) Date: Wed, 01 Oct 2014 17:27:57 +0200 Subject: [ITK] [ITK-users] patch to add a global hierarchical watershed segmentation mode to itksnap In-Reply-To: <53E85181.8040607@mh-hannover.de> References: <53E85181.8040607@mh-hannover.de> Message-ID: <542C1D7D.6000904@mh-hannover.de> Dear mailing list members, Finally, I got my idea about an interactive hierarchical Watershed SegmentationEditor realized. The idea originates from the SegmentationEditor of the InsightApplication demonstrated here: http://www.insight-journal.org/browse/publication/70 I decided to add such functionality to itksnap as it is the successor of the SegmentationEditor. The additions consist of a Click'n'Join mode, which either allows to join or split labels of the current segmentation by clicking, or instead uses a Global Watershed label image as a label source. The great feature of the itkWatershedFilter allows the level of the watershed hierarchy to be changed on-the-fly. The patch is against itksnap-3.0.0 and in beta-testing stage. Loading from files and "back" buttons are not yet implemented. Please feel free to test it too! Regards, Roman On 11/08/14 07:15, Dr. Roman Grothausmann wrote: > Dear mailing list members, > > > For a long time now I've been searching for a replacement of the old > SegmentationEditor (part of the InsightApplications) which I could not get to > work even with older ITK-3.x. Somewhere I was told that it was integrated and > maintained within itksnap. However the only tool in itksnap based on watershed > segmentation seems to be the adaptive brush. It is very handy, but > time-consuming in 3D and only for local segmentations. In contrast the > SegmentationEditor used a global hierarchical watershed segmentation to pick > labels from, see e.g. the video linked here: > http://www.insight-journal.org/browse/publication/70 > Quite often now I've stumbled over data, that would likely have profited a lot > of such a tool for segmentation. > > If such a tool working with ITK-4.x does not exist any more, I thought of > implementing it as a global WS segmentation mode in itksnap. That way making the > tool easier to find, to use and to ensure maintenance (should it be integrated > into the itksnap code base in the end) and also avoiding recoding a GUI with > mouse interaction and such. > > My current idea is to start, similar to the snake-tool, with pre-filtering like > smoothing and optional edge-detection. > Then the main edit mode to consist of the usual 4 subwindows showing an overlay > of the grey-image and the watershed segmentation of the hierarchical WS-filter > (hWS), side-by-side to another label-dataset (loaded like a tiled overlay) which > consist of the actually chosen labels from the hWS as the final data (FD). > The interaction I'm considering would be to LMB click on a label in the hWS > which is then added to the FD as the current fg label, or removed with a RMB. > The hierachrchy level of the hWS could be controlled by a slider or the mouse > wheel + Shift in nearly real time if some region demands higher or lower > detailed segmentation. When the fg label is changed, the segmentation added or > removed with further mouse interactions would modify the new fg label. > When all is done and the global WS mode is left, the FD label-dataset is added > to the main segmentation of itksnap. > > Would that be possible to implement in itksnap 3.x? > What source files of the itksnap code base should I look at for: > - the pre-filtering mode of the snake (for the smoothing and edge detection) > - the mouse interactions (for e.g. adding the whell + Shift interaction) > - possible examples for the dual layout > > Thanks for any comments, help or hints. > Roman > -- Dr. Roman Grothausmann Tomographie und Digitale Bildverarbeitung Tomography and Digital Image Analysis Institut f?r Funktionelle und Angewandte Anatomie, OE 4120 Medizinische Hochschule Hannover Carl-Neuberg-Str. 1 D-30625 Hannover Tel. +49 511 532-9574 -------------- next part -------------- A non-text attachment was scrubbed... Name: itksnap-3.0.0_gWS_53.diff Type: text/x-patch Size: 151111 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Wed Oct 1 15:40:44 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 1 Oct 2014 15:40:44 -0400 Subject: [ITK] [ANNOUNCE] ITK 4.6.1 has been released! Message-ID: On behalf of the Insight Toolkit Community, we are happy to announce the release of ITK 4.6.1! This is a patch release that addresses critical issues. The 4.6.1 release fixes DICOM, MetaIO, TIFF, and PNG IO issues, 32-bit WrapITK build errors, Python wrapping warnings, CMake configuration with COMPONENTS, performance and memory consumption of the ITKv4 implementation of the mutual information matching metric, and a many other issues. Congratulations and thanks to everyone who contributed to this release. We are particularly grateful for the collaborations with the 3D Slicer, Debian, GDCM, and MINC communities to address these issues. Questions and comments are welcome on the ITK mailing lists. The release files can be downloaded from: http://itk.org/ITK/resources/software.html The next feature release of 4.6.0 is scheduled for June. Enjoy ITK! Changes from v4.6.0 to v4.6.1: Arnaud Gelas (5): BUG: fix gdcm version in GDCMImageIO. COMP: missing cast when calling gdcm::DataElement::SetByteValue BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is false BUG: split include directories into appropriate cmake variables HDF5 BUG: missing gdcm libraries when using system GDCM Brad King (2): COMP: Fix vxl_config_macros usage of CMake check macros BUG: Fix itk_module_config for repeated calls Bradley Lowekamp (8): ENH: Adding License file from upstream MetaIO ENH: Adding script to update MetaIO from upstream ENH: Remove ITK MetaIO to prepare for upstream import COMP: Fix variable type for Set/Get macros BUG: Use METER of sCAL scale unit BUG: Use PNG_SCALE_METER for PNG sCAL unit BUG: Fix overflows computing size of read tiff image BUG: Use array delete operator for array new allocations Christopher Mullins (2): COMP: Allows latex to compile for ITKSoftwareGuide COMP: Wrap MeshBase templates David T. Chen (1): DOC: Fixed HistogramThresholdImageFitler Gert Wollny (1): COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) Girish Mallya (1): BUG: Tests added for BinaryImageToLabelMapFilter for single-row images. Hans Johnson (12): COMP: Add tolerance for comparing floating point PERF: Remove non-threadable algorithm components PERF: Remove large foot print of PDF derivatives. PERF: Revert Remove large foot print of PDF derivatives. STYLE: Test against almost equal for floating point values STYLE: Non-exact floating point testing PERF: Distribute initialization per thread buffers ENH: Remove unnecessary mutable qualifier. STYLE: Remove comment with no meaning. ENH: Moved accumlator logic to main MI class ENH: Allow staggering of accumulations per thread. PERF: Zero reset thread buffers during finalize Matthew McCormick (31): BUG: ArchiveTestingData.py future imports must occur at the beginning. DOC: Remove Image2.cxx reference from Book 2. DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. DOC: Remove references to Book 1 sections from Book 2. DOC: Make BinaryThresholdImageFilter not floating. DOC: Fix Software Guide figure caption for FlipImageFilter. DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. DOC: Remove duplicate figure in LaplacianRecursiveGaussianImageFilter2.cxx. DOC: ImageRandomConstIteratorWithIndex table reference. BUG: Bump GCCXML to 2014-08-06. BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. BUG: Call clear instead of empty on PatchBasedDenoising EmptyCaches(). BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. BUG: Fix alpha assignment for RGBA TIFF. BUG: Fix Nifti IO read with large images. BUG: Improve thread-safety and performance of PCAShapeSignedDistanceFunction. DOC: itk::statistics -> itk::Statistics. DOC: Remove duplicate text in LaplacianRecursiveGaussian example. DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. BUG: TransformFileReader does not clear its TransformList. BUG: Prevent dangling pointer in HDF5TransformIO. COMP: Fix missing prefix in ITKv3ImageRegistration20Test. BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform STYLE: Improve style in BinaryImageToLabelMapFilter. BUG: Fix BinaryImageToLabelMapFilter on 1D image. ENH: Improve precision of the joint PDF sum BUG: Fix BinShrinkImageFilter for different input/output image types. COMP: Fix transform type for ITKv3/IterativeClosestPoint2. COMP: Add missing wrapping for TransformIOBaseTemplate. BUG: gdcm::StringFilter recognizes backslash delimiter. ENH: Bump ITK version to 4.6.1. MetaIO Maintainers (1): MetaIO (reduced) Michka Popoff (4): BUG: Improve SWIG version check BUG: Add VTK_VERSION for older VTK versions BUG: Update VTK minimum version (for release) BUG: Fix memory leak in MetaImageIO after exception Vladimir S. FONOV (1): BUG: Fixing incorrect MINC style inverse transform From matt.mccormick at kitware.com Wed Oct 1 15:50:33 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 1 Oct 2014 15:50:33 -0400 Subject: [ITK] [ANNOUNCE] ITK 4.6.1 has been released! In-Reply-To: References: Message-ID: Minor correction: > > The next feature release of 4.6.0 is scheduled for June. > The next feature release of 4.7.0 is scheduled for December. From matt.mccormick at kitware.com Wed Oct 1 18:40:32 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 1 Oct 2014 18:40:32 -0400 Subject: [ITK] Opportunity to share, discuss, design, and learn with other ITK community members Message-ID: On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/u/0/events/c2284tfm9u9t6ft6ghp5u8546mc For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 To get regular invites to these events, join the ITK Bar Camp G+ Community: https://plus.google.com/u/0/communities/111375098792764998322 All are welcome. Hope to talk to you then! From joel.schaerer at laposte.net Thu Oct 2 05:33:06 2014 From: joel.schaerer at laposte.net (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=) Date: Thu, 02 Oct 2014 11:33:06 +0200 Subject: [ITK] [ITK-users] Proper chaining of filters Message-ID: <542D1BD2.40801@laposte.net> Hi all, I've noticed a couple times that when building a pipeline with ITK, you need to keep a reference to all filters before the pipeline is updated. This seems a little counter-intuitive to me, so I would like to better understand the issue and see if there is a way around it. As an example, the following code doesn't work: DilateType::Pointer dilate = DilateType::New(); dilate->SetInput(thresh->GetOutput()); dilate->SetKernel(kernel); dilate_filters.push_back(dilate); for (int i=0; i<14; ++i) { DilateType::Pointer temp = DilateType::New(); temp->SetInput(dilate->GetOutput()); temp->SetKernel(kernel); dilate = temp; } dilate->Update(); Regions don't get propagated properly and I get the following exception when writing the output: C++ exception with description "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not fully contain requested paste IO regionPaste IO region: ImageIORegion (0x7fff9bb72cc0) Dimension: 3 Index: 0 0 0 Size: 0 0 0 Largest possible region: ImageRegion (0x7fff9bb72bc0) Dimension: 3 Index: [0, 0, 0] Size: [0, 0, 0] " thrown in the test body. My guess is that the filters get destroyed before they get a chance to be executed. If I explicitely keep references to each filter, it works: DilateType::Pointer dilate = DilateType::New(); dilate->SetInput(thresh->GetOutput()); dilate->SetKernel(kernel); // We need to keep a reference to each filter in the pipeline before it is updated std::vector dilate_filters; dilate_filters.push_back(dilate); for (int i=0; i<14; ++i) { DilateType::Pointer temp = DilateType::New(); temp->SetInput(dilate_filters.back()->GetOutput()); temp->SetKernel(kernel); dilate = temp; dilate_filters.push_back(temp); } dilate_filters.back()->Update(); My question is, why doesn't a filter keep a reference to the previous filter in the pipeline? Is there a way around this? Thanks! Jo?l _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 pola_88 at hotmail.it Thu Oct 2 05:45:10 2014 From: pola_88 at hotmail.it (Paola Volonghi) Date: Thu, 2 Oct 2014 11:45:10 +0200 Subject: [ITK] (no subject) Message-ID: Hi all, we developed a python program on ubuntu 13.10 using vtk library ver. 5.8.0 and itk library ver. 3.20.1. In our program we used also these command lines: itk.VTKImageToImageFilter.IF3.New() itk.ImageToVTKImageFilter[image_type].New() itk.PyBuffer[image_type].GetArrayFromImage( ?. ) but we discovered that they don't work on itk ver. 4.x. Is there another way to convert images from itk to vtk and vice versa, using the newest versions of vtk and itk? Thanks! Paola -------------- next part -------------- An HTML attachment was scrubbed... URL: From michkapopoff at gmail.com Thu Oct 2 07:11:13 2014 From: michkapopoff at gmail.com (Michka Popoff) Date: Thu, 2 Oct 2014 13:11:13 +0200 Subject: [ITK] (no subject) In-Reply-To: References: Message-ID: <0978546B-55C4-470A-9BE2-C5DD20455818@gmail.com> Hi for the moment, the PyBuffer module has been moved out of ITK, and is no more maintained. There was a port done for ITK4, but it is not tested so I don?t know how well it is working [1] I plan to work a little bit on it one day if I can find some time. The way to move images from itk to vtk is to use the ITKVTKGlue module. You need to build ITK with: Module_ITKVtkGlue=ON Then you can do something like this (for a 2d image for example): image_type = itk.Image[itk.UC, 2] reader = itk.ImageFileReader[image_type].New() reader.SetFileName(?PATH/TO/FILE?) reader.Update() vtk_image = itk.ImageToVTKImageFilter[image_type].New() vtk_image.SetInput(reader.GetOutput()) vtk_image.Update() Then you can use the vtk_image as a vtk object, that you can render or work on. Is there a specific error message you get ? Michka [1] https://github.com/InsightSoftwareConsortium/itkPyBuffer On 2 oct. 2014, at 11:45, Paola Volonghi wrote: > Hi all, > we developed a python program on ubuntu 13.10 using vtk library ver. 5.8.0 and itk library ver. 3.20.1. In our program we used also these command lines: > itk.VTKImageToImageFilter.IF3.New() > itk.ImageToVTKImageFilter[image_type].New() > itk.PyBuffer[image_type].GetArrayFromImage( ?. ) > but we discovered that they don't work on itk ver. 4.x. > Is there another way to convert images from itk to vtk and vice versa, using the newest versions of vtk and itk? > > Thanks! > > Paola > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Thu Oct 2 10:16:08 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 2 Oct 2014 10:16:08 -0400 Subject: [ITK] [ITK-users] Proper chaining of filters In-Reply-To: <542D1BD2.40801@laposte.net> References: <542D1BD2.40801@laposte.net> Message-ID: Hi Jo?l, Calling temp->SetInput(dilate->GetOutput()); Connects the DataObject generated by dilate to the temp filter. temp does not increment dilate's reference count, and it would be difficult to do since the SetInput input is the DataObject, not the ProcessObject. As a consequence, at least one SmartPointer needs to be kept in scope as with your second example. HTH, Matt On Thu, Oct 2, 2014 at 5:33 AM, Jo?l Schaerer wrote: > Hi all, > > I've noticed a couple times that when building a pipeline with ITK, you need > to keep a reference to all filters before the pipeline is updated. This > seems a little counter-intuitive to me, so I would like to better understand > the issue and see if there is a way around it. > > As an example, the following code doesn't work: > > DilateType::Pointer dilate = DilateType::New(); > dilate->SetInput(thresh->GetOutput()); > dilate->SetKernel(kernel); > > dilate_filters.push_back(dilate); > for (int i=0; i<14; ++i) { > DilateType::Pointer temp = DilateType::New(); > temp->SetInput(dilate->GetOutput()); > temp->SetKernel(kernel); > dilate = temp; > } > dilate->Update(); > > Regions don't get propagated properly and I get the following exception when > writing the output: > > C++ exception with description > "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: > itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not > fully contain requested paste IO regionPaste IO region: ImageIORegion > (0x7fff9bb72cc0) > Dimension: 3 > Index: 0 0 0 > Size: 0 0 0 > Largest possible region: ImageRegion (0x7fff9bb72bc0) > Dimension: 3 > Index: [0, 0, 0] > Size: [0, 0, 0] > " thrown in the test body. > > My guess is that the filters get destroyed before they get a chance to be > executed. If I explicitely keep references to each filter, it works: > > DilateType::Pointer dilate = DilateType::New(); > dilate->SetInput(thresh->GetOutput()); > dilate->SetKernel(kernel); > // We need to keep a reference to each filter in the pipeline before it is > updated > std::vector dilate_filters; > dilate_filters.push_back(dilate); > for (int i=0; i<14; ++i) { > DilateType::Pointer temp = DilateType::New(); > temp->SetInput(dilate_filters.back()->GetOutput()); > temp->SetKernel(kernel); > dilate = temp; > dilate_filters.push_back(temp); > } > dilate_filters.back()->Update(); > > My question is, why doesn't a filter keep a reference to the previous filter > in the pipeline? Is there a way around this? > > Thanks! > > Jo?l > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 joel.schaerer at laposte.net Thu Oct 2 10:22:24 2014 From: joel.schaerer at laposte.net (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=) Date: Thu, 02 Oct 2014 16:22:24 +0200 Subject: [ITK] [ITK-users] Proper chaining of filters In-Reply-To: References: <542D1BD2.40801@laposte.net> Message-ID: <542D5FA0.8070903@laposte.net> Hi Matt, Thanks for the confirmation. I was thinking there might be another mechanism I wasn't aware of. Jo?l On 10/02/2014 04:16 PM, Matt McCormick wrote: > Hi Jo?l, > > Calling > > temp->SetInput(dilate->GetOutput()); > > Connects the DataObject generated by dilate to the temp filter. temp > does not increment dilate's reference count, and it would be difficult > to do since the SetInput input is the DataObject, not the > ProcessObject. > > As a consequence, at least one SmartPointer needs to be kept in scope > as with your second example. > > HTH, > Matt > > On Thu, Oct 2, 2014 at 5:33 AM, Jo?l Schaerer wrote: >> Hi all, >> >> I've noticed a couple times that when building a pipeline with ITK, you need >> to keep a reference to all filters before the pipeline is updated. This >> seems a little counter-intuitive to me, so I would like to better understand >> the issue and see if there is a way around it. >> >> As an example, the following code doesn't work: >> >> DilateType::Pointer dilate = DilateType::New(); >> dilate->SetInput(thresh->GetOutput()); >> dilate->SetKernel(kernel); >> >> dilate_filters.push_back(dilate); >> for (int i=0; i<14; ++i) { >> DilateType::Pointer temp = DilateType::New(); >> temp->SetInput(dilate->GetOutput()); >> temp->SetKernel(kernel); >> dilate = temp; >> } >> dilate->Update(); >> >> Regions don't get propagated properly and I get the following exception when >> writing the output: >> >> C++ exception with description >> "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: >> itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not >> fully contain requested paste IO regionPaste IO region: ImageIORegion >> (0x7fff9bb72cc0) >> Dimension: 3 >> Index: 0 0 0 >> Size: 0 0 0 >> Largest possible region: ImageRegion (0x7fff9bb72bc0) >> Dimension: 3 >> Index: [0, 0, 0] >> Size: [0, 0, 0] >> " thrown in the test body. >> >> My guess is that the filters get destroyed before they get a chance to be >> executed. If I explicitely keep references to each filter, it works: >> >> DilateType::Pointer dilate = DilateType::New(); >> dilate->SetInput(thresh->GetOutput()); >> dilate->SetKernel(kernel); >> // We need to keep a reference to each filter in the pipeline before it is >> updated >> std::vector dilate_filters; >> dilate_filters.push_back(dilate); >> for (int i=0; i<14; ++i) { >> DilateType::Pointer temp = DilateType::New(); >> temp->SetInput(dilate_filters.back()->GetOutput()); >> temp->SetKernel(kernel); >> dilate = temp; >> dilate_filters.push_back(temp); >> } >> dilate_filters.back()->Update(); >> >> My question is, why doesn't a filter keep a reference to the previous filter >> in the pipeline? Is there a way around this? >> >> Thanks! >> >> Jo?l >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 pedromorais-17 at hotmail.com Thu Oct 2 12:24:31 2014 From: pedromorais-17 at hotmail.com (Pedro Morais) Date: Thu, 2 Oct 2014 09:24:31 -0700 (PDT) Subject: [ITK] [ITK-users] 3D generalized hough transform Message-ID: <1412267071841-7586297.post@n2.nabble.com> Hi all, I'm wonder if ITK has an implementation of a 3D generalized hough transform. Do you have any idea? Regards, Pedro -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/3D-generalized-hough-transform-tp7586297.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 llliu at umich.edu Thu Oct 2 20:40:16 2014 From: llliu at umich.edu (Lianli Liu) Date: Thu, 2 Oct 2014 20:40:16 -0400 Subject: [ITK] [ITK-users] vector image registration Message-ID: Hi all, I wonder if ITK is supporting vector image registration now? If not, any suggestions to achieve this goal? Thanks! Lianli -------------- 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 ggigi78 at gmail.com Fri Oct 3 05:05:29 2014 From: ggigi78 at gmail.com (Gianluigi Caddeo) Date: Fri, 3 Oct 2014 10:05:29 +0100 Subject: [ITK] [ITK-users] help installing ITK Message-ID: Hi all, during my installation on an ubuntu machine I had this problem: *[100%] Built target ITKv3ThinPlateSplineWarp/bin/sh: 1: DOXYGEN_EXECUTABLE-NOTFOUND: not foundmake[2]: *** [Utilities/Doxygen/CMakeFiles/Documentation] Errore 127make[1]: *** [Utilities/Doxygen/CMakeFiles/Documentation.dir/all] Errore 2make: *** [all] Errore* But doxygen exist and stay in my */usr/bin* directory How can I to force ITK to search doxygen in that directory? thanks a lot Gg -------------- 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 fitz at zhaw.ch Fri Oct 3 09:04:49 2014 From: fitz at zhaw.ch (Fitze Thomas (fitz)) Date: Fri, 3 Oct 2014 13:04:49 +0000 Subject: [ITK] Using filters with images of different dimensions Message-ID: <1BBE26F3-BB10-4BAE-BCFB-B30A2FE8448D@zhaw.ch> Hi all My current situation: 1. 3D inputImage 2. calculate hessian matrix for the image 3. calculate trace of hessian matrix for each voxel 4. use GetAverageSliceImagefilter to get an average (along 1 dimension) of the hessian trace for each voxel in a slice. This reduces the size of this dimension to 1. I will call this the ?averageTracePlane?. Now i want to use the averageTracePlane as a sort of lookup table for my inputImage and apply the corresponding averageTrace value. Or in pseudo code: inputImage(x,y,z) = some_constant * averageTracePlane(x,y,1) How do i set up a image filter that iterates over my inputImage and cycles through the averageTracePlane? I tried using a BinaryFunctorImageFilter, but could not figure out how to get it to ?cycle" trough my averageTracePlane with dimension size 1. Thanks a lot, Thomas From blowekamp at mail.nih.gov Fri Oct 3 09:41:14 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 3 Oct 2014 09:41:14 -0400 Subject: [ITK] Using filters with images of different dimensions (Image broadcast operators?) In-Reply-To: <1BBE26F3-BB10-4BAE-BCFB-B30A2FE8448D@zhaw.ch> References: <1BBE26F3-BB10-4BAE-BCFB-B30A2FE8448D@zhaw.ch> Message-ID: <8BBBA5D3-F1B0-4DC2-8DE3-99F3070B5BDD@mail.nih.gov> Hello, On Oct 3, 2014, at 9:04 AM, Fitze Thomas (fitz) wrote: > Hi all > > My current situation: > 1. 3D inputImage > 2. calculate hessian matrix for the image > 3. calculate trace of hessian matrix for each voxel > 4. use GetAverageSliceImagefilter to get an average (along 1 dimension) of the hessian trace for each voxel in a slice. This reduces the size of this dimension to 1. I will call this the ?averageTracePlane?. Did you consider using a couple MeanProjectionImageFilters[1] to achieve this? > > Now i want to use the averageTracePlane as a sort of lookup table for my inputImage and apply the corresponding averageTrace value. Or in pseudo code: > inputImage(x,y,z) = some_constant * averageTracePlane(x,y,1) > > How do i set up a image filter that iterates over my inputImage and cycles through the averageTracePlane? I tried using a BinaryFunctorImageFilter, but could not figure out how to get it to ?cycle" trough my averageTracePlane with dimension size 1. > You are not going to be able to use any of the Functor based filters as they will expect the images to be the same dimensions. You will need to create a custom filter to do this. You may find the ImageSliceConstItearatorWithIndex[2] use full in combination with a region iterator. Something like this: ImageSliceConstIteratorWithIndex it( image, image->GetRequestedRegion() ); ImageRegionIteratorType it2(projectedImage, projectedImage->GetRequestedRegion() ); it.SetFirstDirection(0); it.SetSecondDirection(1); it.GoToBegin(); it2.GoToBegin(); while( !it.IsAtEnd() && !it2.IsAtEnd() ) { while( !it.IsAtEndOfSlice() ) { while( !it.IsAtEndOfLine() ) { value = it.Get() * it2.Get(); ++it; } it.NextLine(); } it.NextSlice(); ++it2; } This concept of doing operations on different sized images is common in numerical environments such as Matlab, numpy[3] etc..., we don't currently have it in ITK, and I'm not aware of any Insight Journal Article which contributes it either. I think this could be quite a useful filter, say BroadcastingBinaryFunctorImageFilter. Brad > Thanks a lot, > Thomas [1] http://www.itk.org/Doxygen/html/classitk_1_1MeanProjectionImageFilter.html [2] http://www.itk.org/Doxygen/html/classitk_1_1ImageSliceConstIteratorWithIndex.html [3] http://docs.scipy.org/doc/numpy/user/basics.broadcasting.html > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From nicgallego at gmail.com Fri Oct 3 10:29:00 2014 From: nicgallego at gmail.com (Nicolas Gallego) Date: Fri, 3 Oct 2014 16:29:00 +0200 Subject: [ITK] Using filters with images of different dimensions In-Reply-To: <1BBE26F3-BB10-4BAE-BCFB-B30A2FE8448D@zhaw.ch> References: <1BBE26F3-BB10-4BAE-BCFB-B30A2FE8448D@zhaw.ch> Message-ID: Hi Fitze, It seams that what you need is an image iterator. Find some information on classes like itkImageRegionIterator [1] and further information on the software guide [2] on iterators chapter 6. There are different flavors depending on what you need. You may consider the WithIndex iterators since you mentioned you intent to use that image as a lookup table. I hope that helps, [1] http://www.itk.org/Doxygen46/html/classitk_1_1ImageRegionIterator.html [2] http://www.itk.org/ItkSoftwareGuide.pdf Nicol?s Gallego-Ortiz Universit? catholique de Louvain, Belgium 2014-10-03 15:04 GMT+02:00 Fitze Thomas (fitz) : > Hi all > > My current situation: > 1. 3D inputImage > 2. calculate hessian matrix for the image > 3. calculate trace of hessian matrix for each voxel > 4. use GetAverageSliceImagefilter to get an average (along 1 dimension) of > the hessian trace for each voxel in a slice. This reduces the size of this > dimension to 1. I will call this the ?averageTracePlane?. > > Now i want to use the averageTracePlane as a sort of lookup table for my > inputImage and apply the corresponding averageTrace value. Or in pseudo > code: > inputImage(x,y,z) = some_constant * averageTracePlane(x,y,1) > > How do i set up a image filter that iterates over my inputImage and cycles > through the averageTracePlane? I tried using a BinaryFunctorImageFilter, > but could not figure out how to get it to ?cycle" trough my > averageTracePlane with dimension size 1. > > Thanks a lot, > Thomas > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Fri Oct 3 12:57:27 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 3 Oct 2014 12:57:27 -0400 Subject: [ITK] [ITK-dev] Missing "gdcmImageHelper.h" "gdcmSerieHelper.h" on Debian-sid-gcc4-64bit Message-ID: Hi Steve, Mathieu, I noticed that the Debian-sid-gcc4-64bit is having build failures due to missing gdcmImageHelper.h, gdcmSerieHelper.h, since Tuesday, September 30th. Debian-sid-gcc4-32bit ?seems fine. Any ideas on what is happening? Thanks, Matt _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check 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 mathieu.malaterre at gmail.com Sat Oct 4 08:11:09 2014 From: mathieu.malaterre at gmail.com (Mathieu Malaterre) Date: Sat, 4 Oct 2014 14:11:09 +0200 Subject: [ITK] [ITK-dev] Missing "gdcmImageHelper.h" "gdcmSerieHelper.h" on Debian-sid-gcc4-64bit In-Reply-To: <3257282.IFWIHhm9zD@riemann> References: <3257282.IFWIHhm9zD@riemann> Message-ID: On Fri, Oct 3, 2014 at 10:15 PM, Steve M. Robbins wrote: > On October 3, 2014 12:57:27 PM Matt McCormick wrote: >> Hi Steve, Mathieu, >> >> I noticed that the Debian-sid-gcc4-64bit is having build failures due >> to missing gdcmImageHelper.h, gdcmSerieHelper.h, since Tuesday, >> September 30th. Debian-sid-gcc4-32bit seems fine. Any ideas on what >> is happening? > > Well, the difference between the two systems is that I update "Debian-sid- > gcc4-64bit" very regularly, and update "-32bit" very rarely. In particular, > "-64bit" has "gdcm (2.4.4-2)" updated on Sept 30th. > > I'll start looking into the build failure. Thanks for pointing it out. It's there: https://packages.debian.org/sid/amd64/libgdcm2-dev/filelist I guess the cmake cache is still using /usr/include/gdcm-2.2 instead of /usr/include/gdcm-2.4 2cts -- Mathieu _______________________________________________ Powered by www.kitware.com 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 arnaudgelas at gmail.com Mon Oct 6 03:58:09 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Mon, 6 Oct 2014 09:58:09 +0200 Subject: [ITK] [ITK-users] How to remove a tag from MetaDataDictionary? Message-ID: Hi all, I am trying to write a DICOM file in which, the orientation (among others) has changed in my pipeline... 1- After having a look https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919 It appears to me that if the orientation is in the MetaDataDictionary, it is saved anyway into the DICOM image, there is no way to force the ImageIO to recompute it from the image and save it ??? If there is, can anyone give me a pointer? 2- Since I can't find a way to update the image orientation in itk::GDCMImageIO, I have been looking at removing the corresponding tag from the MetaDataDictionary. I could not find any method or any way to do it??? If there is, can anyone give me a pointer? I wish I would not have to copy the dictionary and add if statement to avoid copying the direction... Thanks in advance, Arnaud -------------- 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 emmasaunders123 at gmail.com Mon Oct 6 07:31:03 2014 From: emmasaunders123 at gmail.com (Emma Saunders) Date: Mon, 6 Oct 2014 12:31:03 +0100 Subject: [ITK] [ITK-users] Overlap_image registration metrics Message-ID: Hello all, When computing metrics for image registration, does ITK calculated the metric for only the regions in the image that overlap? If so is this performed on just the initial regions that overlap or will this region of overlap increase during registration and thus require the region in which the metric is calculated to alter? Thanks for any help Emma -------------- 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.ulge at gmail.com Mon Oct 6 09:20:27 2014 From: marco.ulge at gmail.com (Marco Ulge) Date: Mon, 6 Oct 2014 06:20:27 -0700 (MST) Subject: [ITK] [ITK-users] Texture Features extraction Message-ID: <1412601627242-34642.post@n7.nabble.com> Hello, i'm currently working on texture feature extraction and I'm following this examle: http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures It works fine and basically it's all i need. The only problem is that i need to able to specify an arbitrary window size (which is 3 in this example) but as soon as i try to assign it a different value this won't work anymore and i can't figure out why. Can anyone help me with this please? Thanks. Marco -- View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.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 dominique at toepfer-web.de Mon Oct 6 09:47:12 2014 From: dominique at toepfer-web.de (=?ISO-8859-1?Q?Dominique_T=F6pfer?=) Date: Mon, 06 Oct 2014 15:47:12 +0200 Subject: [ITK] [ITK-users] Texture Features extraction In-Reply-To: <1412601627242-34642.post@n7.nabble.com> References: <1412601627242-34642.post@n7.nabble.com> Message-ID: <54329D60.9030004@toepfer-web.de> Hi Marco, you probably forgot to adjust the range of the for-loops. They are running from 1 to size-2 so that the window will not "leave" the image at its boundaries. HTH Dominique On 06.10.2014 15:20, Marco Ulge wrote: > Hello, > > i'm currently working on texture feature extraction and I'm following this > examle: > http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures > > > It works fine and basically it's all i need. The only problem is that i need > to able to specify an arbitrary window size (which is 3 in this example) but > as soon as i try to assign it a different value this won't work anymore and > i can't figure out why. > > Can anyone help me with this please? > > Thanks. > > Marco > > > > -- > View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.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 marco.ulge at gmail.com Mon Oct 6 10:18:26 2014 From: marco.ulge at gmail.com (Marco Ulge) Date: Mon, 6 Oct 2014 07:18:26 -0700 (MST) Subject: [ITK] [ITK-users] Texture Features extraction In-Reply-To: <54329D60.9030004@toepfer-web.de> References: <1412601627242-34642.post@n7.nabble.com> <54329D60.9030004@toepfer-web.de> Message-ID: <1412605106652-34644.post@n7.nabble.com> Thanks for your reply, so if i wanted to specify a window size of 5 (for example) i should iterate from 1 to size - 4? Thanks. Marco -- View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642p34644.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 wjhzwy at gmail.com Mon Oct 6 10:27:10 2014 From: wjhzwy at gmail.com (Jiahui Wang) Date: Mon, 6 Oct 2014 10:27:10 -0400 Subject: [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer Message-ID: Dear All, I modified ImageRegistration8.cxx to run my own rigid registration. However, I found that the processing time of ITKv4 based RegularStepGradientDescentOptimizer is almost 10 times more than that of ITKv3 based one. The program was run on the same machine. The only difference is the ITK libraries. Could anyone give me some suggestions to solve this issue? Thanks, JW -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Mon Oct 6 11:08:10 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 6 Oct 2014 11:08:10 -0400 Subject: [ITK] [ITK-users] How to remove a tag from MetaDataDictionary? In-Reply-To: References: Message-ID: Hi Arnaud, > I am trying to write a DICOM file in which, the orientation (among others) > has changed in my pipeline... > > 1- After having a look > https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919 > > It appears to me that if the orientation is in the MetaDataDictionary, it is > saved anyway into the DICOM image, there is no way to force the ImageIO to > recompute it from the image and save it ??? > If there is, can anyone give me a pointer? If there is a Direction on the input image, it should use it [1]. But the DICOM tag 0020|0037 cannot be present. > 2- Since I can't find a way to update the image orientation in > itk::GDCMImageIO, I have been looking at removing the corresponding tag from > the MetaDataDictionary. I could not find any method or any way to do it??? > If there is, can anyone give me a pointer? > > I wish I would not have to copy the dictionary and add if statement to avoid > copying the direction... This is the method I usually apply... Sorry for the lack of new tricks! Matt [1] https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L816-L828 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Mon Oct 6 11:12:52 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 6 Oct 2014 11:12:52 -0400 Subject: [ITK] [ITK-users] Overlap_image registration metrics In-Reply-To: References: Message-ID: Hi Emma, > When computing metrics for image registration, does ITK calculated the > metric for only the regions in the image that overlap? Yes. See, for example, [1]. > If so is this performed on just the initial regions that overlap or will > this region of overlap increase during registration and thus require the > region in which the metric is calculated to alter? Yes. Ideally, as the registration progresses, the overlap increases, and the registration becomes progressively better. HTH, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.hxx;h=8a6069dde32309a214229968294a14911c701dd0;hb=HEAD#l312 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From lasso at queensu.ca Mon Oct 6 11:44:08 2014 From: lasso at queensu.ca (Andras Lasso) Date: Mon, 6 Oct 2014 15:44:08 +0000 Subject: [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer In-Reply-To: References: Message-ID: See this long thread about this issue: http://slicer-devel.65872.n3.nabble.com/BRAINS-rigid-registration-td4032229.html Short summary: There were some performance regressions in mutual information metric computation, threading, etc. that have been recently fixed, so use the latest ITK version. ITKv4 uses a slightly slower but more accurate optimizer, but if you adjust the number of samples and stopping condition then usually the registration time only increases by about 30-50% (and you might get better quality results). You can see all the changes that have been done in 3D Slicer and BRAINS repositories to go from a 10x-100x slowdown to an approximately equivalent registration speed with ITKv4 compared to ITKv3. Andras From: Community [mailto:community-bounces at itk.org] On Behalf Of Jiahui Wang Sent: Monday, October 06, 2014 10:27 AM To: insight-users at itk.org Subject: [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer Dear All, I modified ImageRegistration8.cxx to run my own rigid registration. However, I found that the processing time of ITKv4 based RegularStepGradientDescentOptimizer is almost 10 times more than that of ITKv3 based one. The program was run on the same machine. The only difference is the ITK libraries. Could anyone give me some suggestions to solve this issue? Thanks, JW -------------- 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 dae.wong at gmail.com Tue Oct 7 03:38:49 2014 From: dae.wong at gmail.com (Fabian Torres) Date: Tue, 7 Oct 2014 15:38:49 +0800 Subject: [ITK] [ITK-users] region inside points Message-ID: Hi all. I have an image that represents some pixels over the surface of an object. Pixels in the surface have value of 1 while any other pixel has value of 0. The pixels are not a continuous line, there are some gaps between pixels. I want to know the region surrounded by the white pixels in my image. I will be working with 2D and 3D data. Is there any class implemented in ITK that I can use? Thanks -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.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 g.bogle at auckland.ac.nz Tue Oct 7 03:40:40 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 7 Oct 2014 07:40:40 +0000 Subject: [ITK] [ITK-users] region inside points In-Reply-To: References: Message-ID: Maybe you could do something with BinaryImageDilateFilter. ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian Torres [dae.wong at gmail.com] Sent: Tuesday, 7 October 2014 8:38 p.m. To: insight-users Subject: [ITK-users] region inside points Hi all. I have an image that represents some pixels over the surface of an object. Pixels in the surface have value of 1 while any other pixel has value of 0. The pixels are not a continuous line, there are some gaps between pixels. I want to know the region surrounded by the white pixels in my image. I will be working with 2D and 3D data. Is there any class implemented in ITK that I can use? Thanks -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.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 g.bogle at auckland.ac.nz Tue Oct 7 03:46:17 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 7 Oct 2014 07:46:17 +0000 Subject: [ITK] [ITK-users] region inside points In-Reply-To: References: , Message-ID: Sorry, I misread your post Fabian - I read it as you wanting the region _surrounding_ the white pixels. But dilate might be usable to fill the gaps, followed by skeletonization. ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Tuesday, 7 October 2014 8:40 p.m. To: Fabian Torres; insight-users Subject: Re: [ITK-users] region inside points Maybe you could do something with BinaryImageDilateFilter. ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian Torres [dae.wong at gmail.com] Sent: Tuesday, 7 October 2014 8:38 p.m. To: insight-users Subject: [ITK-users] region inside points Hi all. I have an image that represents some pixels over the surface of an object. Pixels in the surface have value of 1 while any other pixel has value of 0. The pixels are not a continuous line, there are some gaps between pixels. I want to know the region surrounded by the white pixels in my image. I will be working with 2D and 3D data. Is there any class implemented in ITK that I can use? Thanks -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.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 pola_88 at hotmail.it Tue Oct 7 04:02:39 2014 From: pola_88 at hotmail.it (Paola Volonghi) Date: Tue, 7 Oct 2014 10:02:39 +0200 Subject: [ITK] (no subject) In-Reply-To: <0978546B-55C4-470A-9BE2-C5DD20455818@gmail.com> References: , <0978546B-55C4-470A-9BE2-C5DD20455818@gmail.com> Message-ID: Thanks for your reply.We have just tried before to do what you suggested.Any other idea??ThanksPaola Subject: Re: [ITK] (no subject) From: michkapopoff at gmail.com Date: Thu, 2 Oct 2014 13:11:13 +0200 CC: community at itk.org To: pola_88 at hotmail.it Hi for the moment, the PyBuffer module has been moved out of ITK, and is no more maintained.There was a port done for ITK4, but it is not tested so I don?t know how well it is working [1]I plan to work a little bit on it one day if I can find some time. The way to move images from itk to vtk is to use the ITKVTKGlue module.You need to build ITK with:Module_ITKVtkGlue=ON Then you can do something like this (for a 2d image for example): image_type = itk.Image[itk.UC, 2]reader = itk.ImageFileReader[image_type].New()reader.SetFileName(?PATH/TO/FILE?)reader.Update()vtk_image = itk.ImageToVTKImageFilter[image_type].New()vtk_image.SetInput(reader.GetOutput())vtk_image.Update() Then you can use the vtk_image as a vtk object, that you can render or work on. Is there a specific error message you get ? Michka [1] https://github.com/InsightSoftwareConsortium/itkPyBuffer On 2 oct. 2014, at 11:45, Paola Volonghi wrote:Hi all,we developed a python program on ubuntu 13.10 using vtk library ver. 5.8.0 and itk library ver. 3.20.1. In our program we used also these command lines:itk.VTKImageToImageFilter.IF3.New()itk.ImageToVTKImageFilter[image_type].New()itk.PyBuffer[image_type].GetArrayFromImage( ?. )but we discovered that they don't work on itk ver. 4.x.Is there another way to convert images from itk to vtk and vice versa, using the newest versions of vtk and itk? Thanks! Paola _______________________________________________ Community mailing list Community at itk.org http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From michkapopoff at gmail.com Tue Oct 7 04:04:52 2014 From: michkapopoff at gmail.com (Michka Popoff) Date: Tue, 7 Oct 2014 10:04:52 +0200 Subject: [ITK] (no subject) In-Reply-To: References: , <0978546B-55C4-470A-9BE2-C5DD20455818@gmail.com> Message-ID: What error message are you getting or what is happening ? It?s not really clear to me. When you say ?It doesn?t work?, I need more details to be able to help you. Michka On 7 oct. 2014, at 10:02, Paola Volonghi wrote: > Thanks for your reply. > We have just tried before to do what you suggested. > Any other idea?? > Thanks > Paola > > Subject: Re: [ITK] (no subject) > From: michkapopoff at gmail.com > Date: Thu, 2 Oct 2014 13:11:13 +0200 > CC: community at itk.org > To: pola_88 at hotmail.it > > Hi > > for the moment, the PyBuffer module has been moved out of ITK, and is no more maintained. > There was a port done for ITK4, but it is not tested so I don?t know how well it is working [1] > I plan to work a little bit on it one day if I can find some time. > > The way to move images from itk to vtk is to use the ITKVTKGlue module. > You need to build ITK with: > Module_ITKVtkGlue=ON > > Then you can do something like this (for a 2d image for example): > > image_type = itk.Image[itk.UC, 2] > reader = itk.ImageFileReader[image_type].New() > reader.SetFileName(?PATH/TO/FILE?) > reader.Update() > vtk_image = itk.ImageToVTKImageFilter[image_type].New() > vtk_image.SetInput(reader.GetOutput()) > vtk_image.Update() > > Then you can use the vtk_image as a vtk object, that you can render or work on. > > Is there a specific error message you get ? > > Michka > > [1] https://github.com/InsightSoftwareConsortium/itkPyBuffer > > On 2 oct. 2014, at 11:45, Paola Volonghi wrote: > > Hi all, > we developed a python program on ubuntu 13.10 using vtk library ver. 5.8.0 and itk library ver. 3.20.1. In our program we used also these command lines: > itk.VTKImageToImageFilter.IF3.New() > itk.ImageToVTKImageFilter[image_type].New() > itk.PyBuffer[image_type].GetArrayFromImage( ?. ) > but we discovered that they don't work on itk ver. 4.x. > Is there another way to convert images from itk to vtk and vice versa, using the newest versions of vtk and itk? > > Thanks! > > Paola > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community -------------- next part -------------- An HTML attachment was scrubbed... URL: From dae.wong at gmail.com Tue Oct 7 04:05:24 2014 From: dae.wong at gmail.com (Fabian Torres) Date: Tue, 7 Oct 2014 16:05:24 +0800 Subject: [ITK] [ITK-users] region inside points In-Reply-To: References: Message-ID: Hi Gib. Thanks for the quick response. The problem of using dilation and skeletonization is that some times the gap between pixels is big, and I will have to work with different and big structural elements to be sure that all the gaps were eliminated. I was hoping to find a class that works similar to a convex hull (it does not have to be convex) algorithm and then find the region surrounded by the hull. Thanks On Tue, Oct 7, 2014 at 3:46 PM, Gib Bogle wrote: > Sorry, I misread your post Fabian - I read it as you wanting the region > _surrounding_ the white pixels. But dilate might be usable to fill the > gaps, followed by skeletonization. > ------------------------------ > *From:* Insight-users [insight-users-bounces at itk.org] on behalf of Gib > Bogle [g.bogle at auckland.ac.nz] > *Sent:* Tuesday, 7 October 2014 8:40 p.m. > *To:* Fabian Torres; insight-users > *Subject:* Re: [ITK-users] region inside points > > Maybe you could do something with BinaryImageDilateFilter. > ------------------------------ > *From:* Insight-users [insight-users-bounces at itk.org] on behalf of Fabian > Torres [dae.wong at gmail.com] > *Sent:* Tuesday, 7 October 2014 8:38 p.m. > *To:* insight-users > *Subject:* [ITK-users] region inside points > > Hi all. > > I have an image that represents some pixels over the surface of an > object. Pixels in the surface have value of 1 while any other pixel has > value of 0. > The pixels are not a continuous line, there are some gaps between pixels. > I want to know the region surrounded by the white pixels in my image. > > I will be working with 2D and 3D data. Is there any class implemented in > ITK that I can use? > > Thanks > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.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 g.bogle at auckland.ac.nz Tue Oct 7 04:08:23 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Tue, 7 Oct 2014 08:08:23 +0000 Subject: [ITK] [ITK-users] region inside points In-Reply-To: References: , Message-ID: Maybe there is a way to use a rolling ball. Richard Beare has some morphological filters that might be applicable, but I think it will always be a bit complicated. ________________________________ From: Fabian Torres [dae.wong at gmail.com] Sent: Tuesday, 7 October 2014 9:05 p.m. To: Gib Bogle Cc: insight-users Subject: Re: [ITK-users] region inside points Hi Gib. Thanks for the quick response. The problem of using dilation and skeletonization is that some times the gap between pixels is big, and I will have to work with different and big structural elements to be sure that all the gaps were eliminated. I was hoping to find a class that works similar to a convex hull (it does not have to be convex) algorithm and then find the region surrounded by the hull. Thanks On Tue, Oct 7, 2014 at 3:46 PM, Gib Bogle > wrote: Sorry, I misread your post Fabian - I read it as you wanting the region _surrounding_ the white pixels. But dilate might be usable to fill the gaps, followed by skeletonization. ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Gib Bogle [g.bogle at auckland.ac.nz] Sent: Tuesday, 7 October 2014 8:40 p.m. To: Fabian Torres; insight-users Subject: Re: [ITK-users] region inside points Maybe you could do something with BinaryImageDilateFilter. ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian Torres [dae.wong at gmail.com] Sent: Tuesday, 7 October 2014 8:38 p.m. To: insight-users Subject: [ITK-users] region inside points Hi all. I have an image that represents some pixels over the surface of an object. Pixels in the surface have value of 1 while any other pixel has value of 0. The pixels are not a continuous line, there are some gaps between pixels. I want to know the region surrounded by the white pixels in my image. I will be working with 2D and 3D data. Is there any class implemented in ITK that I can use? Thanks -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.com -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.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 rousseau at unistra.fr Tue Oct 7 04:11:03 2014 From: rousseau at unistra.fr (francois rousseau) Date: Tue, 7 Oct 2014 10:11:03 +0200 Subject: [ITK] [ITK-users] Segmentation fault when using BSplineScatteredDataPointSetToImageFilter for 3D image Message-ID: <44223E94-F14E-4CF5-A0D6-C667CD3DDE29@unistra.fr> Hi everyone, I?m trying to use the BSplineScatteredDataPointSetToImageFilter. No problem when applying it on 2D images (using itkBSplineScatteredDataPointSetToImageFilterTest.cxx). However, after setting const unsigned int ParametricDimension = 3; it crashes when I try to apply it on 3D image (segmentation fault). Can this code be used for 3D images? Thank you Fran?ois -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 2828 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From ggigi78 at gmail.com Tue Oct 7 09:12:21 2014 From: ggigi78 at gmail.com (Gianluigi Caddeo) Date: Tue, 7 Oct 2014 14:12:21 +0100 Subject: [ITK] [ITK-users] 8. help installing ITK (Gianluigi Caddeo) solved Message-ID: Hi all, I solved my problem, I gave the correct path to the DOXYGEN_EXECUTABLE variable. Gg On Tue, Oct 7, 2014 at 9:05 AM, wrote: > Send Insight-users mailing list submissions to > insight-users at itk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/mailman/listinfo/insight-users > or, via email, send a message with subject or body 'help' to > insight-users-request at itk.org > > You can reach the person managing the list at > insight-users-owner at itk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Insight-users digest..." > > > Today's Topics: > > 1. [ANNOUNCE] ITK 4.6.1 has been released! (Matt McCormick) > 2. Re: [ANNOUNCE] ITK 4.6.1 has been released! (Matt McCormick) > 3. Proper chaining of filters (Jo?l Schaerer) > 4. Re: [ITK] Proper chaining of filters (Matt McCormick) > 5. Re: [ITK] Proper chaining of filters (Jo?l Schaerer) > 6. 3D generalized hough transform (Pedro Morais) > 7. vector image registration (Lianli Liu) > 8. help installing ITK (Gianluigi Caddeo) > 9. How to remove a tag from MetaDataDictionary? (Arnaud Gelas) > 10. Overlap_image registration metrics (Emma Saunders) > 11. Texture Features extraction (Marco Ulge) > 12. Re: Texture Features extraction (Dominique T?pfer) > 13. Re: Texture Features extraction (Marco Ulge) > 14. Speed of ITKv4 based Gradient Descent Optimizer (Jiahui Wang) > 15. Re: How to remove a tag from MetaDataDictionary? (Matt McCormick) > 16. Re: Overlap_image registration metrics (Matt McCormick) > 17. Re: [ITK] Speed of ITKv4 based Gradient Descent Optimizer > (Andras Lasso) > 18. Polygon inside point (Fabian Torres) > 19. region inside points (Fabian Torres) > 20. Re: region inside points (Gib Bogle) > 21. Re: region inside points (Gib Bogle) > 22. Re: region inside points (Fabian Torres) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 1 Oct 2014 15:40:44 -0400 > From: Matt McCormick > To: "community at itk.org" , "insight-users at itk.org" > , ITK > Subject: [ITK-users] [ANNOUNCE] ITK 4.6.1 has been released! > Message-ID: > < > CALzTN-TXyhZ2aDaA-UQoFgbg3fPPCPzYKKFpAmKvuquf1EXgrw at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > On behalf of the Insight Toolkit Community, we are happy to announce > the release of ITK 4.6.1! > > This is a patch release that addresses critical issues. The 4.6.1 > release fixes DICOM, MetaIO, TIFF, and PNG IO issues, 32-bit WrapITK > build errors, Python wrapping warnings, CMake configuration with > COMPONENTS, performance and memory consumption of the ITKv4 > implementation of the mutual information matching metric, and a many > other issues. > > Congratulations and thanks to everyone who contributed to this > release. We are particularly grateful for the collaborations with the > 3D Slicer, Debian, GDCM, and MINC communities to address these issues. > Questions and comments are welcome on the ITK mailing lists. > > The release files can be downloaded from: > > http://itk.org/ITK/resources/software.html > > > The next feature release of 4.6.0 is scheduled for June. > > > Enjoy ITK! > > > > Changes from v4.6.0 to v4.6.1: > > Arnaud Gelas (5): > BUG: fix gdcm version in GDCMImageIO. > COMP: missing cast when calling gdcm::DataElement::SetByteValue > BUG: GDCMImageIO was not working properly when m_KeepOriginalUID is > false > BUG: split include directories into appropriate cmake variables HDF5 > BUG: missing gdcm libraries when using system GDCM > > Brad King (2): > COMP: Fix vxl_config_macros usage of CMake check macros > BUG: Fix itk_module_config for repeated calls > > Bradley Lowekamp (8): > ENH: Adding License file from upstream MetaIO > ENH: Adding script to update MetaIO from upstream > ENH: Remove ITK MetaIO to prepare for upstream import > COMP: Fix variable type for Set/Get macros > BUG: Use METER of sCAL scale unit > BUG: Use PNG_SCALE_METER for PNG sCAL unit > BUG: Fix overflows computing size of read tiff image > BUG: Use array delete operator for array new allocations > > Christopher Mullins (2): > COMP: Allows latex to compile for ITKSoftwareGuide > COMP: Wrap MeshBase templates > > David T. Chen (1): > DOC: Fixed HistogramThresholdImageFitler > > Gert Wollny (1): > COMP: Fix SSE2 build errors with WrapITK on GCC 4.9. (ForRelease) > > Girish Mallya (1): > BUG: Tests added for BinaryImageToLabelMapFilter for single-row > images. > > Hans Johnson (12): > COMP: Add tolerance for comparing floating point > PERF: Remove non-threadable algorithm components > PERF: Remove large foot print of PDF derivatives. > PERF: Revert Remove large foot print of PDF derivatives. > STYLE: Test against almost equal for floating point values > STYLE: Non-exact floating point testing > PERF: Distribute initialization per thread buffers > ENH: Remove unnecessary mutable qualifier. > STYLE: Remove comment with no meaning. > ENH: Moved accumlator logic to main MI class > ENH: Allow staggering of accumulations per thread. > PERF: Zero reset thread buffers during finalize > > Matthew McCormick (31): > BUG: ArchiveTestingData.py future imports must occur at the > beginning. > DOC: Remove Image2.cxx reference from Book 2. > DOC: Fix Software Guide page overruns in IterativeClosestPoint3.cxx. > DOC: Remove references to Book 1 sections from Book 2. > DOC: Make BinaryThresholdImageFilter not floating. > DOC: Fix Software Guide figure caption for FlipImageFilter. > DOC: Avoid duplicate figure description in ResampleImageFilter2.cxx. > DOC: Remove duplicate figure in > LaplacianRecursiveGaussianImageFilter2.cxx. > DOC: ImageRandomConstIteratorWithIndex table reference. > BUG: Bump GCCXML to 2014-08-06. > BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. > BUG: Call clear instead of empty on PatchBasedDenoising > EmptyCaches(). > BUG: Fix Size() in ImageToListSampleAdaptor for VectorImage's. > BUG: Fix alpha assignment for RGBA TIFF. > BUG: Fix Nifti IO read with large images. > BUG: Improve thread-safety and performance of > PCAShapeSignedDistanceFunction. > DOC: itk::statistics -> itk::Statistics. > DOC: Remove duplicate text in LaplacianRecursiveGaussian example. > DOC: Fix Software Guide page overruns in > IterativeClosestPoint{1,2}.cxx. > BUG: TransformFileReader does not clear its TransformList. > BUG: Prevent dangling pointer in HDF5TransformIO. > COMP: Fix missing prefix in ITKv3ImageRegistration20Test. > BUG: Do not return SmartPointers in TimeVaryingVelocityFieldTransform > STYLE: Improve style in BinaryImageToLabelMapFilter. > BUG: Fix BinaryImageToLabelMapFilter on 1D image. > ENH: Improve precision of the joint PDF sum > BUG: Fix BinShrinkImageFilter for different input/output image types. > COMP: Fix transform type for ITKv3/IterativeClosestPoint2. > COMP: Add missing wrapping for TransformIOBaseTemplate. > BUG: gdcm::StringFilter recognizes backslash delimiter. > ENH: Bump ITK version to 4.6.1. > > MetaIO Maintainers (1): > MetaIO (reduced) > > Michka Popoff (4): > BUG: Improve SWIG version check > BUG: Add VTK_VERSION for older VTK versions > BUG: Update VTK minimum version (for release) > BUG: Fix memory leak in MetaImageIO after exception > > Vladimir S. FONOV (1): > BUG: Fixing incorrect MINC style inverse transform > > > ------------------------------ > > Message: 2 > Date: Wed, 1 Oct 2014 15:50:33 -0400 > From: Matt McCormick > To: "community at itk.org" , "insight-users at itk.org" > , ITK > Subject: Re: [ITK-users] [ANNOUNCE] ITK 4.6.1 has been released! > Message-ID: > < > CALzTN-S9DU8K8ACbgVP6L0ozXQGvcbnfXC7nz8iu_xqLTVtHsw at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Minor correction: > > > > > The next feature release of 4.6.0 is scheduled for June. > > > > The next feature release of 4.7.0 is scheduled for December. > > > ------------------------------ > > Message: 3 > Date: Thu, 02 Oct 2014 11:33:06 +0200 > From: Jo?l Schaerer > To: itk > Subject: [ITK-users] Proper chaining of filters > Message-ID: <542D1BD2.40801 at laposte.net> > Content-Type: text/plain; charset=utf-8; format=flowed > > Hi all, > > I've noticed a couple times that when building a pipeline with ITK, you > need to keep a reference to all filters before the pipeline is updated. > This seems a little counter-intuitive to me, so I would like to better > understand the issue and see if there is a way around it. > > As an example, the following code doesn't work: > > DilateType::Pointer dilate = DilateType::New(); > dilate->SetInput(thresh->GetOutput()); > dilate->SetKernel(kernel); > > dilate_filters.push_back(dilate); > for (int i=0; i<14; ++i) { > DilateType::Pointer temp = DilateType::New(); > temp->SetInput(dilate->GetOutput()); > temp->SetKernel(kernel); > dilate = temp; > } > dilate->Update(); > > Regions don't get propagated properly and I get the following exception > when writing the output: > > C++ exception with description > > "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: > itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not > fully contain requested paste IO regionPaste IO region: ImageIORegion > (0x7fff9bb72cc0) > Dimension: 3 > Index: 0 0 0 > Size: 0 0 0 > Largest possible region: ImageRegion (0x7fff9bb72bc0) > Dimension: 3 > Index: [0, 0, 0] > Size: [0, 0, 0] > " thrown in the test body. > > My guess is that the filters get destroyed before they get a chance to > be executed. If I explicitely keep references to each filter, it works: > > DilateType::Pointer dilate = DilateType::New(); > dilate->SetInput(thresh->GetOutput()); > dilate->SetKernel(kernel); > // We need to keep a reference to each filter in the pipeline before > it is updated > std::vector dilate_filters; > dilate_filters.push_back(dilate); > for (int i=0; i<14; ++i) { > DilateType::Pointer temp = DilateType::New(); > temp->SetInput(dilate_filters.back()->GetOutput()); > temp->SetKernel(kernel); > dilate = temp; > dilate_filters.push_back(temp); > } > dilate_filters.back()->Update(); > > My question is, why doesn't a filter keep a reference to the previous > filter in the pipeline? Is there a way around this? > > Thanks! > > Jo?l > > > ------------------------------ > > Message: 4 > Date: Thu, 2 Oct 2014 10:16:08 -0400 > From: Matt McCormick > To: Jo?l Schaerer > Cc: itk > Subject: Re: [ITK-users] [ITK] Proper chaining of filters > Message-ID: > v6XSg at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Jo?l, > > Calling > > temp->SetInput(dilate->GetOutput()); > > Connects the DataObject generated by dilate to the temp filter. temp > does not increment dilate's reference count, and it would be difficult > to do since the SetInput input is the DataObject, not the > ProcessObject. > > As a consequence, at least one SmartPointer needs to be kept in scope > as with your second example. > > HTH, > Matt > > On Thu, Oct 2, 2014 at 5:33 AM, Jo?l Schaerer > wrote: > > Hi all, > > > > I've noticed a couple times that when building a pipeline with ITK, you > need > > to keep a reference to all filters before the pipeline is updated. This > > seems a little counter-intuitive to me, so I would like to better > understand > > the issue and see if there is a way around it. > > > > As an example, the following code doesn't work: > > > > DilateType::Pointer dilate = DilateType::New(); > > dilate->SetInput(thresh->GetOutput()); > > dilate->SetKernel(kernel); > > > > dilate_filters.push_back(dilate); > > for (int i=0; i<14; ++i) { > > DilateType::Pointer temp = DilateType::New(); > > temp->SetInput(dilate->GetOutput()); > > temp->SetKernel(kernel); > > dilate = temp; > > } > > dilate->Update(); > > > > Regions don't get propagated properly and I get the following exception > when > > writing the output: > > > > C++ exception with description > > > "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: > > itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not > > fully contain requested paste IO regionPaste IO region: ImageIORegion > > (0x7fff9bb72cc0) > > Dimension: 3 > > Index: 0 0 0 > > Size: 0 0 0 > > Largest possible region: ImageRegion (0x7fff9bb72bc0) > > Dimension: 3 > > Index: [0, 0, 0] > > Size: [0, 0, 0] > > " thrown in the test body. > > > > My guess is that the filters get destroyed before they get a chance to be > > executed. If I explicitely keep references to each filter, it works: > > > > DilateType::Pointer dilate = DilateType::New(); > > dilate->SetInput(thresh->GetOutput()); > > dilate->SetKernel(kernel); > > // We need to keep a reference to each filter in the pipeline before > it is > > updated > > std::vector dilate_filters; > > dilate_filters.push_back(dilate); > > for (int i=0; i<14; ++i) { > > DilateType::Pointer temp = DilateType::New(); > > temp->SetInput(dilate_filters.back()->GetOutput()); > > temp->SetKernel(kernel); > > dilate = temp; > > dilate_filters.push_back(temp); > > } > > dilate_filters.back()->Update(); > > > > My question is, why doesn't a filter keep a reference to the previous > filter > > in the pipeline? Is there a way around this? > > > > Thanks! > > > > Jo?l > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the 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 > > > ------------------------------ > > Message: 5 > Date: Thu, 02 Oct 2014 16:22:24 +0200 > From: Jo?l Schaerer > To: Matt McCormick > Cc: itk > Subject: Re: [ITK-users] [ITK] Proper chaining of filters > Message-ID: <542D5FA0.8070903 at laposte.net> > Content-Type: text/plain; charset=utf-8; format=flowed > > Hi Matt, > > Thanks for the confirmation. I was thinking there might be another > mechanism I wasn't aware of. > > Jo?l > > On 10/02/2014 04:16 PM, Matt McCormick wrote: > > Hi Jo?l, > > > > Calling > > > > temp->SetInput(dilate->GetOutput()); > > > > Connects the DataObject generated by dilate to the temp filter. temp > > does not increment dilate's reference count, and it would be difficult > > to do since the SetInput input is the DataObject, not the > > ProcessObject. > > > > As a consequence, at least one SmartPointer needs to be kept in scope > > as with your second example. > > > > HTH, > > Matt > > > > On Thu, Oct 2, 2014 at 5:33 AM, Jo?l Schaerer > wrote: > >> Hi all, > >> > >> I've noticed a couple times that when building a pipeline with ITK, you > need > >> to keep a reference to all filters before the pipeline is updated. This > >> seems a little counter-intuitive to me, so I would like to better > understand > >> the issue and see if there is a way around it. > >> > >> As an example, the following code doesn't work: > >> > >> DilateType::Pointer dilate = DilateType::New(); > >> dilate->SetInput(thresh->GetOutput()); > >> dilate->SetKernel(kernel); > >> > >> dilate_filters.push_back(dilate); > >> for (int i=0; i<14; ++i) { > >> DilateType::Pointer temp = DilateType::New(); > >> temp->SetInput(dilate->GetOutput()); > >> temp->SetKernel(kernel); > >> dilate = temp; > >> } > >> dilate->Update(); > >> > >> Regions don't get propagated properly and I get the following exception > when > >> writing the output: > >> > >> C++ exception with description > >> > "/home/joel/workspace/ITK/Modules/IO/ImageBase/include/itkImageFileWriter.hxx:290: > >> itk::ERROR: ImageFileWriter(0x3130460): Largest possible region does not > >> fully contain requested paste IO regionPaste IO region: ImageIORegion > >> (0x7fff9bb72cc0) > >> Dimension: 3 > >> Index: 0 0 0 > >> Size: 0 0 0 > >> Largest possible region: ImageRegion (0x7fff9bb72bc0) > >> Dimension: 3 > >> Index: [0, 0, 0] > >> Size: [0, 0, 0] > >> " thrown in the test body. > >> > >> My guess is that the filters get destroyed before they get a chance to > be > >> executed. If I explicitely keep references to each filter, it works: > >> > >> DilateType::Pointer dilate = DilateType::New(); > >> dilate->SetInput(thresh->GetOutput()); > >> dilate->SetKernel(kernel); > >> // We need to keep a reference to each filter in the pipeline before > it is > >> updated > >> std::vector dilate_filters; > >> dilate_filters.push_back(dilate); > >> for (int i=0; i<14; ++i) { > >> DilateType::Pointer temp = DilateType::New(); > >> temp->SetInput(dilate_filters.back()->GetOutput()); > >> temp->SetKernel(kernel); > >> dilate = temp; > >> dilate_filters.push_back(temp); > >> } > >> dilate_filters.back()->Update(); > >> > >> My question is, why doesn't a filter keep a reference to the previous > filter > >> in the pipeline? Is there a way around this? > >> > >> Thanks! > >> > >> Jo?l > >> _____________________________________ > >> Powered by www.kitware.com > >> > >> Visit other Kitware open-source projects at > >> http://www.kitware.com/opensource/opensource.html > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> http://www.kitware.com/products/protraining.php > >> > >> Please keep messages on-topic and check the 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 > > > > ------------------------------ > > Message: 6 > Date: Thu, 2 Oct 2014 09:24:31 -0700 (PDT) > From: Pedro Morais > To: insight-users at itk.org > Subject: [ITK-users] 3D generalized hough transform > Message-ID: <1412267071841-7586297.post at n2.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Hi all, > > I'm wonder if ITK has an implementation of a 3D generalized hough > transform. > Do you have any idea? > > Regards, > Pedro > > > > -- > View this message in context: > http://itk-insight-users.2283740.n2.nabble.com/3D-generalized-hough-transform-tp7586297.html > Sent from the ITK Insight Users mailing list archive at Nabble.com. > > > ------------------------------ > > Message: 7 > Date: Thu, 2 Oct 2014 20:40:16 -0400 > From: Lianli Liu > To: "insight-users at itk.org" > Subject: [ITK-users] vector image registration > Message-ID: > < > CAGKqDmfV89qpnVG5tq4bvZrc6FDHhNRHrkvWg7qEXjh_pObKsQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I wonder if ITK is supporting vector image registration now? If not, any > suggestions to achieve this goal? > > Thanks! > Lianli > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141002/87f15593/attachment-0001.html > > > > ------------------------------ > > Message: 8 > Date: Fri, 3 Oct 2014 10:05:29 +0100 > From: Gianluigi Caddeo > To: insight-users at itk.org > Subject: [ITK-users] help installing ITK > Message-ID: > < > CADeTECOS-PqOswWC4H2Wo_f8eKjd24eN+eSDfRG+YK8LKF7+CA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > during my installation on an ubuntu machine I had this problem: > > > > > > > *[100%] Built target ITKv3ThinPlateSplineWarp/bin/sh: 1: > DOXYGEN_EXECUTABLE-NOTFOUND: not foundmake[2]: *** > [Utilities/Doxygen/CMakeFiles/Documentation] Errore 127make[1]: *** > [Utilities/Doxygen/CMakeFiles/Documentation.dir/all] Errore 2make: *** > [all] Errore* > But doxygen exist and stay in my */usr/bin* directory > > How can I to force ITK to search doxygen in that directory? > > thanks a lot > > Gg > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141003/ec1ddfe8/attachment-0001.html > > > > ------------------------------ > > Message: 9 > Date: Mon, 6 Oct 2014 09:58:09 +0200 > From: Arnaud Gelas > To: insight-users > Cc: Mathieu Malaterre > Subject: [ITK-users] How to remove a tag from MetaDataDictionary? > Message-ID: > < > CAK3qF+8e1kg7bN4EcM2FUYy_e3AYz-M3ZrGGwkssWz0Kvz4y2Q at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all, > > I am trying to write a DICOM file in which, the orientation (among others) > has changed in my pipeline... > > 1- After having a look > > https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919 > > It appears to me that if the orientation is in the MetaDataDictionary, it > is saved anyway into the DICOM image, there is no way to force the ImageIO > to recompute it from the image and save it ??? > If there is, can anyone give me a pointer? > > 2- Since I can't find a way to update the image orientation in > itk::GDCMImageIO, I have been looking at removing the corresponding tag > from the MetaDataDictionary. I could not find any method or any way to do > it??? > If there is, can anyone give me a pointer? > > I wish I would not have to copy the dictionary and add if statement to > avoid copying the direction... > > Thanks in advance, > Arnaud > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141006/51ca077c/attachment-0001.html > > > > ------------------------------ > > Message: 10 > Date: Mon, 6 Oct 2014 12:31:03 +0100 > From: Emma Saunders > To: "insight-users at itk.org Users" > Subject: [ITK-users] Overlap_image registration metrics > Message-ID: > 1as4oZLo5UXQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello all, > > When computing metrics for image registration, does ITK calculated the > metric for only the regions in the image that overlap? > > If so is this performed on just the initial regions that overlap or will > this region of overlap increase during registration and thus require the > region in which the metric is calculated to alter? > > Thanks for any help > > Emma > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141006/639045b5/attachment-0001.html > > > > ------------------------------ > > Message: 11 > Date: Mon, 6 Oct 2014 06:20:27 -0700 (MST) > From: Marco Ulge > To: insight-users at itk.org > Subject: [ITK-users] Texture Features extraction > Message-ID: <1412601627242-34642.post at n7.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Hello, > > i'm currently working on texture feature extraction and I'm following this > examle: > http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures > > > It works fine and basically it's all i need. The only problem is that i > need > to able to specify an arbitrary window size (which is 3 in this example) > but > as soon as i try to assign it a different value this won't work anymore and > i can't figure out why. > > Can anyone help me with this please? > > Thanks. > > Marco > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.html > Sent from the ITK - Users mailing list archive at Nabble.com. > > > ------------------------------ > > Message: 12 > Date: Mon, 06 Oct 2014 15:47:12 +0200 > From: Dominique T?pfer > To: Marco Ulge , insight-users at itk.org > Subject: Re: [ITK-users] Texture Features extraction > Message-ID: <54329D60.9030004 at toepfer-web.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Marco, > > you probably forgot to adjust the range of the for-loops. They are > running from 1 to size-2 so that the window will not "leave" the image > at its boundaries. > > HTH > Dominique > > > On 06.10.2014 15:20, Marco Ulge wrote: > > Hello, > > > > i'm currently working on texture feature extraction and I'm following > this > > examle: > > http://www.itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures > > > > > > It works fine and basically it's all i need. The only problem is that i > need > > to able to specify an arbitrary window size (which is 3 in this example) > but > > as soon as i try to assign it a different value this won't work anymore > and > > i can't figure out why. > > > > Can anyone help me with this please? > > > > Thanks. > > > > Marco > > > > > > > > -- > > View this message in context: > http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642.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 > > > > ------------------------------ > > Message: 13 > Date: Mon, 6 Oct 2014 07:18:26 -0700 (MST) > From: Marco Ulge > To: insight-users at itk.org > Subject: Re: [ITK-users] Texture Features extraction > Message-ID: <1412605106652-34644.post at n7.nabble.com> > Content-Type: text/plain; charset=us-ascii > > Thanks for your reply, so if i wanted to specify a window size of 5 (for > example) i should iterate from 1 to size - 4? > > Thanks. > > Marco > > > > -- > View this message in context: > http://itk-users.7.n7.nabble.com/ITK-users-Texture-Features-extraction-tp34642p34644.html > Sent from the ITK - Users mailing list archive at Nabble.com. > > > ------------------------------ > > Message: 14 > Date: Mon, 6 Oct 2014 10:27:10 -0400 > From: Jiahui Wang > To: insight-users at itk.org > Subject: [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer > Message-ID: > UPK2wK-ksA6v1vKak75aE1f3ea-de7sLQSTrGiQwxEpQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear All, > > I modified ImageRegistration8.cxx to run my own rigid registration. > > However, I found that the processing time of ITKv4 based > RegularStepGradientDescentOptimizer is almost 10 times more than that of > ITKv3 based one. > > The program was run on the same machine. The only difference is the ITK > libraries. > > Could anyone give me some suggestions to solve this issue? > > Thanks, > > JW > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141006/40c2b5ce/attachment-0001.html > > > > ------------------------------ > > Message: 15 > Date: Mon, 6 Oct 2014 11:08:10 -0400 > From: Matt McCormick > To: Arnaud Gelas > Cc: insight-users , Mathieu Malaterre > > Subject: Re: [ITK-users] How to remove a tag from MetaDataDictionary? > Message-ID: > < > CALzTN-TjoXUpe16JNsViVH0srU_q1oTJpVYG94G3S6a0mUD3Eg at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Arnaud, > > > > I am trying to write a DICOM file in which, the orientation (among > others) > > has changed in my pipeline... > > > > 1- After having a look > > > https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L883-L919 > > > > It appears to me that if the orientation is in the MetaDataDictionary, > it is > > saved anyway into the DICOM image, there is no way to force the ImageIO > to > > recompute it from the image and save it ??? > > If there is, can anyone give me a pointer? > > If there is a Direction on the input image, it should use it [1]. But > the DICOM tag 0020|0037 cannot be present. > > > > 2- Since I can't find a way to update the image orientation in > > itk::GDCMImageIO, I have been looking at removing the corresponding tag > from > > the MetaDataDictionary. I could not find any method or any way to do > it??? > > If there is, can anyone give me a pointer? > > > > I wish I would not have to copy the dictionary and add if statement to > avoid > > copying the direction... > > This is the method I usually apply... > > Sorry for the lack of new tricks! > Matt > > [1] > https://github.com/Kitware/ITK/blob/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L816-L828 > > > ------------------------------ > > Message: 16 > Date: Mon, 6 Oct 2014 11:12:52 -0400 > From: Matt McCormick > To: Emma Saunders > Cc: "insight-users at itk.org Users" > Subject: Re: [ITK-users] Overlap_image registration metrics > Message-ID: > < > CALzTN-SrbFWD0R7-GAPxxT0ssf2fzLN_bATjtHB+ZAyHYZjk+w at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Emma, > > > When computing metrics for image registration, does ITK calculated the > > metric for only the regions in the image that overlap? > > Yes. See, for example, [1]. > > > If so is this performed on just the initial regions that overlap or > will > > this region of overlap increase during registration and thus require the > > region in which the metric is calculated to alter? > > Yes. Ideally, as the registration progresses, the overlap increases, > and the registration becomes progressively better. > > HTH, > Matt > > [1] > http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Registration/Metricsv4/include/itkImageToImageMetricv4.hxx;h=8a6069dde32309a214229968294a14911c701dd0;hb=HEAD#l312 > > > ------------------------------ > > Message: 17 > Date: Mon, 6 Oct 2014 15:44:08 +0000 > From: Andras Lasso > To: Jiahui Wang , "insight-users at itk.org" > > Subject: Re: [ITK-users] [ITK] Speed of ITKv4 based Gradient Descent > Optimizer > Message-ID: > < > B6FC5543F5C41E479B8B89158B0C58FF179374D9 at MP-DUP-MBX-02.AD.QUEENSU.CA> > Content-Type: text/plain; charset="utf-8" > > See this long thread about this issue: > > http://slicer-devel.65872.n3.nabble.com/BRAINS-rigid-registration-td4032229.html > > Short summary: There were some performance regressions in mutual > information metric computation, threading, etc. that have been recently > fixed, so use the latest ITK version. ITKv4 uses a slightly slower but more > accurate optimizer, but if you adjust the number of samples and stopping > condition then usually the registration time only increases by about 30-50% > (and you might get better quality results). > > You can see all the changes that have been done in 3D Slicer and BRAINS > repositories to go from a 10x-100x slowdown to an approximately equivalent > registration speed with ITKv4 compared to ITKv3. > > Andras > > From: Community [mailto:community-bounces at itk.org] On Behalf Of Jiahui > Wang > Sent: Monday, October 06, 2014 10:27 AM > To: insight-users at itk.org > Subject: [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer > > Dear All, > I modified ImageRegistration8.cxx to run my own rigid registration. > > However, I found that the processing time of ITKv4 based > RegularStepGradientDescentOptimizer is almost 10 times more than that of > ITKv3 based one. > > The program was run on the same machine. The only difference is the ITK > libraries. > > Could anyone give me some suggestions to solve this issue? > Thanks, > JW > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141006/230f318a/attachment-0001.html > > > > ------------------------------ > > Message: 18 > Date: Tue, 7 Oct 2014 15:13:06 +0800 > From: Fabian Torres > To: insight-users at itk.org > Subject: [ITK-users] Polygon inside point > Message-ID: > KP5XsjnYeFWGwWbifQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all. > > I have an image that represents some pixels over the surface of an object. > Pixels in the surface have value of 1 while any other pixel has value of 0. > The pixels are not a continuous line, there are some gaps between pixels. I > want to know the region surrounded by the white pixels in my image. > > I will be working with 2D and 3D data. Is there any class implemented in > ITK that I can use? > > Thanks > > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141007/152068ea/attachment-0001.html > > > > ------------------------------ > > Message: 19 > Date: Tue, 7 Oct 2014 15:38:49 +0800 > From: Fabian Torres > To: insight-users > Subject: [ITK-users] region inside points > Message-ID: > < > CALD_Ep+OEAE8Jik0hsy8PWYGBmxTHYWoRZOoFQaP2OqT1P_GyQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi all. > > I have an image that represents some pixels over the surface of an object. > Pixels in the surface have value of 1 while any other pixel has value of 0. > The pixels are not a continuous line, there are some gaps between pixels. I > want to know the region surrounded by the white pixels in my image. > > I will be working with 2D and 3D data. Is there any class implemented in > ITK that I can use? > > Thanks > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141007/2f835b53/attachment-0001.html > > > > ------------------------------ > > Message: 20 > Date: Tue, 7 Oct 2014 07:40:40 +0000 > From: Gib Bogle > To: Fabian Torres , insight-users > > Subject: Re: [ITK-users] region inside points > Message-ID: > < > BD80F91C3E2E394894ED4780703D7F9E826C670A at uxcn10-tdc06.UoA.auckland.ac.nz> > > Content-Type: text/plain; charset="iso-8859-1" > > Maybe you could do something with BinaryImageDilateFilter. > ________________________________ > From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian > Torres [dae.wong at gmail.com] > Sent: Tuesday, 7 October 2014 8:38 p.m. > To: insight-users > Subject: [ITK-users] region inside points > > Hi all. > > I have an image that represents some pixels over the surface of an object. > Pixels in the surface have value of 1 while any other pixel has value of 0. > The pixels are not a continuous line, there are some gaps between pixels. > I want to know the region surrounded by the white pixels in my image. > > I will be working with 2D and 3D data. Is there any class implemented in > ITK that I can use? > > Thanks > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, > dae.wong at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141007/4f28baa5/attachment-0001.html > > > > ------------------------------ > > Message: 21 > Date: Tue, 7 Oct 2014 07:46:17 +0000 > From: Gib Bogle > To: Fabian Torres , insight-users > > Subject: Re: [ITK-users] region inside points > Message-ID: > < > BD80F91C3E2E394894ED4780703D7F9E826C671B at uxcn10-tdc06.UoA.auckland.ac.nz> > > Content-Type: text/plain; charset="iso-8859-1" > > Sorry, I misread your post Fabian - I read it as you wanting the region > _surrounding_ the white pixels. But dilate might be usable to fill the > gaps, followed by skeletonization. > ________________________________ > From: Insight-users [insight-users-bounces at itk.org] on behalf of Gib > Bogle [g.bogle at auckland.ac.nz] > Sent: Tuesday, 7 October 2014 8:40 p.m. > To: Fabian Torres; insight-users > Subject: Re: [ITK-users] region inside points > > Maybe you could do something with BinaryImageDilateFilter. > ________________________________ > From: Insight-users [insight-users-bounces at itk.org] on behalf of Fabian > Torres [dae.wong at gmail.com] > Sent: Tuesday, 7 October 2014 8:38 p.m. > To: insight-users > Subject: [ITK-users] region inside points > > Hi all. > > I have an image that represents some pixels over the surface of an object. > Pixels in the surface have value of 1 while any other pixel has value of 0. > The pixels are not a continuous line, there are some gaps between pixels. > I want to know the region surrounded by the white pixels in my image. > > I will be working with 2D and 3D data. Is there any class implemented in > ITK that I can use? > > Thanks > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, > dae.wong at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141007/4dee4e3f/attachment-0001.html > > > > ------------------------------ > > Message: 22 > Date: Tue, 7 Oct 2014 16:05:24 +0800 > From: Fabian Torres > To: Gib Bogle > Cc: insight-users > Subject: Re: [ITK-users] region inside points > Message-ID: > < > CALD_Ep+NkNKwMdz18XLQ3ygxBAdCwK0AGFBZcNPT3MfUpC_ARA at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Gib. > > Thanks for the quick response. The problem of using dilation and > skeletonization is that some times the gap between pixels is big, and I > will have to work with different and big structural elements to be sure > that all the gaps were eliminated. > > I was hoping to find a class that works similar to a convex hull (it does > not have to be convex) algorithm and then find the region surrounded by the > hull. > > Thanks > > On Tue, Oct 7, 2014 at 3:46 PM, Gib Bogle wrote: > > > Sorry, I misread your post Fabian - I read it as you wanting the region > > _surrounding_ the white pixels. But dilate might be usable to fill the > > gaps, followed by skeletonization. > > ------------------------------ > > *From:* Insight-users [insight-users-bounces at itk.org] on behalf of Gib > > Bogle [g.bogle at auckland.ac.nz] > > *Sent:* Tuesday, 7 October 2014 8:40 p.m. > > *To:* Fabian Torres; insight-users > > *Subject:* Re: [ITK-users] region inside points > > > > Maybe you could do something with BinaryImageDilateFilter. > > ------------------------------ > > *From:* Insight-users [insight-users-bounces at itk.org] on behalf of > Fabian > > Torres [dae.wong at gmail.com] > > *Sent:* Tuesday, 7 October 2014 8:38 p.m. > > *To:* insight-users > > *Subject:* [ITK-users] region inside points > > > > Hi all. > > > > I have an image that represents some pixels over the surface of an > > object. Pixels in the surface have value of 1 while any other pixel has > > value of 0. > > The pixels are not a continuous line, there are some gaps between pixels. > > I want to know the region surrounded by the white pixels in my image. > > > > I will be working with 2D and 3D data. Is there any class implemented in > > ITK that I can use? > > > > Thanks > > -- > > Fabi?n Torres Robles > > Maestria en Ciencias en Ingenier?a Electr?nica > > Ingenier?a en Sistemas Electr?nicos > > tel. 58081280, 0445534661338 > > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > > > > > > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://public.kitware.com/pipermail/insight-users/attachments/20141007/6202b2cc/attachment.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Insight-users mailing list > Insight-users at itk.org > http://public.kitware.com/mailman/listinfo/insight-users > > > ------------------------------ > > End of Insight-users Digest, Vol 126, Issue 2 > ********************************************* > -------------- 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 65104355 at qq.com Tue Oct 7 10:06:17 2014 From: 65104355 at qq.com (=?ISO-8859-1?B?SmVycnk=?=) Date: Tue, 7 Oct 2014 22:06:17 +0800 Subject: [ITK] [ITK-users] Detect tube and ball typed objects in airway CT image. Message-ID: I am developing a segmentation algorithm that requires detect tube and ball typed airways in CT image. I tried canny, log, hessian etc. None of them looks promising. Any advice will be appreicated. Regards, Jerry -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: B3AB03A0 at 8E359815.59F33354.jpg Type: image/jpeg Size: 79219 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: tubecircle.jpg Type: application/octet-stream Size: 79219 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From blowekamp at mail.nih.gov Tue Oct 7 10:18:10 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 7 Oct 2014 10:18:10 -0400 Subject: [ITK] [ITK-users] Detect tube and ball typed objects in airway CT image. In-Reply-To: References: Message-ID: <6FF244AB-597A-4CFB-8644-3E918F42F938@mail.nih.gov> Interesting. Have you considered looking at the ratio of a gaussian and a laplacian at certain scales to detect the feature you are interested in? Brad Brad On Oct 7, 2014, at 10:06 AM, Jerry <65104355 at qq.com> wrote: > I am developing a segmentation algorithm that requires detect tube and ball typed airways in CT image. I tried canny, log, hessian etc. None of them looks promising. Any advice will be appreicated. > > Regards, > > Jerry > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 matt.mccormick at kitware.com Tue Oct 7 10:28:40 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 7 Oct 2014 10:28:40 -0400 Subject: [ITK] [ITK-users] Segmentation fault when using BSplineScatteredDataPointSetToImageFilter for 3D image In-Reply-To: <44223E94-F14E-4CF5-A0D6-C667CD3DDE29@unistra.fr> References: <44223E94-F14E-4CF5-A0D6-C667CD3DDE29@unistra.fr> Message-ID: Hi Fran?ois, Yes, it should work on a 3D Image -- itkBSplineScatteredDataPointSetToImageFilterTest4.cxx is for ParametericDimension = 3. HTH, Matt On Tue, Oct 7, 2014 at 4:11 AM, francois rousseau wrote: > Hi everyone, > > I?m trying to use the BSplineScatteredDataPointSetToImageFilter. No problem > when applying it on 2D images (using > itkBSplineScatteredDataPointSetToImageFilterTest.cxx). > However, after setting const unsigned int ParametricDimension = 3; it > crashes when I try to apply it on 3D image (segmentation fault). Can this > code be used for 3D images? > > Thank you > Fran?ois > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 Tue Oct 7 10:43:55 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 7 Oct 2014 10:43:55 -0400 Subject: [ITK] [ITK-users] Detect tube and ball typed objects in airway CT image. In-Reply-To: References: Message-ID: Hi Jerry, The LesionSizingToolkit [1], and TubeTK [2], both based on ITK, may be helpful here. The LesionSizeToolkit is available as a Remote Module. It can be built by setting Module_LesionSizingToolkit=ON in your CMake configuration. HTH, Matt [1] http://public.kitware.com/LesionSizingKit/index.php/Main_Page [2] http://tubetk.org/ On Tue, Oct 7, 2014 at 10:06 AM, Jerry <65104355 at qq.com> wrote: > I am developing a segmentation algorithm that requires detect tube and > ball typed airways in CT image. I tried canny, log, hessian etc. None of > them looks promising. Any advice will be appreicated. > > Regards, > > Jerry > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 -------------- A non-text attachment was scrubbed... Name: B3AB03A0 at 8E359815.59F33354.jpg Type: image/jpeg Size: 79219 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Oct 7 11:52:56 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 7 Oct 2014 11:52:56 -0400 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/u/0/events/cs71fpcqpa7l9me2vq45mi61mq8 To get regular invites to these events, join the ITK Bar Camp G+ Community: https://plus.google.com/u/0/communities/111375098792764998322 All are welcome. Hope to talk to you then! From wjhzwy at gmail.com Tue Oct 7 13:44:47 2014 From: wjhzwy at gmail.com (Jiahui Wang) Date: Tue, 7 Oct 2014 13:44:47 -0400 Subject: [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent Optimizer In-Reply-To: References: Message-ID: Thank you very much, Andras. Jiahui On Mon, Oct 6, 2014 at 11:44 AM, Andras Lasso wrote: > See this long thread about this issue: > > > http://slicer-devel.65872.n3.nabble.com/BRAINS-rigid-registration-td4032229.html > > > > Short summary: There were some performance regressions in mutual > information metric computation, threading, etc. that have been recently > fixed, so use the latest ITK version. ITKv4 uses a slightly slower but more > accurate optimizer, but if you adjust the number of samples and stopping > condition then usually the registration time only increases by about 30-50% > (and you might get better quality results). > > > > You can see all the changes that have been done in 3D Slicer and BRAINS > repositories to go from a 10x-100x slowdown to an approximately equivalent > registration speed with ITKv4 compared to ITKv3. > > > > Andras > > > > *From:* Community [mailto:community-bounces at itk.org] *On Behalf Of *Jiahui > Wang > *Sent:* Monday, October 06, 2014 10:27 AM > *To:* insight-users at itk.org > *Subject:* [ITK] [ITK-users] Speed of ITKv4 based Gradient Descent > Optimizer > > > > Dear All, > > I modified ImageRegistration8.cxx to run my own rigid registration. > > > However, I found that the processing time of ITKv4 based > RegularStepGradientDescentOptimizer is almost 10 times more than that of > ITKv3 based one. > > > The program was run on the same machine. The only difference is the ITK > libraries. > > Could anyone give me some suggestions to solve this issue? > > Thanks, > > JW > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Tue Oct 7 17:00:32 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 7 Oct 2014 17:00:32 -0400 Subject: [ITK] Network Resources Down Thursday, 5:30 PM Message-ID: Hi, A note that there will be a scheduled downtime for ITK network resources such as CDash Git Wiki Homepage Gerrit on Thursday, October 9th, 5:30 PM lasting approximately 10-20 minutes. Thanks, Matt From dae.wong at gmail.com Wed Oct 8 06:51:51 2014 From: dae.wong at gmail.com (Fabian Torres) Date: Wed, 8 Oct 2014 18:51:51 +0800 Subject: [ITK] [ITK-users] region inside points In-Reply-To: References: Message-ID: Hi all. Just wanted to let you know I solved the problem for 2D by doing the next: Arrange the white pixels in clockwise order 1. Calculate the centroid of the region define by the white pixels 2. Calculate the angle between the white pixels and the centroid using atan2( ) 3. Sort the white pixels in clockwise order. Draw a line between the pixels to fill the gap between points to obtain a closed contour 1. Using LineIterator to draw lines between the clockwise ordered points Fill the region inside the close contour. 1. Using GrayScaleFillholeImageFilter. I don?t know if this is a nice solution but it works for now. I will try to use this approach for 3D images, processing them slice by slice. I think I can use the itkSliceBySliceImageFilter, since I create an itk filter that outputs the closed contour image, but I don?t know if this is going to work. If any one have any advice on this matter it would be appreciated. Greetings On Tue, Oct 7, 2014 at 4:08 PM, Gib Bogle wrote: > Maybe there is a way to use a rolling ball. Richard Beare has some > morphological filters that might be applicable, but I think it will always > be a bit complicated. > ------------------------------ > *From:* Fabian Torres [dae.wong at gmail.com] > *Sent:* Tuesday, 7 October 2014 9:05 p.m. > *To:* Gib Bogle > *Cc:* insight-users > > *Subject:* Re: [ITK-users] region inside points > > Hi Gib. > > Thanks for the quick response. The problem of using dilation and > skeletonization is that some times the gap between pixels is big, and I > will have to work with different and big structural elements to be sure > that all the gaps were eliminated. > > I was hoping to find a class that works similar to a convex hull (it > does not have to be convex) algorithm and then find the region surrounded > by the hull. > > Thanks > > On Tue, Oct 7, 2014 at 3:46 PM, Gib Bogle wrote: > >> Sorry, I misread your post Fabian - I read it as you wanting the region >> _surrounding_ the white pixels. But dilate might be usable to fill the >> gaps, followed by skeletonization. >> ------------------------------ >> *From:* Insight-users [insight-users-bounces at itk.org] on behalf of Gib >> Bogle [g.bogle at auckland.ac.nz] >> *Sent:* Tuesday, 7 October 2014 8:40 p.m. >> *To:* Fabian Torres; insight-users >> *Subject:* Re: [ITK-users] region inside points >> >> Maybe you could do something with BinaryImageDilateFilter. >> ------------------------------ >> *From:* Insight-users [insight-users-bounces at itk.org] on behalf of >> Fabian Torres [dae.wong at gmail.com] >> *Sent:* Tuesday, 7 October 2014 8:38 p.m. >> *To:* insight-users >> *Subject:* [ITK-users] region inside points >> >> Hi all. >> >> I have an image that represents some pixels over the surface of an >> object. Pixels in the surface have value of 1 while any other pixel has >> value of 0. >> The pixels are not a continuous line, there are some gaps between pixels. >> I want to know the region surrounded by the white pixels in my image. >> >> I will be working with 2D and 3D data. Is there any class implemented >> in ITK that I can use? >> >> Thanks >> -- >> Fabi?n Torres Robles >> Maestria en Ciencias en Ingenier?a Electr?nica >> Ingenier?a en Sistemas Electr?nicos >> tel. 58081280, 0445534661338 >> e-mail fabian.trobles at gmail.com, dae.wong at gmail.com >> > > > > -- > Fabi?n Torres Robles > Maestria en Ciencias en Ingenier?a Electr?nica > Ingenier?a en Sistemas Electr?nicos > tel. 58081280, 0445534661338 > e-mail fabian.trobles at gmail.com, dae.wong at gmail.com > -- Fabi?n Torres Robles Maestria en Ciencias en Ingenier?a Electr?nica Ingenier?a en Sistemas Electr?nicos tel. 58081280, 0445534661338 e-mail fabian.trobles at gmail.com, dae.wong at gmail.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 alfonso.castro at udc.es Wed Oct 8 14:13:43 2014 From: alfonso.castro at udc.es (Alfonso Castro) Date: Wed, 08 Oct 2014 20:13:43 +0200 Subject: [ITK] [ITK-users] Problem compiling ITK 4.6.1 Message-ID: <2757769.bt995I62FB@hinata> Hi. I'm trying to compile ITK 4.6.1 on OpenSuSE 13.1 with CUDA 6.5 from NVIDIA. Whwn I turn on the option of Module_SmoothingRecursiveYvvGaussianFilter and Module_VariationalRegistration with ITK_USE_GPU option. Make gives the follow errors: Building CXX object Modules/Remote/SmoothingRecursiveYvvGaussianFilter/src/CMakeFiles/SmoothingRecursiveYvvGaussianFilter.dir/GPUSmoothingRecursiveYvvGaussianImageFilterKernel.cxx.o In file included from /usr/local/cuda-6.5/include/CL/opencl.h:44:0, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkOpenCLUtil.h:36, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/SmoothingRecursiveYvvGaussianFilter/include/itkGPUSmoothingRecursiveYvvGaussianImageFilter.h:29, from /opt/mia/itk/Modules/Remote/SmoothingRecursiveYvvGaussianFilter/src/GPUSmoothingRecursiveYvvGaussianImageFilterKernel.cxx:1: /usr/local/cuda-6.5/include/CL/cl_gl_ext.h:44:4: warning: "/*" within comment [-Wcomment] * /* cl_VEN_extname extension */ ^ In file included from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkGPUImage.h:284:0, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkGPUKernelManager.h:30, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkGPUImageToImageFilter.h:22, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/SmoothingRecursiveYvvGaussianFilter/include/itkGPUSmoothingRecursiveYvvGaussianImageFilter.h:30, from /opt/mia/itk/Modules/Remote/SmoothingRecursiveYvvGaussianFilter/src/GPUSmoothingRecursiveYvvGaussianImageFilterKernel.cxx:1: /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkGPUImage.hxx: In member function ?virtual void itk::GPUImage::Graft(const itk::DataObject*)?: /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Core/GPUCommon/include/itkGPUImage.hxx:188:56: warning: typedef ?GPUImageDataSuperclassPointer? locally defined but not used [-Wunused-local-typedefs] typedef typename GPUImageDataSuperclass::Pointer GPUImageDataSuperclassPointer; ^ Linking CXX static library ../../../../lib/libSmoothingRecursiveYvvGaussianFilter.a [100%] Built target SmoothingRecursiveYvvGaussianFilter Scanning dependencies of target SplitComponents-all [100%] Built target SplitComponents-all Scanning dependencies of target VariationalRegistration-all [100%] Built target VariationalRegistration-all Scanning dependencies of target VariationalRegistration [100%] Building CXX object Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/VariationalRegistrationMain.cxx.o In file included from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationFilter.h:24:0, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationMultiResolutionFilter.h:24, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/src/VariationalRegistrationMain.cxx:60: /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationFunction.h:156:11: error: duplicate ?virtual? virtual virtual void InitializeIteration(); ^ make[2]: *** [Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/VariationalRegistrationMain.cxx.o] Erro 1 make[1]: *** [Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/all] Erro 2 make: *** [all] Erro 2 If I deactivated the GPU option only, I obtained: [ 18%] Building CXX object Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/VariationalRegistrationMain.cxx.o In file included from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationFilter.h:24:0, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationMultiResolutionFilter.h:24, from /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/src/VariationalRegistrationMain.cxx:60: /opt/mia/fuentes/InsightToolkit-4.6.1/Modules/Remote/VariationalRegistration/include/itkVariationalRegistrationFunction.h:156:11: error: duplicate ?virtual? virtual virtual void InitializeIteration(); ^ make[2]: *** [Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/VariationalRegistrationMain.cxx.o] Erro 1 make[1]: *** [Modules/Remote/VariationalRegistration/src/CMakeFiles/VariationalRegistration.dir/all] Erro 2 make: *** [all] Erro 2 If I deactivated GPU and Module_VariationalRegistration, ITK compile without problem. Is there some solution or walk around for those errors? Thanks. Alfonso Faculty of Computer Science University of A Coruna _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 curiale at gmail.com Thu Oct 9 10:43:03 2014 From: curiale at gmail.com (=?iso-8859-1?Q?Ariel_Hern=E1n_Curiale?=) Date: Thu, 9 Oct 2014 16:43:03 +0200 Subject: [ITK] [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members In-Reply-To: References: Message-ID: <2A6589EB-D292-4362-8863-D4804ADE41EC@gmail.com> Hi Matt, Is there any chance to see the video of the meeting on you tube, for example ? Cheers __________________________________ | Ariel Hern?n Curiale Ph.D Candidate | ETSI Telecomunicaci?n | Universidad de Valladolid | Campus Miguel Delibes | 47011 Valladolid, Spain | Phone: 983-423000 ext. 5590 | Web: www.curiale.com.ar |_________________________________ On 07/10/2014, at 17:52, Matt McCormick wrote: > On Friday, 11:00 AM Eastern USA time, an ITK development conference, > > https://plus.google.com/u/0/events/cs71fpcqpa7l9me2vq45mi61mq8 > > > To get regular invites to these events, join the ITK Bar Camp G+ Community: > > https://plus.google.com/u/0/communities/111375098792764998322 > > > All are welcome. Hope to talk to you then! > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From handongfeng at gmail.com Thu Oct 9 15:54:20 2014 From: handongfeng at gmail.com (Dongfeng Han) Date: Thu, 9 Oct 2014 15:54:20 -0400 Subject: [ITK] [ITK-users] TransformMatrix order in MHD file Message-ID: Dear ITK users, Now I have a 3x3 TransformMatrix , when I write to mhd file, it just one line. I should write as row order or column order? thanks dongfeng - -------------- 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 fbudin at email.unc.edu Fri Oct 10 08:35:04 2014 From: fbudin at email.unc.edu (Budin, Francois) Date: Fri, 10 Oct 2014 12:35:04 +0000 Subject: [ITK] [ITK-users] itkTransformFileReaderTemplate In-Reply-To: <4FAFFD37-9479-4FF9-ACB7-27C50195B685@unc.edu> References: <4FAFFD37-9479-4FF9-ACB7-27C50195B685@unc.edu> Message-ID: Hello, I use to read transform files with itkTransformFileReader, but I discovered the new class in itk4.5 and above called itkTransformFileReaderTemplate. This class seems very convenient as it converts my transforms from let?s say float to double automatically if my transform file is a float transform, but if my reader is instantiated as double. However, I was wondering if there is a way to know the original type in which the transform in the file is encoded. I would like to be able to know if my file contains a float or a double transform (without manually reading the transform file myself). Sincerely, Francois _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From hans-johnson at uiowa.edu Fri Oct 10 08:37:26 2014 From: hans-johnson at uiowa.edu (Johnson, Hans J) Date: Fri, 10 Oct 2014 12:37:26 +0000 Subject: [ITK] [ITK-users] itkTransformFileReaderTemplate Message-ID: Ali Ghayoor in my lab did this work. I?ll allow him to respond appropriately today. Hans On 10/10/14, 7:35 AM, "Budin, Francois" wrote: >Hello, > >I use to read transform files with itkTransformFileReader, but I >discovered the new class in itk4.5 and above called >itkTransformFileReaderTemplate. This class seems very convenient as it >converts my transforms from let?s say float to double automatically if my >transform file is a float transform, but if my reader is instantiated as >double. However, I was wondering if there is a way to know the original >type in which the transform in the file is encoded. I would like to be >able to know if my file contains a float or a double transform (without >manually reading the transform file myself). >Sincerely, > >Francois >_____________________________________ >Powered by www.kitware.com > >Visit other Kitware open-source projects at >http://www.kitware.com/opensource/opensource.html > >Kitware offers ITK Training Courses, for more information visit: >http://www.kitware.com/products/protraining.php > >Please keep messages on-topic and check the ITK FAQ at: >http://www.itk.org/Wiki/ITK_FAQ > >Follow this link to subscribe/unsubscribe: >http://public.kitware.com/mailman/listinfo/insight-users ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 alii.ghayoor at gmail.com Fri Oct 10 14:40:55 2014 From: alii.ghayoor at gmail.com (Ali Ghayoor) Date: Fri, 10 Oct 2014 13:40:55 -0500 Subject: [ITK] [ITK-users] itkTransformFileReaderTemplate In-Reply-To: References: Message-ID: Well, I am not sure whether there is a way to know about the original precision type of transform parameters before reading them in ITK. Based on the reader class implementation, the parameters precision types are casted to the request type (float or double) instantly while reading the parameters from the transform buffer, so we don?t need any knowledge about their current type. Ali On 10/10/14, 7:37 AM, "Johnson, Hans J" wrote: >Ali Ghayoor in my lab did this work. I?ll allow him to respond >appropriately today. > >Hans > > >On 10/10/14, 7:35 AM, "Budin, Francois" wrote: > >>Hello, >> >>I use to read transform files with itkTransformFileReader, but I >>discovered the new class in itk4.5 and above called >>itkTransformFileReaderTemplate. This class seems very convenient as it >>converts my transforms from let?s say float to double automatically if my >>transform file is a float transform, but if my reader is instantiated as >>double. However, I was wondering if there is a way to know the original >>type in which the transform in the file is encoded. I would like to be >>able to know if my file contains a float or a double transform (without >>manually reading the transform file myself). >>Sincerely, >> >>Francois >>_____________________________________ >>Powered by www.kitware.com >> >>Visit other Kitware open-source projects at >>http://www.kitware.com/opensource/opensource.html >> >>Kitware offers ITK Training Courses, for more information visit: >>http://www.kitware.com/products/protraining.php >> >>Please keep messages on-topic and check the ITK FAQ at: >>http://www.itk.org/Wiki/ITK_FAQ >> >>Follow this link to subscribe/unsubscribe: >>http://public.kitware.com/mailman/listinfo/insight-users > > > >________________________________ >Notice: This UI Health Care e-mail (including attachments) is covered by >the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is >confidential and may be legally privileged. If you are not the intended >recipient, you are hereby notified that any retention, dissemination, >distribution, or copying of this communication is strictly prohibited. >Please reply to the sender that you have received the message in error, >then delete it. Thank you. >________________________________ >_____________________________________ >Powered by www.kitware.com > >Visit other Kitware open-source projects at >http://www.kitware.com/opensource/opensource.html > >Kitware offers ITK Training Courses, for more information visit: >http://www.kitware.com/products/protraining.php > >Please keep messages on-topic and check the 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 bschaffer at superstem.org Sat Oct 11 14:59:03 2014 From: bschaffer at superstem.org (Dr Bernhard Schaffer) Date: Sat, 11 Oct 2014 20:59:03 +0200 Subject: [ITK] Hello & beginners question Message-ID: <004c01cfe585$6e5fb1d0$4b1f1570$@superstem.org> Hi to all, I've just signed up to this list, so please be patient with me and presumably dumb questions. Potentially a lot of questions. I'm still trying to get a grip on ITK in general. I'm using it as an extension in another application, where I already have images & visualization, so I'm mainly interest in utilizing some of the more advanced image-computation algorithms. So far I've been to the usual suspects of information (ITK webpage, itkWiki, InsightSoftwarGuide-Book, Doxygen documentation) and I've been able to get ITK compiled and incorporated in my project (on a basic level). However, quite a lot of itk-concepts are strange/new to me and the syntax is not always clear to me neither. Upfront question: Is it generally better to ask (itk) coding-related questions in this group, or on a more general platform like StackOverlow with the [itk] tag ? (First) coding question: Right now, I'm looking for simple code/syntax example for the use of EvaluatePosition(). I've seen the method in the Doxygen documentation, but so far I've not found a good example code anywhere and the parameters are a bit obscure to me. What I'm trying to do is the following: 1. Load a set of vertices (2D) into the VoronoiDiagram2DGenerator 2. Generate the diagram (using the size of an existing image as outer boundary) 3. Test points of the image ( a subset ) against the generated VoronoiDiagram to label them with the VoronoiCellIndex 4. Eventually label all of the points of my image to create a simple Voronoi label map from my image. Steps 1 & 2 are pretty clear to me, as they are in the VoronoiDiagram WikiExample (http://www.itk.org/Wiki/ITK/Examples/Segmentation/WishList/VoronoiDiagram2D Generator) Step 3 is where I would need some example code. (Maybe as an extension to the example above?) Step 4 would follow, but if there is a smarter/faster way of creating such a "pixelated" VoronoiDiagram, I would love to see some example code as well. Thanks in advance, Bernhard -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Sun Oct 12 22:49:24 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 12 Oct 2014 22:49:24 -0400 Subject: [ITK] [ITK-users] vector image registration In-Reply-To: References: Message-ID: Hi Lianli, No, ITK does not have any vector image registration methods yet. There could be many approaches here that are often problem specific. Extracting a scalar pixel value from the vectors for application in the metric is a workable approach. Hope this helps, Matt On Thu, Oct 2, 2014 at 8:40 PM, Lianli Liu wrote: > Hi all, > > I wonder if ITK is supporting vector image registration now? If not, any > suggestions to achieve this goal? > > Thanks! > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 stnava at gmail.com Sun Oct 12 22:59:29 2014 From: stnava at gmail.com (brian avants) Date: Sun, 12 Oct 2014 22:59:29 -0400 Subject: [ITK] [ITK-users] vector image registration In-Reply-To: References: Message-ID: Both: itkMultiGradientImageToImageMetricv4RegistrationTest.cxx and itkMeanSquaresImageToImageMetricv4VectorRegistrationTest.cxx can achieve some form of vector image registration. but it depends on what you mean by *vector*. brian On Sun, Oct 12, 2014 at 10:49 PM, Matt McCormick wrote: > Hi Lianli, > > No, ITK does not have any vector image registration methods yet. > There could be many approaches here that are often problem specific. > Extracting a scalar pixel value from the vectors for application in > the metric is a workable approach. > > Hope this helps, > Matt > > On Thu, Oct 2, 2014 at 8:40 PM, Lianli Liu wrote: > > Hi all, > > > > I wonder if ITK is supporting vector image registration now? If not, any > > suggestions to achieve this goal? > > > > Thanks! > > Lianli > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Mon Oct 13 11:11:20 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 13 Oct 2014 11:11:20 -0400 Subject: [ITK] [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members In-Reply-To: <2A6589EB-D292-4362-8863-D4804ADE41EC@gmail.com> References: <2A6589EB-D292-4362-8863-D4804ADE41EC@gmail.com> Message-ID: Hi Ariel, I'll see if we can record and upload the audio next time. Thanks, Matt On Thu, Oct 9, 2014 at 10:43 AM, Ariel Hern?n Curiale wrote: > Hi Matt, > Is there any chance to see the video of the meeting on you tube, for example > ? > > Cheers > __________________________________ > | Ariel Hern?n Curiale Ph.D Candidate > | ETSI Telecomunicaci?n > | Universidad de Valladolid > | Campus Miguel Delibes > | 47011 Valladolid, Spain > | Phone: 983-423000 ext. 5590 > | Web: www.curiale.com.ar > |_________________________________ > > On 07/10/2014, at 17:52, Matt McCormick wrote: > > On Friday, 11:00 AM Eastern USA time, an ITK development conference, > > https://plus.google.com/u/0/events/cs71fpcqpa7l9me2vq45mi61mq8 > > > To get regular invites to these events, join the ITK Bar Camp G+ Community: > > https://plus.google.com/u/0/communities/111375098792764998322 > > > All are welcome. Hope to talk to you then! > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > From matt.mccormick at kitware.com Mon Oct 13 11:20:13 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 13 Oct 2014 11:20:13 -0400 Subject: [ITK] [ITK-users] TransformMatrix order in MHD file In-Reply-To: References: Message-ID: Hi Dongfeng, Column order. See itkImageIODirection3DTest [1] [2] for reference. HTH, Matt [1] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/IO/ImageBase/test/itkImageIODirection3DTest.cxx;h=dc0f351944bc9dc293d95cf6ffb01bb832059bf8;hb=HEAD [2] http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/IO/ImageBase/test/CMakeLists.txt;h=1f8c20ec0ade96b860d000e3a777ee0d613cc467;hb=HEAD#l217 On Thu, Oct 9, 2014 at 3:54 PM, Dongfeng Han wrote: > Dear ITK users, > > Now I have a 3x3 TransformMatrix , when I write to mhd file, it just one > line. > I should write as row order or column order? > > thanks > > dongfeng > - > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 noreply at insightsoftwareconsortium.org Mon Oct 13 14:29:18 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 14:29:18 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Challenge on Endocardial Three-dimensional Ultrasound Segmentation (CETUS) Message-ID: <20141013182918.87F7E3D6C171@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Challenge on Endocardial Three-dimensional Ultrasound Segmentation (CETUS) Authors: Bernard O., Heyde B., Alessandrini M., Barbosa D., Camarasu-Pop S., Cervenansky F., Valette S., Mirea O., Galli E., Geleijnse M., Papachristidis A., Bosch J.G., D'hooge J. Abstract: Real-time 3D echocardiography has already been shown to be an accurate tool for left ventricular (LV) volume assessment. However, LV border identification remains a challenging task, mainly because of the low contrast of the images combined with drop-out artifacts. Many (semi-)automatic algorithms have been proposed to segment the LV border, but a systematic and fair comparison between such methods has so far been impossible due to a lack of publicly available common database. The aim of this MICCAI challenge was to gather researchers around the field of LV segmentation in 3D cardiac ultrasound by providing a common database to compare algorithms directly. The proposed platform will allow a consistent evaluation and ranking of the current state-of-the-art segmentation solutions and will contribute to a faster clinical translation of groundbreaking technical advances. The purpose of this paper is to describe the technical aspects of the generation of the database, give an ov erview of the ranking strategy and the outline of the challenge itself. Download and review this publication at: http://hdl.handle.net/10380/3479 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 15:20:14 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 15:20:14 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Clinical Expert Delineation of 3D Left Ventricular Echocardiograms for the CETUS Segmentation Challenge Message-ID: <20141013192014.688FB3D6C4F4@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Clinical Expert Delineation of 3D Left Ventricular Echocardiograms for the CETUS Segmentation Challenge Authors: Papachristidis A., Geleijnse M.L., Galli E., Heyde B., Alessandrini M., Barbosa D., Monaghan M.J., Bernard O., D'hooge J., Bosch J.G. Abstract: Within the framework of the CETUS challenge, forty-five 3D echocardiographic datasets have been acquired and segmented independently by three clinical experts from different hospitals. The goal was to generate a well-established ground truth of validated expert contours on this broad range of images from different ultrasound vendors, for a number of common pathologies. Image data were acquired and segmented according to a specifically designed protocol. Since there is no clear standard or guideline for segmentation for 3DUS, we defined a tracing consensus which results in clinically acceptable and reproducible contours. Tracing was performed in four longitudinal and five transversal 3D-derived 2D planes in ED and ES. 3D contours were constructed from these tracings. If the contours or their clinical parameters differed by more than a predefined level, the tracings were compared and the experts would reach a consensus interpretation on the best segmentation. One or more experts would then adapt their tracings. Final distance differences in contours were 0.77??0.18mm for the training set and 0.82??0.27mmfor the testing set. For the training set, 69% of contours were retraced. For the testing set, 76% of contours were retraced. The used protocol resulted in well-established ground truth contours. Download and review this publication at: http://hdl.handle.net/10380/3480 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 15:40:38 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 15:40:38 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Fast Tracking of the Left Ventricle Using Global Anatomical Affine Optical Flow and Local Recursive Block Matching Message-ID: <20141013194038.520803D6C2EB@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Fast Tracking of the Left Ventricle Using Global Anatomical Affine Optical Flow and Local Recursive Block Matching Authors: Barbosa D., Friboulet D., D'hooge J., Bernard O. Abstract: We present a novel method for segmentation and tracking of the left ventricle (LV) in 4D ultrasound sequences using a combination of automatic segmentation at the end-diastolic frame and tracking using both a global optical flow-based tracker and local block matching. The core novelty of the proposed algorithm relies on the recursive formulation of the block-matching problem, which introduces temporal consistency on the patterns being tracked. The proposed method offers a competitive solution, with average segmentation errors of 2.29 and 2.26mm in the training (#=15) and testing (#=15) datasets respectively. Download and review this publication at: http://hdl.handle.net/10380/3481 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 15:47:08 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 15:47:08 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Automatized Evaluation of the Left Ventricular Ejection Fraction from Echocardiographic Images Using Graph Cut Message-ID: <20141013194708.C4BD63D6C4EC@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Automatized Evaluation of the Left Ventricular Ejection Fraction from Echocardiographic Images Using Graph Cut Authors: Bernier M., Jodoin P., Lalande A. Abstract: In this paper, we present a fast and interactive graph cut method for 3D segmentation of the endocardial wall of the left ventricle (LV) given 3D echocardiographic images. This is a challenging task due to the poor contrast and the low signal-to-noise ratio typical of echocardiographic images. The method is carried out in 3 steps. First, 3D sampling of the LV cavity is made in a spherical-cylindrical coordinate system. Then, a gradient-based energy term is assigned to each voxel, some of which being given an infinite energy to make sure the resulting volume passes through key anatomical points. Then, a graph-cut procedure provides delineation of the endocardial surface. Results obtained on 30 exams from the 2014 CETUS MICCAI challenge dataset reveal that our method takes between 5 and 10 seconds to segment a 3D volume with an overall mean surface distance lower than 2.3 mm and an ejection fraction error of less than 5% compared to a manual tracing by an expert. Download and review this publication at: http://hdl.handle.net/10380/3482 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 15:56:17 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 15:56:17 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Endocardial Segmentation using Structured Random Forests in 3D Echocardiography Message-ID: <20141013195617.B23403D6C4DA@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Endocardial Segmentation using Structured Random Forests in 3D Echocardiography Authors: Domingos J.S., Stebbing R.V., Noble A.J. Abstract: Segmentation of the left ventricle endocardium in 3D echocardiography is a critical step for the diagnosis of heart disease. Although recent work has shown effective endocardial edge detection, these techniques still preserve spurious anatomical edge responses that undermine overall ventricle segmentation. In this paper we propose a robust semiautomatic framework based on 2D structured learning that facilitates full 3D model-based endocardial segmentation. This method is evaluated on 30 publicly available datasets from different brands of ultrasound machines. Results show that the proposed method accurately finds the endocardium and effectively converges an explicit and continuous surface model to it. Download and review this publication at: http://hdl.handle.net/10380/3483 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 16:25:11 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:25:11 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Endocardial 3D Ultrasound Segmentation using Autocontext Random Forests Message-ID: <20141013202511.6AA1B3D6C291@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Endocardial 3D Ultrasound Segmentation using Autocontext Random Forests Authors: Keraudren K., Oktay O., Shi W., Hajnal J.V., Rueckert D. Abstract: In this paper, we present the use of a generic image segmentation method, namely a succession of Random Forest classifiers in an autocontext framework, for the MICCAI 2014 Challenge on Endocardial 3D Ultrasound Segmentation (CETUS). The proposed method segments each frame independently in 90 sec, without requiring temporal information such as end-diastolic or end-systolic time points nor any registration. For better segmentation accuracy, non-local means denoising can be applied to the images at the cost of an increased run-time. The mean Dice score on the testing dataset was 84.4% without denoising and 86.4% with denoising. The originality of our approach lies in the introduction of two classes, the myocardium and the mitral valve, in addition to the left ventricle and the background classes, in order to gain contextual information for the segmentation task. Download and review this publication at: http://hdl.handle.net/10380/3484 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 16:30:11 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:30:11 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Left Ventricle Segmentation in Cardiac Ultrasound Using Hough-Forests With Implicit Shape and Appearance Priors Message-ID: <20141013203011.25A3E3D6C3C2@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Left Ventricle Segmentation in Cardiac Ultrasound Using Hough-Forests With Implicit Shape and Appearance Priors Authors: Milletari F., Yigitsoy M., Navab N., Ahmadi S. Abstract: We propose a learning based approach to perform automatic segmentation of the left ventricle in 3D cardiac ultrasound images. The segmentation contour is estimated through the use of a variant of Hough forests whose object localization capabilities are coupled with a patch-wise, appearance driven, contour estimation strategy. The performance of the proposed method is evaluated on a dataset of 30 images acquired from 15 patients using different equipment and settings. Download and review this publication at: http://hdl.handle.net/10380/3485 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 16:34:43 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:34:43 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Learning Shape Representations for Multi-Atlas Endocardium Segmentation in 3D Echo Images Message-ID: <20141013203443.D24FA3D6C55B@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Learning Shape Representations for Multi-Atlas Endocardium Segmentation in 3D Echo Images Authors: Oktay O., Shi W., Keraudren K., Caballero J., Rueckert D. Abstract: As part of the CETUS challenge, we present a multi-atlas segmentation framework to delineate the left-ventricle endocardium in echocardiographic images. To increase the robustness of the registration step, we introduce a speckle reduction step and a new shape representation based on sparse coding and manifold approximation in dictionary space. The shape representation, unlike intensity values, provides consistent shape information across different images. The validation results on the test set show that registration based on our shape representation significantly improves the performance of multi-atlas segmentation compared to intensity based registration. To our knowledge it is the first time that multi-atlas segmentation achieves state-of-the-art results for echocardiographic images. Download and review this publication at: http://hdl.handle.net/10380/3486 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 16:38:35 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:38:35 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Real-time Tracking of the Left Ventricle in 3D Ultrasound Using Kalman Filter and Mean Value Coordinates Message-ID: <20141013203835.114943D6C407@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Real-time Tracking of the Left Ventricle in 3D Ultrasound Using Kalman Filter and Mean Value Coordinates Authors: Smistad E., Lindseth F. Abstract: A method for real-time automatic tracking of the left ventricle (LV) in 3D ultrasound is presented. A mesh model of the LV is deformed using mean value coordinates enabling large variations. Kalman filtering and edge detection is used to track the mesh in each frame. The method is evaluated using the framework of the Challenge on Endocardial Three-dimensional Ultrasound Segmentation (CETUS). The results show that the method is able to robustly track the LV in all sequences with a mean mesh difference of about 2.5 mm Download and review this publication at: http://hdl.handle.net/10380/3487 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 16:45:33 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:45:33 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Segmentation of Multi-Center 3D Left Ventricular Echocardiograms by Active Appearance Models Message-ID: <20141013204533.E60203D6C46C@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Segmentation of Multi-Center 3D Left Ventricular Echocardiograms by Active Appearance Models Authors: Van Stralen M., Haak A., Leung E.K., Van Burken G., Bosch J.G. Abstract: Segmentation of 3D echocardiograms (3DEs) is still a challenging task due to the low signal-to-noise ratio, the limited field of view, and typical ultrasound artifacts. We propose to segment the left ventricular endocardial surface by using Active Appearance Models (AAMs). Separate end-diastolic (ED) and end-systolic (ES) AAMs were built from presegmented 3DEs of the CETUS training data and 25 previously acquired 3DEs, imaged using various 3DE equipment. The AAMs fully automatically segmented the 15 training sets in a leave-one-out cross validation, comparing two training populations and various initialization strategies. All segmentations took about 15 seconds per patient. The comparison on the CETUS training data shows that the AAM benefits from additional training data and more accurate initialization. The results on the CETUS training and testing data confirm good ED and ES segmentation accuracy on multi-center, multi-vendor, multi-pathology data, and corresponding EF e stimation. Selection from different initialization strategies, based on the minimal residual error, and propagation of detected ED contours to initialize ES detection, contributed to more accurate segmentations in this heterogeneous population. Download and review this publication at: http://hdl.handle.net/10380/3488 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Mon Oct 13 16:51:08 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 13 Oct 2014 16:51:08 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Model-based left ventricle segmentation in 3D ultrasound using phase image Message-ID: <20141013205108.426C23D6C7AE@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Model-based left ventricle segmentation in 3D ultrasound using phase image Authors: Wang C., Smedby O. Abstract: In this paper, we propose a semi-automatic method for left ventricle segmentation. The proposed method utilizes a multi-scale quadrature filter method to enhance the 3D volume, followed by a model-based level set method to segment the endocardial surface of the left ventricle. The phase map from the quadrature filters is also used to weight the influence of contour points when updating the statistical model. Download and review this publication at: http://hdl.handle.net/10380/3489 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Mon Oct 13 17:39:15 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 13 Oct 2014 17:39:15 -0400 Subject: [ITK] Gerrit Down Time Message-ID: Hi, Gerrit will be down tonight for a few hours starting at 7:00 PM Eastern USA time for infrastructure upgrades. Sorry for any inconvenience. Matt From davis.vigneault at gmail.com Tue Oct 14 11:31:09 2014 From: davis.vigneault at gmail.com (DVigneault) Date: Tue, 14 Oct 2014 08:31:09 -0700 (PDT) Subject: [ITK] [ITK-users] Operator overloading in ITK objects. Message-ID: <1413300669946-7586346.post@n2.nabble.com> All-- I've defined an ITK object inheriting from itk::DataObject (full header file copied below). The object has two properties: Index and Value. I've tried to overload the == and < operators (basing my syntax off of itk::Point) so that the two objects would be equal if they have the same index, and one would be less than the other if one's value is less than the other's: bool operator==(const Self & pt) const { return this->GetIndex() == pt->GetIndex(); } bool operator<(const Self & pt) const { return this->GetValue() < pt->GetValue(); } However, the less than operator isn't functioning as intended: typedef IndexValuePair< IndexType, PixelType > PairType; typename PairType::Pointer pair1 = PairType::New(); IndexType index1; pair1->SetIndex( index1.Fill( 0 ) ); pair1->SetValue( 1 ); typename PairType::Pointer pair2 = PairType::New(); IndexType index2; pair2->SetIndex( index2.Fill( 1 ) ); pair2->SetValue( 0 ); std::cout << (pair1 == pair2) << std::endl; // 0 std::cout << (pair1 == pair1) << std::endl; // 1 std::cout << (pair1 < pair2) << std::endl; // 1 Interestingly, the results do not change if I comment out the overloading operators in the header file, or if I change the values of the pairs, suggesting that the program is comparing the objects based on some other criteria. Any ideas what I'm doing wrong? Apologies in advance if this is more of a c++ question and less of an ITK question--I'm sometimes not sure whether my problem is due to my misunderstanding the language or the library. Best, --Davis Best, and thanks, --Davis *** Header ** #ifndef __itkIndexValuePair_h #define __itkIndexValuePair_h #include "itkDataObject.h" namespace itk { template < typename IndexType, typename ValueType > class IndexValuePair:public DataObject { public: /** Standard class typedefs. */ typedef IndexValuePair Self; typedef DataObject Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; /** Method for creation through the object factory. */ itkNewMacro(Self); /** Standard part of every itk Object. */ itkTypeMacro(IndexValuePair, DataObject); itkSetMacro( Index, IndexType ); itkGetMacro( Index, IndexType ); itkSetMacro( Value, ValueType ); itkGetMacro( Value, ValueType ); /** Compare two points for equality. */ bool operator==(const Self & pt) const { return this->GetIndex() == pt->GetIndex(); } /** Less than. */ bool operator<(const Self & pt) const { return this->GetValue() < pt->GetValue(); } protected: /** Constructor for use by New() method. */ IndexValuePair() {} ~IndexValuePair() {} // virtual void PrintSelf(std::ostream & os, Indent indent) const; IndexType m_Index; ValueType m_Value; private: IndexValuePair(const Self &); //purposely not implemented void operator=(const Self &); //purposely not implemented }; } #endif -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Operator-overloading-in-ITK-objects-tp7586346.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 blowekamp at mail.nih.gov Tue Oct 14 11:38:49 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 14 Oct 2014 11:38:49 -0400 Subject: [ITK] [ITK-users] Operator overloading in ITK objects. In-Reply-To: <1413300669946-7586346.post@n2.nabble.com> References: <1413300669946-7586346.post@n2.nabble.com> Message-ID: <47CDDE20-C688-4DA0-A28B-AAEE0BBAC93A@mail.nih.gov> Hello, I think the issue is that the variables pair1 and pair2 are SmartPointers not the derived data object type, so your operators are working on a different object type than you expected. ITK was not designed for use with overloaded operators with it's data objects and process objects. You could likely hack it by doing (*pair1) == (*pair2), if you really want to use overloaded operators. Otherwise a conventional member function could just as easily be used. Brad On Oct 14, 2014, at 11:31 AM, DVigneault wrote: > All-- > > I've defined an ITK object inheriting from itk::DataObject (full header file > copied below). The object has two properties: Index and Value. I've tried > to overload the == and < operators (basing my syntax off of itk::Point) so > that the two objects would be equal if they have the same index, and one > would be less than the other if one's value is less than the other's: > > bool operator==(const Self & pt) const { > return this->GetIndex() == pt->GetIndex(); } > > bool operator<(const Self & pt) const { > return this->GetValue() < pt->GetValue(); } > > However, the less than operator isn't functioning as intended: > > typedef IndexValuePair< IndexType, PixelType > PairType; > typename PairType::Pointer pair1 = PairType::New(); > IndexType index1; > pair1->SetIndex( index1.Fill( 0 ) ); > pair1->SetValue( 1 ); > > typename PairType::Pointer pair2 = PairType::New(); > IndexType index2; > pair2->SetIndex( index2.Fill( 1 ) ); > pair2->SetValue( 0 ); > > std::cout << (pair1 == pair2) << std::endl; // 0 > std::cout << (pair1 == pair1) << std::endl; // 1 > std::cout << (pair1 < pair2) << std::endl; // 1 > > Interestingly, the results do not change if I comment out the overloading > operators in the header file, or if I change the values of the pairs, > suggesting that the program is comparing the objects based on some other > criteria. Any ideas what I'm doing wrong? Apologies in advance if this is > more of a c++ question and less of an ITK question--I'm sometimes not sure > whether my problem is due to my misunderstanding the language or the > library. > > Best, > > --Davis > > Best, and thanks, > > --Davis > > *** Header ** > > #ifndef __itkIndexValuePair_h > #define __itkIndexValuePair_h > > #include "itkDataObject.h" > > namespace itk > { > > template < typename IndexType, typename ValueType > > class IndexValuePair:public DataObject > { > > public: > > /** Standard class typedefs. */ > typedef IndexValuePair Self; > typedef DataObject Superclass; > typedef SmartPointer< Self > Pointer; > typedef SmartPointer< const Self > ConstPointer; > > /** Method for creation through the object factory. */ > itkNewMacro(Self); > > /** Standard part of every itk Object. */ > itkTypeMacro(IndexValuePair, DataObject); > > itkSetMacro( Index, IndexType ); > itkGetMacro( Index, IndexType ); > > itkSetMacro( Value, ValueType ); > itkGetMacro( Value, ValueType ); > > > /** Compare two points for equality. */ > bool > operator==(const Self & pt) const > { > return this->GetIndex() == pt->GetIndex(); > } > > /** Less than. */ > bool > operator<(const Self & pt) const > { > return this->GetValue() < pt->GetValue(); > } > > protected: > /** Constructor for use by New() method. */ > IndexValuePair() {} > ~IndexValuePair() {} > // virtual void PrintSelf(std::ostream & os, Indent indent) const; > > IndexType m_Index; > ValueType m_Value; > > private: > IndexValuePair(const Self &); //purposely not implemented > void operator=(const Self &); //purposely not implemented > > }; > > } > > #endif > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Operator-overloading-in-ITK-objects-tp7586346.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 gaetano.esposito at outlook.com Tue Oct 14 18:23:07 2014 From: gaetano.esposito at outlook.com (Gaetano Esposito) Date: Tue, 14 Oct 2014 22:23:07 +0000 Subject: [ITK] ITK -- Transform an image with a change of coordinates Message-ID: Hello, I apologize in advance for using a vague language, but I just started to play with image processing and segmentation. Given an image, I would like to define an arbitrary origin, get the coordinates of every pixel from Cartesian (x,y) to polar(rho, theta), and then create a new image whose x axis is "rho" and whose y axis is "theta". In other words, I would like to map a circular image in Cartesian Coordinates to a periodic line in polar coordinates. I am a little confused about how I would achieve this in ITK. I believe that I can take advantage of a couple of Transform based Polar-Cartesian algorithms out there, some of them published on the Insight Journal. The transform typically seems to act on a single point. Is using a transform the right approach? If yes, once I have the correct transform from Cartesian to Polar, how do I create the "polar" image that I am seeking? Thanks for your feedback, Gaetano -------------- next part -------------- An HTML attachment was scrubbed... URL: From gabrielgimenez85 at gmail.com Tue Oct 14 19:51:39 2014 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Tue, 14 Oct 2014 16:51:39 -0700 (PDT) Subject: [ITK] [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform Message-ID: <1413330699438-7586348.post@n2.nabble.com> Hello everyone, I modified the example 8 for use OnePlusOneEvolutionaryOptimizer and itkMattesMutualInformationImageToImageMetric, this worked for me. Now, i try to use itkRegistrationParameterScalesFromPhysicalShift for to estimate the parameters of scale. I adapted my code to use the ITKv4, but, but I have this error: *Optimizer stop condition: OnePlusOneEvolutionaryOptimizerv4: Fnorm (0.000777958) is less than Epsilon (1 at iteration #0* I found almost no documentation of ITK version 4, why ?In Manuals not found anything. This is the part of code to configure the estimation scale (based on examples found in the DoxyGen): typedef itk::RegistrationParameterScalesFromPhysicalShift ScalesEstimatorType; ScalesEstimatorType::Pointer scalesEstimator = ScalesEstimatorType::New(); scalesEstimator->SetMetric( metric ); scalesEstimator->SetTransformForward( true ); scalesEstimator->SetSmallParameterVariation( 1.0 ); optimizer->SetScalesEstimator( scalesEstimator ); optimizer->SetDoEstimateScales(true); Hopefully someone can help me with something, thanks. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348.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 j.plumat at auckland.ac.nz Tue Oct 14 21:42:19 2014 From: j.plumat at auckland.ac.nz (Jerome Plumat) Date: Wed, 15 Oct 2014 14:42:19 +1300 Subject: [ITK] [ITK-users] how to visualise deformed volume along registration process Message-ID: <543DD0FB.1040609@auckland.ac.nz> Hello everyone, I'm facing to a problem and I hope some may have ideas to help me. I'm using Multi Resolution Symmetric Log-Domain Diffeomorphic Demons Algorithm (http://www.insight-journal.org/browse/publication/644) to register volumes. The current results are not very good and I would like to observe them along the registration process. My current solution uses object to display metrics and information along pyramid levels: template class ShowProgressObject { public: ShowProgressLevelObject(TRegistration* o) { m_Process = o; } void ShowProgress() { std::cout << "Level: " << m_Process->GetCurrentLevel() << " "; std::cout << "Progress: " << m_Process->GetProgress() << " "; std::cout << "Starting Metric: " << m_Process->GetRegistrationFilter()->GetMetric() << " "; std::cout << std::endl; } typename TRegistration::Pointer m_Process; }; .... typedef ShowProgressObject ProgressType; ProgressType progressWatch(registrator); itk::SimpleMemberCommand::Pointer command; command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(&progressWatch, &ProgressType::ShowProgress); I would like to use this object to display the current deformed image at each level of the pyramid. My current (not so good) idea is to use fixed and moving images and current deformation field. I'm using warper to deform the moving image in the ShowProgressObject::ShowProgress function: warper->SetInput( m_originalMoving ); warper->SetInterpolator( interpolator ); warper->SetOutputSpacing( m_fixed->GetSpacing() ); warper->SetOutputOrigin( m_fixed->GetOrigin() ); warper->SetOutputDirection( m_fixed->GetDirection() ); warper->SetDisplacementField( m_Process->GetRegistrationFilter()->GetDeformationField() ); warper->Update(); Then the result would be display with QuickView. But ... it appears that using fixed and moving images in this process makes them unavailable for the registration. I can make copies of them but this seems very inefficient. Any recommendations or advices to achieve to display deformed image along process? Thanks a lot. -- Jerome ------- School of Medical Sciences University of Auckland If I am not for myself, who will be for me? And if I am only for myself, then what an I? And if not now when? ? Hillel HaZaken _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 shinya.onogi at live.jp Wed Oct 15 05:45:39 2014 From: shinya.onogi at live.jp (Shinya Onogi) Date: Wed, 15 Oct 2014 02:45:39 -0700 (MST) Subject: [ITK] [ITK-users] ITK build failed in using ITK_USE_FLOAT_SPACE_PRECISION Message-ID: <1413366339221-34689.post@n7.nabble.com> Hi, When ITK_USE_FLOAT_SPACE_PRECISION is TRUE, Compilation error occurs in itkTransformFactoryBase.cxx at L274 and L275. I could not find the issue in Google; therefore, I will note it here for anyone. L274: TransformFactory< GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform >::RegisterTransform (); L275 TransformFactory< GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform >::RegisterTransform (); My env is followings. OS: Windows 8.1 Platform: Visual Studio 2013 ITK: ITK-4.6.1 -- View this message in context: http://itk-users.7.n7.nabble.com/ITK-build-failed-in-using-ITK-USE-FLOAT-SPACE-PRECISION-tp34689.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 Wed Oct 15 08:32:47 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 15 Oct 2014 08:32:47 -0400 Subject: [ITK] [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: <1413330699438-7586348.post@n2.nabble.com> References: <1413330699438-7586348.post@n2.nabble.com> Message-ID: <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> Hello, > > *Optimizer stop condition: OnePlusOneEvolutionaryOptimizerv4: Fnorm > (0.000777958) is less than Epsilon (1 at iteration #0* This message may mean that the scales are not correctly set, and the the initial search area failed to yield a significant change. Things that can impact the scales include the metric used and the spacing of your image. This can some times be a difficult thing to track down. Would the spacing of you image happen to be very large or very small? Also keep in mind that the Versor transforms are not Euclidean spaces and a best suited for use with the regular step gradient descent optimizers as only that optimizer takes into consideration the correct normalization of the versor space. In short I think you have picked three challenging components that may just now work well together. Brad > > I found almost no documentation of ITK version 4, why ?In Manuals not found > anything. > > This is the part of code to configure the estimation scale (based on > examples found in the DoxyGen): > > typedef itk::RegistrationParameterScalesFromPhysicalShift > ScalesEstimatorType; > ScalesEstimatorType::Pointer scalesEstimator = > ScalesEstimatorType::New(); > scalesEstimator->SetMetric( metric ); > scalesEstimator->SetTransformForward( true ); > scalesEstimator->SetSmallParameterVariation( 1.0 ); > > optimizer->SetScalesEstimator( scalesEstimator ); > optimizer->SetDoEstimateScales(true); > > Hopefully someone can help me with something, thanks. > > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348.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 emmasaunders123 at gmail.com Wed Oct 15 08:56:33 2014 From: emmasaunders123 at gmail.com (Emma Saunders) Date: Wed, 15 Oct 2014 13:56:33 +0100 Subject: [ITK] [ITK-users] Metric Distance on Manifold Message-ID: Hello all, ITK offers numerous diffeomorphic registration algorithms, is there a mechanism within ITK to calculate the distance each transformation has moved along the diffeomorphic manifold? If not is it possible to perform such a calculation on the displacement fields themselves. Thanks for any help Emma -------------- 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 Wed Oct 15 09:14:25 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 15 Oct 2014 09:14:25 -0400 Subject: [ITK] [ITK-users] ITK build failed in using ITK_USE_FLOAT_SPACE_PRECISION In-Reply-To: <1413366339221-34689.post@n7.nabble.com> References: <1413366339221-34689.post@n7.nabble.com> Message-ID: Hello, I tried compiling with this options with gcc 4.8.2 on Linux and I am getting a large number of compilation errors too. Looks like it would requite a bit of work to get this working again. Perhaps This option worked with the ITK 4.5 release? Brad On Oct 15, 2014, at 5:45 AM, Shinya Onogi wrote: > Hi, > > When ITK_USE_FLOAT_SPACE_PRECISION is TRUE, Compilation error occurs in > itkTransformFactoryBase.cxx at L274 and L275. I could not find the issue in > Google; therefore, I will note it here for anyone. > > L274: > TransformFactory< > GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform >> ::RegisterTransform (); > > L275 > TransformFactory< > GaussianSmoothingOnUpdateTimeVaryingVelocityFieldTransform >> ::RegisterTransform (); > > > My env is followings. > OS: Windows 8.1 > Platform: Visual Studio 2013 > ITK: ITK-4.6.1 > > > > > -- > View this message in context: http://itk-users.7.n7.nabble.com/ITK-build-failed-in-using-ITK-USE-FLOAT-SPACE-PRECISION-tp34689.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 gabrielgimenez85 at gmail.com Wed Oct 15 10:26:00 2014 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Wed, 15 Oct 2014 07:26:00 -0700 (PDT) Subject: [ITK] [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> References: <1413330699438-7586348.post@n2.nabble.com> <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> Message-ID: <1413383160042-7586354.post@n2.nabble.com> Hello Brad ,thanks for answering, I need the definition of scales Optimizer (translation and rotation) to be dynamic, not hard, so I use the RegistrationParameterScalesFromPhysicalShift class. Any other alternatives for my problem?. Nor do I find much information about how to define these scales and even less dynamically. Theoretically ITK architecture is fully modular and low-coupling, then, should be no problem to combine different types of optimizers, transformations, etc, or am I wrong? -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348p7586354.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 blowekamp at mail.nih.gov Wed Oct 15 10:43:45 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 15 Oct 2014 10:43:45 -0400 Subject: [ITK] [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: <1413383160042-7586354.post@n2.nabble.com> References: <1413330699438-7586348.post@n2.nabble.com> <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> <1413383160042-7586354.post@n2.nabble.com> Message-ID: <7F36D103-169A-415A-8FB4-0585E40876EB@mail.nih.gov> Hello, The scales are going to be for the serializable optimization parameters for the Transform defined in the doxygen[1]. You may wish to try the other scales estimators: RegistrationPatameterScalesFromIndexShift, RegistrationParameterScalesFromJacobian Also the other parameters for your optimizer may need to be adjusted such as InitialRadius, ShrinkFactor and the GrowthFactor. I have not investigated if these optimizer parameters are correctly scales into the parameter space when applied, but they should be. As you are doing you can theoretically plug any combination of components together. However the results may not be robust or stable. Again I will urge caution with using the Versor transforms with an optimizer other than the RegularStepGradientDescent as there is some coupling of these two to do the correct normalization in the versor space. Brad [1] http://www.itk.org/Doxygen/html/classitk_1_1VersorRigid3DTransform.html On Oct 15, 2014, at 10:26 AM, Gabriel A. Gim?nez wrote: > Hello Brad ,thanks for answering, > > I need the definition of scales Optimizer (translation and rotation) to be > dynamic, not hard, so I use the RegistrationParameterScalesFromPhysicalShift > class. Any other alternatives for my problem?. Nor do I find much > information about how to define these scales and even less dynamically. > > > Theoretically ITK architecture is fully modular and low-coupling, then, > should be no problem to combine different types of optimizers, > transformations, etc, or am I wrong? > > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348p7586354.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 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Wed Oct 15 15:34:19 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Wed, 15 Oct 2014 19:34:19 +0000 Subject: [ITK] Stitching Message-ID: Hi all, This is not really an ITK question, but it's on a topic that will be familiar to many here. There are several algorithms and programs for stitching together image pieces to create a whole image. As far as I can tell, these tend to assume that the pieces overlap. We are exploring a course of action in which a fluorescently-labelled biological sample is cut into slices (e.g. 100 microns thick) in order to image with confocal microscopy. I have been asked about the feasibility of joining the thick image slices together to reconstitute the whole sample. The problem, of course, is matching the non-overlapping cut surfaces, since there will be inevitable distortion and loss of information. I'd like to know of any publications on this kind of stitching. Thanks Gib -------------- next part -------------- An HTML attachment was scrubbed... URL: From llliu at umich.edu Wed Oct 15 18:13:19 2014 From: llliu at umich.edu (Lianli Liu) Date: Wed, 15 Oct 2014 18:13:19 -0400 Subject: [ITK] [ITK-users] get B spline coefficients Message-ID: Hi all, I have a deformation field (m*n*k*3 vector image) obtained from B spline registration and I want to get the B spline coefficient from the deformation field. Here are my questions: Shall I use the itkBSplineDecompositionImageFilter to do this? If so, do I need to decompose it along each dimension all just input the entire vector image? Do I need to down sample the image first before decomposition? How should I save my decomposition results? Thanks! Lianli -------------- 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 gabrielgimenez85 at gmail.com Wed Oct 15 21:40:06 2014 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Wed, 15 Oct 2014 18:40:06 -0700 (PDT) Subject: [ITK] [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: <7F36D103-169A-415A-8FB4-0585E40876EB@mail.nih.gov> References: <1413330699438-7586348.post@n2.nabble.com> <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> <1413383160042-7586354.post@n2.nabble.com> <7F36D103-169A-415A-8FB4-0585E40876EB@mail.nih.gov> Message-ID: <1413423606327-7586357.post@n2.nabble.com> thank you very much Brad! Some documentation on how to configure these scales (translation and rotation) manually? -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348p7586357.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 Thu Oct 16 00:05:07 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 16 Oct 2014 00:05:07 -0400 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: There are a couple of upcoming opportunities to share, discuss, design, and learn with your fellow ITK community members. On Thursday (tomorrow), 1:00 PM Eastern USA time, there will be a Google+ Hangout where we will be doing code reviews: https://plus.google.com/events/cg7hf091i0k638gm43n3ktkfic0 On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/events/c3fr7aeqa06lhp2j1r601586o1s For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 To get regular invites to these events, join the ITK Bar Camp G+ Community: https://plus.google.com/u/0/communities/111375098792764998322 All are welcome. Hope to talk to you then! From matt.mccormick at kitware.com Thu Oct 16 00:14:17 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 16 Oct 2014 00:14:17 -0400 Subject: [ITK] ITK -- Transform an image with a change of coordinates In-Reply-To: References: Message-ID: Hi Gaetano, Yes, using a Transform is one way to go. See this Insight Journal article [1] and this class [2]. Hope this helps, Matt [1] http://insight-journal.org/browse/publication/722 [2] http://www.itk.org/Doxygen/html/classitk_1_1AzimuthElevationToCartesianTransform.html On Tue, Oct 14, 2014 at 6:23 PM, Gaetano Esposito wrote: > Hello, > > I apologize in advance for using a vague language, but I just started to > play with image processing and segmentation. > > Given an image, I would like to define an arbitrary origin, get the > coordinates of every pixel from Cartesian (x,y) to polar(rho, theta), and > then create a new image whose x axis is "rho" and whose y axis is "theta". > In other words, I would like to map a circular image in Cartesian > Coordinates to a periodic line in polar coordinates. > > I am a little confused about how I would achieve this in ITK. > I believe that I can take advantage of a couple of Transform based > Polar-Cartesian algorithms out there, some of them published on the Insight > Journal. The transform typically seems to act on a single point. > > Is using a transform the right approach? If yes, once I have the correct > transform from Cartesian to Polar, how do I create the "polar" image that I > am seeking? > > Thanks for your feedback, > > Gaetano > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From matt.mccormick at kitware.com Thu Oct 16 00:25:03 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 16 Oct 2014 00:25:03 -0400 Subject: [ITK] [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: <1413423606327-7586357.post@n2.nabble.com> References: <1413330699438-7586348.post@n2.nabble.com> <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> <1413383160042-7586354.post@n2.nabble.com> <7F36D103-169A-415A-8FB4-0585E40876EB@mail.nih.gov> <1413423606327-7586357.post@n2.nabble.com> Message-ID: Hi Gabriel, Documentation on the ITKv4 registration scale estimation can be found in the Nightly build of the ITK Software Guide. There is is usually a link to the Nightly PDF builds of the ITK Software Guide on the dashboard [1], but it is currently not available due to some build issues. The code for the examples in the software guide can be found in the Examples/Registrationv4/ direction of ITK Git master [2]. Hope this helps, Matt [1] http://open.cdash.org/index.php?project=Insight [2] http://www.itk.org/Wiki/ITK/Git On Wed, Oct 15, 2014 at 9:40 PM, Gabriel A. Gim?nez wrote: > thank you very much Brad! > Some documentation on how to configure these scales (translation and > rotation) manually? > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348p7586357.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 matt.mccormick at kitware.com Thu Oct 16 00:34:11 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 16 Oct 2014 00:34:11 -0400 Subject: [ITK] [ITK-users] how to visualise deformed volume along registration process In-Reply-To: <543DD0FB.1040609@auckland.ac.nz> References: <543DD0FB.1040609@auckland.ac.nz> Message-ID: Hi Jerome, Writing out the Transform as the program progresses may work. Then, use a separate program to generate the resampled images from the input images and the transform. Also, the Transform Visualizer [1] available in the current Slicer Nightly build [2] (soon to be 4.4.0), is a great tool. Hope this helps, Matt [1] http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/TransformVisualizer [2] http://download.slicer.org/ On Tue, Oct 14, 2014 at 9:42 PM, Jerome Plumat wrote: > Hello everyone, > I'm facing to a problem and I hope some may have ideas to help me. > > I'm using Multi Resolution Symmetric Log-Domain Diffeomorphic Demons > Algorithm (http://www.insight-journal.org/browse/publication/644) to > register volumes. The current results are not very good and I would like to > observe them along the registration process. > > My current solution uses object to display metrics and information along > pyramid levels: > > template > class ShowProgressObject > { > public: > ShowProgressLevelObject(TRegistration* o) > { > m_Process = o; > } > > void ShowProgress() > { > std::cout << "Level: " << m_Process->GetCurrentLevel() << " "; > std::cout << "Progress: " << m_Process->GetProgress() << " "; > std::cout << "Starting Metric: " << > m_Process->GetRegistrationFilter()->GetMetric() << " "; > std::cout << std::endl; > > } > > typename TRegistration::Pointer m_Process; > }; > > .... > > typedef ShowProgressObject ProgressType; > ProgressType progressWatch(registrator); > > itk::SimpleMemberCommand::Pointer command; > command = itk::SimpleMemberCommand::New(); > command->SetCallbackFunction(&progressWatch, &ProgressType::ShowProgress); > > > I would like to use this object to display the current deformed image at > each level of the pyramid. My current (not so good) idea is to use fixed and > moving images and current deformation field. I'm using warper to deform the > moving image in the ShowProgressObject::ShowProgress function: > warper->SetInput( m_originalMoving ); > warper->SetInterpolator( interpolator ); > warper->SetOutputSpacing( m_fixed->GetSpacing() ); > warper->SetOutputOrigin( m_fixed->GetOrigin() ); > warper->SetOutputDirection( m_fixed->GetDirection() ); > warper->SetDisplacementField( > m_Process->GetRegistrationFilter()->GetDeformationField() ); > warper->Update(); > > Then the result would be display with QuickView. > > But ... it appears that using fixed and moving images in this process makes > them unavailable for the registration. I can make copies of them but this > seems very inefficient. > > Any recommendations or advices to achieve to display deformed image along > process? > > Thanks a lot. > > -- > > Jerome > ------- > > School of Medical Sciences > University of Auckland > > If I am not for myself, who will be for me? And if I am only for myself, > then what an I? And if not now when? ? Hillel HaZaken > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 Thu Oct 16 15:30:10 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 16 Oct 2014 15:30:10 -0400 Subject: [ITK] [ITK-users] Opportunities to share, discuss, design, and learn with other ITK community members In-Reply-To: References: <2A6589EB-D292-4362-8863-D4804ADE41EC@gmail.com> Message-ID: Based on feedback at the Code Review Hangout today, to respect the privacy of participants, we are not going to record the audio tomorrow. Matt On Mon, Oct 13, 2014 at 11:11 AM, Matt McCormick wrote: > Hi Ariel, > > I'll see if we can record and upload the audio next time. > > Thanks, > Matt > > On Thu, Oct 9, 2014 at 10:43 AM, Ariel Hern?n Curiale wrote: >> Hi Matt, >> Is there any chance to see the video of the meeting on you tube, for example >> ? >> >> Cheers >> __________________________________ >> | Ariel Hern?n Curiale Ph.D Candidate >> | ETSI Telecomunicaci?n >> | Universidad de Valladolid >> | Campus Miguel Delibes >> | 47011 Valladolid, Spain >> | Phone: 983-423000 ext. 5590 >> | Web: www.curiale.com.ar >> |_________________________________ >> >> On 07/10/2014, at 17:52, Matt McCormick wrote: >> >> On Friday, 11:00 AM Eastern USA time, an ITK development conference, >> >> https://plus.google.com/u/0/events/cs71fpcqpa7l9me2vq45mi61mq8 >> >> >> To get regular invites to these events, join the ITK Bar Camp G+ Community: >> >> https://plus.google.com/u/0/communities/111375098792764998322 >> >> >> All are welcome. Hope to talk to you then! >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 boll0107 at umn.edu Thu Oct 16 16:00:17 2014 From: boll0107 at umn.edu (Evan Bollig PhD) Date: Thu, 16 Oct 2014 15:00:17 -0500 Subject: [ITK] [ITK-users] SimpleITK python3.4 OSX egg/homebrew Message-ID: Can someone generate a SimpleITK egg for python3.4 on OSX? easy_install SimpleITK comes back with 0 hits for me, and I'd rather not try to figure out how to reproduce your builds. By the way, you should also consider writing a Homebrew recipe to build and install the library as well. I can provide an example recipe for another CMake project that provides Python (SWIG wrapped) libraries if you're interested. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan at msi.umn.edu boll0107 at umn.edu _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 gabrielgimenez85 at gmail.com Thu Oct 16 20:36:42 2014 From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=) Date: Thu, 16 Oct 2014 17:36:42 -0700 (PDT) Subject: [ITK] [ITK-users] RegistrationParameterScalesFromPhysicalShif and itkVersorRigid3DTransform In-Reply-To: References: <1413330699438-7586348.post@n2.nabble.com> <12562DA0-849A-4BB6-8CE0-BD89D7836D08@mail.nih.gov> <1413383160042-7586354.post@n2.nabble.com> <7F36D103-169A-415A-8FB4-0585E40876EB@mail.nih.gov> <1413423606327-7586357.post@n2.nabble.com> Message-ID: <1413506202830-7586363.post@n2.nabble.com> Thanks Matt, I sure will be very useful! I'm working on my thesis, I would like to implement a GA optimizer for ITK. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/RegistrationParameterScalesFromPhysicalShif-and-itkVersorRigid3DTransform-tp7586348p7586363.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 blowekamp at mail.nih.gov Fri Oct 17 08:12:16 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 17 Oct 2014 08:12:16 -0400 Subject: [ITK] [ITK-users] SimpleITK python3.4 OSX egg/homebrew In-Reply-To: References: Message-ID: Hello, There are quite a large number of different binary distributions of Python and not all of them can be supported. Currently the the binaries are compatible with OSX's system python. It is not too hard to build SimpleITK itself for you custom installation. Information on how to do that can be found here [1]. If you are familiar with Homebrew then it should not be too hard to write a recipe for that packaging system. Contributing this to the community would be very welcomed and appreciated by many. There is a recipe for the anaconda python distribution that may be a good basis for Homebrew[2]. Brad [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself [2] https://github.com/conda/conda-recipes/blob/master/simpleitk/build.sh On Oct 16, 2014, at 4:00 PM, Evan Bollig PhD wrote: > Can someone generate a SimpleITK egg for python3.4 on OSX? > easy_install SimpleITK comes back with 0 hits for me, and I'd rather > not try to figure out how to reproduce your builds. > > By the way, you should also consider writing a Homebrew recipe to > build and install the library as well. I can provide an example recipe > for another CMake project that provides Python (SWIG wrapped) > libraries if you're interested. > > Cheers, > -Evan Bollig > Research Associate | Application Developer | User Support Consultant > Minnesota Supercomputing Institute > 599 Walter Library > 612 624 1447 > evan at msi.umn.edu > boll0107 at umn.edu > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 gaetano.esposito at outlook.com Fri Oct 17 08:38:23 2014 From: gaetano.esposito at outlook.com (Gaetano Esposito) Date: Fri, 17 Oct 2014 12:38:23 +0000 Subject: [ITK] ITK -- Transform an image with a change of coordinates In-Reply-To: References: , Message-ID: Thank you for the pointer. I will update this thread as I go. > Date: Thu, 16 Oct 2014 00:14:17 -0400 > Subject: Re: [ITK] ITK -- Transform an image with a change of coordinates > From: matt.mccormick at kitware.com > To: gaetano.esposito at outlook.com > CC: community at itk.org > > Hi Gaetano, > > Yes, using a Transform is one way to go. See this Insight Journal > article [1] and this class [2]. > > Hope this helps, > Matt > > [1] http://insight-journal.org/browse/publication/722 > > [2] http://www.itk.org/Doxygen/html/classitk_1_1AzimuthElevationToCartesianTransform.html > > On Tue, Oct 14, 2014 at 6:23 PM, Gaetano Esposito > wrote: > > Hello, > > > > I apologize in advance for using a vague language, but I just started to > > play with image processing and segmentation. > > > > Given an image, I would like to define an arbitrary origin, get the > > coordinates of every pixel from Cartesian (x,y) to polar(rho, theta), and > > then create a new image whose x axis is "rho" and whose y axis is "theta". > > In other words, I would like to map a circular image in Cartesian > > Coordinates to a periodic line in polar coordinates. > > > > I am a little confused about how I would achieve this in ITK. > > I believe that I can take advantage of a couple of Transform based > > Polar-Cartesian algorithms out there, some of them published on the Insight > > Journal. The transform typically seems to act on a single point. > > > > Is using a transform the right approach? If yes, once I have the correct > > transform from Cartesian to Polar, how do I create the "polar" image that I > > am seeking? > > > > Thanks for your feedback, > > > > Gaetano > > > > _______________________________________________ > > Community mailing list > > Community at itk.org > > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joel.schaerer at laposte.net Fri Oct 17 12:03:49 2014 From: joel.schaerer at laposte.net (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=) Date: Fri, 17 Oct 2014 18:03:49 +0200 Subject: [ITK] [ITK-users] Possible missing method in itkImageSource Message-ID: <54413DE5.1050108@laposte.net> Hi all, I've run into a problem with named outputs, which I believe could be a bug in ITK. When using named outputs, one is supposed to create the output data objects in the constructor using the MakeOutput method (see http://www.itk.org/Wiki/ITK/Examples/Developer/ImageFilterMultipleOutputs for an example). The MakeOutput method exists for both indexed and named outputs. . These methods are declared and defined first in itkProcessObject: .h: * ... * ProcessObject::MakeOutput. Note that MakeOutput always returns a * itkSmartPointer to a DataObject. ImageSource and MeshSource override * this method to create the correct type of image and mesh respectively. * If a filter has multiple outputs of different types, then that * filter must provide an implementation of MakeOutput(). */ virtual DataObjectPointer MakeOutput( const DataObjectIdentifierType & ); virtual DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx); .cxx DataObject::Pointer ProcessObject ::MakeOutput( const DataObjectIdentifierType & name ) { itkDebugMacro("MakeOutput(" << name << ")"); if( this->IsIndexedOutputName(name) ) { return this->MakeOutput( this->MakeIndexFromOutputName(name) ); } return static_cast(DataObject::New().GetPointer()); } DataObject::Pointer ProcessObject ::MakeOutput(DataObjectPointerArraySizeType) { return static_cast(DataObject::New().GetPointer()); } For indexed outputs, it is redefined in ImageSource in order to create an image object of the correct type. template< typename TOutputImage > ProcessObject::DataObjectPointer ImageSource< TOutputImage > ::MakeOutput(ProcessObject::DataObjectPointerArraySizeType) { return TOutputImage::New().GetPointer(); } So far, so good. However, the named output version of MakeOutput is not redefined in ImageSource, contrary to what the comment in itkProcessObject.h says. And so if someone tries to use it in an ImageToImageFilter, it will crash. Any reason for this behavior? Is this an oversight? Thanks, Jo?l _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From millerjv at gmail.com Fri Oct 17 17:01:57 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 17 Oct 2014 17:01:57 -0400 Subject: [ITK] [ITK-users] Possible missing method in itkImageSource In-Reply-To: <54413DE5.1050108@laposte.net> References: <54413DE5.1050108@laposte.net> Message-ID: <3271CF4A-5DCC-47A5-8456-05BB9325FC4C@gmail.com> At first glance it looks like an oversight. I would expect, however, that we should be seeing warnings about the named version of MakeOutput in ProcessObject being hidden. Jim > On Oct 17, 2014, at 12:03 PM, Jo?l Schaerer wrote: > > Hi all, > > I've run into a problem with named outputs, which I believe could be a bug in ITK. > > When using named outputs, one is supposed to create the output data objects in the constructor using the MakeOutput method (see http://www.itk.org/Wiki/ITK/Examples/Developer/ImageFilterMultipleOutputs for an example). The MakeOutput method exists for both indexed and named outputs. > . > These methods are declared and defined first in itkProcessObject: > > .h: > * ... > * ProcessObject::MakeOutput. Note that MakeOutput always returns a > * itkSmartPointer to a DataObject. ImageSource and MeshSource override > * this method to create the correct type of image and mesh respectively. > * If a filter has multiple outputs of different types, then that > * filter must provide an implementation of MakeOutput(). */ > virtual DataObjectPointer MakeOutput( const DataObjectIdentifierType & ); > virtual DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx); > > .cxx > DataObject::Pointer > ProcessObject > ::MakeOutput( const DataObjectIdentifierType & name ) > { > itkDebugMacro("MakeOutput(" << name << ")"); > if( this->IsIndexedOutputName(name) ) > { > return this->MakeOutput( this->MakeIndexFromOutputName(name) ); > } > return static_cast(DataObject::New().GetPointer()); > } > > DataObject::Pointer > ProcessObject > ::MakeOutput(DataObjectPointerArraySizeType) > { > return static_cast(DataObject::New().GetPointer()); > } > > > For indexed outputs, it is redefined in ImageSource in order to create an image object of the correct type. > > template< typename TOutputImage > > ProcessObject::DataObjectPointer > ImageSource< TOutputImage > > ::MakeOutput(ProcessObject::DataObjectPointerArraySizeType) > { > return TOutputImage::New().GetPointer(); > } > > So far, so good. However, the named output version of MakeOutput is not redefined in ImageSource, contrary to what the comment in itkProcessObject.h says. And so if someone tries to use it in an ImageToImageFilter, it will crash. > > Any reason for this behavior? Is this an oversight? > > Thanks, > > Jo?l > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 gralewskik at email.chop.edu Sun Oct 19 20:13:09 2014 From: gralewskik at email.chop.edu (Kevin) Date: Sun, 19 Oct 2014 17:13:09 -0700 (MST) Subject: [ITK] [ITK-users] Error running Exmaple code -- ICP2.cxx Message-ID: <1413763989914-34707.post@n7.nabble.com> Hello, Just started working with ITK and could use help from this nice community getting up to speed. As the subject reads, I'm currently trying to run iterativeclosestpoint2.cxx from the example source code to register 2 volume meshes. Below is the copied error message I keep getting (ClosestPoint3D is the executable name, obviously): /ClosestPoint3D(15746,0x7fff79138310) malloc: *** error for object 0x7f818d00e328: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Abort trap: 6/ I haven't coded in about 10 years and was never great at debugging so I'm at a bit of a loss. I'm running the official release 4.6.1 on OS X 10.9.5 with clang, Apple LLVM 6.0 (based on 3.5). Here are a few more details/curious notes: when I would pass it the mesh files in either .STL or .vtk format the code would get stuck in the indexing function (I just dropped and returned an counter in the while loop). It never kicked out even after running for iterations orders of magnitude more than the points (and edges for that matter). I then passed it a point cloud file as both a .txt and .xyz (a 3D point plot from MeshLab 1.3.3). This is when I get the checksum error. The code indexed and returned the points tally fine, and initiated a matrix transform, but would the abort. Even more oddly, when I run the executable again (with the same files) to make sure I got the error message right it returned a solution with the .txt, along with the checksum error, but not the .xyz point cloud. Lastly, I lowered the convergence criterion, epsilon, to .001 thinking maybe it wasn't converging before the number of iterations was hit, but that didn't alleviate the issue. In fact, it wouldn't return the initial identity matrix. -- View this message in context: http://itk-users.7.n7.nabble.com/Error-running-Exmaple-code-ICP2-cxx-tp34707.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 matt.mccormick at kitware.com Sun Oct 19 23:47:47 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Sun, 19 Oct 2014 23:47:47 -0400 Subject: [ITK] [ITK-users] Error running Exmaple code -- ICP2.cxx In-Reply-To: <1413763989914-34707.post@n7.nabble.com> References: <1413763989914-34707.post@n7.nabble.com> Message-ID: Hi Kevin, Welcome to ITK! Please send your CMakeLists.txt, code, data, and the command that you run so that others may understand the problem. Thanks, Matt On Sun, Oct 19, 2014 at 8:13 PM, Kevin wrote: > Hello, > > Just started working with ITK and could use help from this nice community > getting up to speed. > > As the subject reads, I'm currently trying to run iterativeclosestpoint2.cxx > from the example source code to register 2 volume meshes. Below is the > copied error message I keep getting (ClosestPoint3D is the executable name, > obviously): > > /ClosestPoint3D(15746,0x7fff79138310) malloc: *** error for object > 0x7f818d00e328: incorrect checksum for freed object - object was probably > modified after being freed. > *** set a breakpoint in malloc_error_break to debug > Abort trap: 6/ > > I haven't coded in about 10 years and was never great at debugging so I'm > at a bit of a loss. I'm running the official release 4.6.1 on OS X 10.9.5 > with clang, Apple LLVM 6.0 (based on 3.5). > > Here are a few more details/curious notes: when I would pass it the mesh > files in either .STL or .vtk format the code would get stuck in the indexing > function (I just dropped and returned an counter in the while loop). It > never kicked out even after running for iterations orders of magnitude more > than the points (and edges for that matter). > > I then passed it a point cloud file as both a .txt and .xyz (a 3D point plot > from MeshLab 1.3.3). This is when I get the checksum error. The code indexed > and returned the points tally fine, and initiated a matrix transform, but > would the abort. Even more oddly, when I run the executable again (with the > same files) to make sure I got the error message right it returned a > solution with the .txt, along with the checksum error, but not the .xyz > point cloud. > > Lastly, I lowered the convergence criterion, epsilon, to .001 thinking maybe > it wasn't converging before the number of iterations was hit, but that > didn't alleviate the issue. In fact, it wouldn't return the initial identity > matrix. > > > > > -- > View this message in context: http://itk-users.7.n7.nabble.com/Error-running-Exmaple-code-ICP2-cxx-tp34707.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 gralewskik at email.chop.edu Mon Oct 20 21:43:38 2014 From: gralewskik at email.chop.edu (Kevin) Date: Mon, 20 Oct 2014 18:43:38 -0700 (MST) Subject: [ITK] [ITK-users] Error running Exmaple code -- ICP2.cxx In-Reply-To: References: <1413763989914-34707.post@n7.nabble.com> Message-ID: <1413855818662-34709.post@n7.nabble.com> Thanks, Matt. And thanks for the quick reply. Attached are the requested files: CMakeLists.txt IterativeClosestPoint2.cxx (directly from source package) Data_1.txt Data_2.txt Again, I'm running OS x and follow the method outlined in the manual to configure, compile and run. The line commands are: ccmake ../(directory containing CMakelists.txt and code) make ./(executable name) (file 1) (file 2) -- View this message in context: http://itk-users.7.n7.nabble.com/Error-running-Exmaple-code-ICP2-cxx-tp34707p34709.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 lefebvre at imnc.in2p3.fr Tue Oct 21 12:18:02 2014 From: lefebvre at imnc.in2p3.fr (=?ISO-8859-1?Q?Fran=E7oise_Lefebvre?=) Date: Tue, 21 Oct 2014 18:18:02 +0200 Subject: [ITK] [ITK-users] Error compiling msvc2010 + ITK4.6 + Qt Message-ID: <5446873A.7070500@imnc.in2p3.fr> Hi, ITK 4.6 was succesfully build using cmake2.8.10.2, the default parameters and the Module_ITKReview on. I am now trying to compile a program developed in C++ using Qt5.1.1 and Microsoft Visual C++ express 2010 on Windows 7. I get the following link error : 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: static class itksys::Encoding::CommandLineArguments __cdecl itksys::Encoding::CommandLineArguments::Main(int,char const * const *)" (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) I didn't get this error when compiling with itk4.3 . Any hint ? Thank you for your help, F. Lefebvre _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 Oct 21 13:18:05 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 21 Oct 2014 13:18:05 -0400 Subject: [ITK] [ITK-users] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: <5446873A.7070500@imnc.in2p3.fr> References: <5446873A.7070500@imnc.in2p3.fr> Message-ID: <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> Did you try the latest 4.6.1 release? Brad On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre wrote: > > Hi, > > ITK 4.6 was succesfully build using cmake2.8.10.2, the default parameters and the Module_ITKReview on. > > I am now trying to compile a program developed in C++ using Qt5.1.1 and Microsoft Visual C++ express 2010 on Windows 7. > > I get the following link error : > > 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: static class itksys::Encoding::CommandLineArguments __cdecl itksys::Encoding::CommandLineArguments::Main(int,char const * const *)" (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) > > I didn't get this error when compiling with itk4.3 . > > Any hint ? > > Thank you for your help, > > F. Lefebvre > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 marina.bendersky at gmail.com Tue Oct 21 18:05:00 2014 From: marina.bendersky at gmail.com (Marina Bendersky) Date: Tue, 21 Oct 2014 15:05:00 -0700 Subject: [ITK] [ITK-users] Find corresponding slices in two different volumes Message-ID: Hi all, I need to find corresponding slices in 2 different volumes. I used the ImageRegistration20.cxx example to register "volumeSource" and "volumeTarget". My question is, then, to which slice in "volumeTarget" does ?slice 10? in "volumeSource" correspond? Is there an ITK example/hints that could guide me in the right direction? I?ve just started using ITK and would be grateful for any help. Thank you very much! Marina -------------- 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 rsvpitt at gmail.com Tue Oct 21 18:06:54 2014 From: rsvpitt at gmail.com (Vikas) Date: Tue, 21 Oct 2014 18:06:54 -0400 Subject: [ITK] [ITK-users] Problem applying landmarks in FEM registration Message-ID: Hi, I am having issues applying landmarks to FEM registration and would appreciate any help to resolve it. I am following the example in RegistrationITKv4/DeformableRegistration11 with the following modification: //Add landmartks RegistrationType::PointType SourceLandmark; RegistrationType::PointType TargetLandmark; SourceLandmark[0] = 23;SourceLandmark[1] = 12;SourceLandmark[2] = 41; TargetLandmark[0] = 26;TargetLandmark[1] = 16;TargetLandmark[2] = 45; registrationFilter->AddLandmark(SourceLandmark,TargetLandmark); registrationFilter->SetUseLandmarks(true); I get a run time error: "Vector subscript out of range". The call stack is as follows: > msvcp90d.dll!std::_Debug_message(const wchar_t * message=0x000000013fa48fc8, const wchar_t * file=0x000000013fa49010, unsigned int line=779) Line 24 C++ HybridRegistration.exe!std::vector >::operator[](unsigned __int64 _Pos=0) Line 780 C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::ApplyLoads(itk::Size<3> ImgSz={...}, double * scaling=0x0000000000000000) Line 410 + 0x35 bytes C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::MultiResSolve() Line 1173 C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::RunRegistration() Line 169 C++ HybridRegistration.exe!main(int argc=1, char * * argv=0x0000000002546b40) Line 225 C++ HybridRegistration.exe!__tmainCRTStartup() Line 586 + 0x19 bytes C HybridRegistration.exe!mainCRTStartup() Line 403 C Thanks Vikas -------------- 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 lefebvre at imnc.in2p3.fr Wed Oct 22 03:23:48 2014 From: lefebvre at imnc.in2p3.fr (=?ISO-8859-1?Q?Fran=E7oise_Lefebvre?=) Date: Wed, 22 Oct 2014 09:23:48 +0200 Subject: [ITK] [ITK-users] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> Message-ID: <54475B84.5020906@imnc.in2p3.fr> Yes I did. Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : > Did you try the latest 4.6.1 release? > > Brad > > On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre wrote: > >> Hi, >> >> ITK 4.6 was succesfully build using cmake2.8.10.2, the default parameters and the Module_ITKReview on. >> >> I am now trying to compile a program developed in C++ using Qt5.1.1 and Microsoft Visual C++ express 2010 on Windows 7. >> >> I get the following link error : >> >> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: static class itksys::Encoding::CommandLineArguments __cdecl itksys::Encoding::CommandLineArguments::Main(int,char const * const *)" (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) >> >> I didn't get this error when compiling with itk4.3 . >> >> Any hint ? >> >> Thank you for your help, >> >> F. Lefebvre >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 -- Fran?oise LEFEBVRE IMNC (Imagerie et Mod?lisation en Neurobiologie et Canc?rologie) Campus d'Orsay - B?t 440 91405 ORSAY Cedex 01 69 15 51 87 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 Wed Oct 22 09:44:15 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Wed, 22 Oct 2014 09:44:15 -0400 Subject: [ITK] [ITK-users] Possible missing method in itkImageSource In-Reply-To: <3271CF4A-5DCC-47A5-8456-05BB9325FC4C@gmail.com> References: <54413DE5.1050108@laposte.net> <3271CF4A-5DCC-47A5-8456-05BB9325FC4C@gmail.com> Message-ID: <0023FC88-13F9-4ED2-9767-FB324A2EE0CB@mail.nih.gov> Hello, I'm going to take a look at this issue. Brad On Oct 17, 2014, at 5:01 PM, Jim Miller wrote: > At first glance it looks like an oversight. I would expect, however, that we should be seeing warnings about the named version of MakeOutput in ProcessObject being hidden. > > Jim > >> On Oct 17, 2014, at 12:03 PM, Jo?l Schaerer wrote: >> >> Hi all, >> >> I've run into a problem with named outputs, which I believe could be a bug in ITK. >> >> When using named outputs, one is supposed to create the output data objects in the constructor using the MakeOutput method (see http://www.itk.org/Wiki/ITK/Examples/Developer/ImageFilterMultipleOutputs for an example). The MakeOutput method exists for both indexed and named outputs. >> . >> These methods are declared and defined first in itkProcessObject: >> >> .h: >> * ... >> * ProcessObject::MakeOutput. Note that MakeOutput always returns a >> * itkSmartPointer to a DataObject. ImageSource and MeshSource override >> * this method to create the correct type of image and mesh respectively. >> * If a filter has multiple outputs of different types, then that >> * filter must provide an implementation of MakeOutput(). */ >> virtual DataObjectPointer MakeOutput( const DataObjectIdentifierType & ); >> virtual DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx); >> >> .cxx >> DataObject::Pointer >> ProcessObject >> ::MakeOutput( const DataObjectIdentifierType & name ) >> { >> itkDebugMacro("MakeOutput(" << name << ")"); >> if( this->IsIndexedOutputName(name) ) >> { >> return this->MakeOutput( this->MakeIndexFromOutputName(name) ); >> } >> return static_cast(DataObject::New().GetPointer()); >> } >> >> DataObject::Pointer >> ProcessObject >> ::MakeOutput(DataObjectPointerArraySizeType) >> { >> return static_cast(DataObject::New().GetPointer()); >> } >> >> >> For indexed outputs, it is redefined in ImageSource in order to create an image object of the correct type. >> >> template< typename TOutputImage > >> ProcessObject::DataObjectPointer >> ImageSource< TOutputImage > >> ::MakeOutput(ProcessObject::DataObjectPointerArraySizeType) >> { >> return TOutputImage::New().GetPointer(); >> } >> >> So far, so good. However, the named output version of MakeOutput is not redefined in ImageSource, contrary to what the comment in itkProcessObject.h says. And so if someone tries to use it in an ImageToImageFilter, it will crash. >> >> Any reason for this behavior? Is this an oversight? >> >> Thanks, >> >> Jo?l >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 norman-k-williams at uiowa.edu Wed Oct 22 14:35:12 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Wed, 22 Oct 2014 18:35:12 +0000 Subject: [ITK] [ITK-dev] Can I get permission to upload a file to http://midas3.kitware.com? Message-ID: I have an account, I can upload my own public & private files, but I don?t have permission to add new test Data. Can I be added to the permitted uploaders? Thanks! ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Wed Oct 22 14:41:19 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 22 Oct 2014 14:41:19 -0400 Subject: [ITK] [ITK-dev] Can I get permission to upload a file to http://midas3.kitware.com? In-Reply-To: References: Message-ID: Hi Kent, You have been added to the Community Moderator group. Please try to upload again and let use know if you have any difficulties. Thanks, Matt On Wed, Oct 22, 2014 at 2:35 PM, Williams, Norman K wrote: > I have an account, I can upload my own public & private files, but I don?t > have permission to add new test Data. Can I be added to the permitted > uploaders? > > Thanks! > > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the > Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential > and may be legally privileged. If you are not the intended recipient, you > are hereby notified that any retention, dissemination, distribution, or > copying of this communication is strictly prohibited. Please reply to the > sender that you have received the message in error, then delete it. Thank > you. > ________________________________ > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From nikita at iitj.ac.in Wed Oct 22 18:33:23 2014 From: nikita at iitj.ac.in (Nikita Chopra) Date: Wed, 22 Oct 2014 18:33:23 -0400 Subject: [ITK] [ITK-users] Data Structure to save Vectors obtained from Demons Registration. Message-ID: Hello All I'm using itk:DemonsRegistrationFilter to apply registration on each successive frame that I obtain from Video .Please tell me how can I save the vector obtained from registration, what is the data structure I should use for saving the vector field. If it is saved automatically let me know how can I retrieve it . Also ,Please suggest me how to visualize these vectors as well. Thanks for the help in advance. Regards Nikita -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From lasso at queensu.ca Wed Oct 22 18:56:44 2014 From: lasso at queensu.ca (Andras Lasso) Date: Wed, 22 Oct 2014 22:56:44 +0000 Subject: [ITK] [ITK-users] Data Structure to save Vectors obtained from Demons Registration. In-Reply-To: References: Message-ID: If you save the transform as a displacement field (in a nrrd or mha file) then you can load it into 3D Slicer as a transform and visualize it in 2D and 3D (as glyphs, deformed grid, or contour lines) overlaid with your images, segmentation results, landmarks, etc. See more info and some examples here: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms Andras ________________________________ From: Nikita Chopra Sent: ?2014-?10-?22 18:33 To: insight-users at itk.org Subject: [ITK] [ITK-users] Data Structure to save Vectors obtained from Demons Registration. Hello All I'm using itk:DemonsRegistrationFilter to apply registration on each successive frame that I obtain from Video .Please tell me how can I save the vector obtained from registration, what is the data structure I should use for saving the vector field. If it is saved automatically let me know how can I retrieve it . Also ,Please suggest me how to visualize these vectors as well. Thanks for the help in advance. Regards Nikita -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Thu Oct 23 00:54:06 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 23 Oct 2014 00:54:06 -0400 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: There are a couple of upcoming opportunities to share, discuss, design, and learn with your fellow ITK community members. On Thursday (tomorrow), 1:00 PM Eastern USA time, there will be a Google+ Hangout where we will be doing code reviews: https://plus.google.com/events/cn4gsqfr90k9ssa0jogal8vobco On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/events/c2qo0onsh06h3adslvkcj66nr7k? For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 To get regular invites to these events, join the ITK Bar Camp G+ Community: https://plus.google.com/u/0/communities/111375098792764998322 All are welcome. Hope to talk to you then! From g.lemaitre58 at gmail.com Thu Oct 23 04:43:23 2014 From: g.lemaitre58 at gmail.com (=?UTF-8?Q?Guillaume_Lema=C3=AEtre?=) Date: Thu, 23 Oct 2014 10:43:23 +0200 Subject: [ITK] [ITK-users] Issue installing SimpleITK via conda-recipe Message-ID: Hi all, First, I am a newbie in Python and anaconda and sorry in advance if things seems trivial I tried to install SimpleITK through conda-recipe. The installation by itself seems to be fined but the test is failling: ==== testing package: simpleitk-0.8.0.post29-py27_0 ===== import: u'SimpleITK' Traceback (most recent call last): File "/home/lemaitre/anaconda/conda-bld/test-tmp_dir/run_test.py", line 25, in import SimpleITK File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/__init__.py", line 1, in from .SimpleITK import * File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 28, in _SimpleITK = swig_import_helper() File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 24, in swig_import_helper _mod = imp.load_module('_SimpleITK', fp, pathname, description) ImportError: /home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: symbol TIFFFieldDataType, version LIBTIFF_4.0 not defined in file libtiff.so.5 with link time reference TESTS FAILED: simpleitk-0.8.0.post29-py27_0 I got that the issue is linked with the libtiff but I believed that anaconda would manage the installation of the dependencies needed. My system is: Ubuntu 14.04 Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 Cheers, -- *LEMA?TRE GuillaumePhD CandiateMSc Erasmus Mundus ViBOT (Vision-roBOTic)MSc Business Innovation and Technology Management* g.lemaitre58 at gmail.com *ViCOROB - Computer Vision and Robotic Team* Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 http://vicorob.udg.es/ *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 http://le2i.cnrs.fr https://sites.google.com/site/glemaitre58/ Vice - Chairman of A.S.C. Fours UFOLEP Chairman of A.S.C. Fours FFC Webmaster of http://ascfours.free.fr -------------- 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 rsvpitt at gmail.com Thu Oct 23 07:04:10 2014 From: rsvpitt at gmail.com (Vikas) Date: Thu, 23 Oct 2014 07:04:10 -0400 Subject: [ITK] [ITK-users] Problem applying landmarks in FEM registration Message-ID: Hi, I am having issues applying landmarks to FEM registration and would appreciate any help to resolve it. I am following the example in RegistrationITKv4/DeformableRegistration11 with the following modification: //Add landmartks RegistrationType::PointType SourceLandmark; RegistrationType::PointType TargetLandmark; SourceLandmark[0] = 23;SourceLandmark[1] = 12;SourceLandmark[2] = 41; TargetLandmark[0] = 26;TargetLandmark[1] = 16;TargetLandmark[2] = 45; registrationFilter->AddLandmark(SourceLandmark,TargetLandmark); registrationFilter->SetUseLandmarks(true); I get a run time error: "Vector subscript out of range". The call stack is as follows: > msvcp90d.dll!std::_Debug_message(const wchar_t * message=0x000000013fa48fc8, const wchar_t * file=0x000000013fa49010, unsigned int line=779) Line 24 C++ HybridRegistration.exe!std::vector >::operator[](unsigned __int64 _Pos=0) Line 780 C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::ApplyLoads(itk::Size<3> ImgSz={...}, double * scaling=0x0000000000000000) Line 410 + 0x35 bytes C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::MultiResSolve() Line 1173 C++ HybridRegistration.exe!itk::fem::FEMRegistrationFilter,itk::Image,itk::fem::FEMObject<3> >::RunRegistration() Line 169 C++ HybridRegistration.exe!main(int argc=1, char * * argv=0x0000000002546b40) Line 225 C++ HybridRegistration.exe!__tmainCRTStartup() Line 586 + 0x19 bytes C HybridRegistration.exe!mainCRTStartup() Line 403 C Thanks Vikas -------------- 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 Oct 23 08:52:07 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 23 Oct 2014 08:52:07 -0400 Subject: [ITK] [ITK-users] Issue installing SimpleITK via conda-recipe In-Reply-To: References: Message-ID: <4129C8F3-7952-4104-94E4-A4407A40D41C@mail.nih.gov> Hello, Can you please send me you CMakeCache.txt file from the build directory. The simplest thing to do may be to remote using the anaconda "system" tiff library and just use the one ITK has. This can be done by modifying the conda recipe build script here [1]. Most likely there is some confusion which occurs during the CMake configuration about which tiff library to use. Brad [1] https://github.com/conda/conda-recipes/blob/master/simpleitk/build.sh#L35 On Oct 23, 2014, at 4:43 AM, Guillaume Lema?tre wrote: > Hi all, > > First, I am a newbie in Python and anaconda and sorry in advance if things seems trivial > I tried to install SimpleITK through conda-recipe. The installation by itself seems to be fined but the test is failling: > > ==== testing package: simpleitk-0.8.0.post29-py27_0 ===== > import: u'SimpleITK' > Traceback (most recent call last): > File "/home/lemaitre/anaconda/conda-bld/test-tmp_dir/run_test.py", line 25, in > import SimpleITK > File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/__init__.py", line 1, in > from .SimpleITK import * > File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 28, in > _SimpleITK = swig_import_helper() > File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 24, in swig_import_helper > _mod = imp.load_module('_SimpleITK', fp, pathname, description) > ImportError: /home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: symbol TIFFFieldDataType, version LIBTIFF_4.0 not defined in file libtiff.so.5 with link time reference > TESTS FAILED: simpleitk-0.8.0.post29-py27_0 > > I got that the issue is linked with the libtiff but I believed that anaconda would manage the installation of the dependencies needed. > > My system is: > Ubuntu 14.04 > Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21) > [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 > > Cheers, > > -- > LEMA?TRE Guillaume > PhD Candiate > MSc Erasmus Mundus ViBOT (Vision-roBOTic) > MSc Business Innovation and Technology Management > > g.lemaitre58 at gmail.com > > > ViCOROB - Computer Vision and Robotic Team > Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona > Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 > http://vicorob.udg.es/ > LE2I - Le Creusot > IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot > Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 > http://le2i.cnrs.fr > > https://sites.google.com/site/glemaitre58/ > Vice - Chairman of A.S.C. Fours UFOLEP > Chairman of A.S.C. Fours FFC > Webmaster of http://ascfours.free.fr > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.lemaitre58 at gmail.com Thu Oct 23 09:00:13 2014 From: g.lemaitre58 at gmail.com (=?UTF-8?Q?Guillaume_Lema=C3=AEtre?=) Date: Thu, 23 Oct 2014 15:00:13 +0200 Subject: [ITK] [ITK-users] Issue installing SimpleITK via conda-recipe In-Reply-To: <4129C8F3-7952-4104-94E4-A4407A40D41C@mail.nih.gov> References: <4129C8F3-7952-4104-94E4-A4407A40D41C@mail.nih.gov> Message-ID: Hi Brad, Find attached the CMakeCache.txt from ./anaconda/conda-bld/work/build In this file it seems that, ITK_USE_SYSTEM_TIFF:BOOL=ON Does it mean that the TIFF used is from the anaconda "system"? I assume that I have to try to put the boolean to OFF to use the one of ITK. Thanks, On 23 October 2014 14:52, Bradley Lowekamp wrote: > Hello, > > Can you please send me you CMakeCache.txt file from the build directory. > > The simplest thing to do may be to remote using the anaconda "system" tiff > library and just use the one ITK has. This can be done by modifying the > conda recipe build script here [1]. > > Most likely there is some confusion which occurs during the CMake > configuration about which tiff library to use. > > Brad > > [1] > https://github.com/conda/conda-recipes/blob/master/simpleitk/build.sh#L35 > > On Oct 23, 2014, at 4:43 AM, Guillaume Lema?tre > wrote: > > Hi all, > > First, I am a newbie in Python and anaconda and sorry in advance if things > seems trivial > I tried to install SimpleITK through conda-recipe. The installation by > itself seems to be fined but the test is failling: > > ==== testing package: simpleitk-0.8.0.post29-py27_0 ===== > import: u'SimpleITK' > Traceback (most recent call last): > File "/home/lemaitre/anaconda/conda-bld/test-tmp_dir/run_test.py", line > 25, in > import SimpleITK > File > "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/__init__.py", > line 1, in > from .SimpleITK import * > File > "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", > line 28, in > _SimpleITK = swig_import_helper() > File > "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", > line 24, in swig_import_helper > _mod = imp.load_module('_SimpleITK', fp, pathname, description) > ImportError: > /home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: > symbol TIFFFieldDataType, version LIBTIFF_4.0 not defined in file > libtiff.so.5 with link time reference > TESTS FAILED: simpleitk-0.8.0.post29-py27_0 > > I got that the issue is linked with the libtiff but I believed that > anaconda would manage the installation of the dependencies needed. > > My system is: > Ubuntu 14.04 > Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21) > [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 > > Cheers, > > -- > > > > > *LEMA?TRE GuillaumePhD CandiateMSc Erasmus Mundus ViBOT > (Vision-roBOTic)MSc Business Innovation and Technology Management* > g.lemaitre58 at gmail.com > > > *ViCOROB - Computer Vision and Robotic Team* > Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona > Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 > http://vicorob.udg.es/ > > *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la > Fonderie, 71200 Le Creusot > Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 > http://le2i.cnrs.fr > > https://sites.google.com/site/glemaitre58/ > Vice - Chairman of A.S.C. Fours UFOLEP > Chairman of A.S.C. Fours FFC > Webmaster of http://ascfours.free.fr > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > > -- *LEMA?TRE GuillaumePhD CandiateMSc Erasmus Mundus ViBOT (Vision-roBOTic)MSc Business Innovation and Technology Management* g.lemaitre58 at gmail.com *ViCOROB - Computer Vision and Robotic Team* Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 http://vicorob.udg.es/ *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 http://le2i.cnrs.fr https://sites.google.com/site/glemaitre58/ Vice - Chairman of A.S.C. Fours UFOLEP Chairman of A.S.C. Fours FFC Webmaster of http://ascfours.free.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- # This is the CMakeCache file. # For build in directory: /home/lemaitre/anaconda/conda-bld/work/build # It was generated by CMake: /home/lemaitre/anaconda/envs/_build/bin/cmake # You can edit this file to change values found and used by cmake. # If you do not want to change any of the values, simply exit the editor. # If you do want to change a value, simply edit, save, and exit the editor. # The syntax for the file is as follows: # KEY:TYPE=VALUE # KEY is the name of a variable in the cache. # TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!. # VALUE is the current value for the KEY. ######################## # EXTERNAL cache entries ######################## //path to the bison executable BISON_EXECUTABLE:FILEPATH=/usr/bin/bison //Flags used by bison BISON_FLAGS:STRING= //Enable Building of the SimpleITK Examples as a separate project. BUILD_EXAMPLES:BOOL=ON //Build SimpleITK ITK with shared libraries. This does not effect // wrapped languages. BUILD_SHARED_LIBS:BOOL=OFF //Turn on Testing for SimpleITK BUILD_TESTING:BOOL=OFF //Path to a program. CMAKE_AR:FILEPATH=/usr/bin/ar //No help, variable specified on the command line. CMAKE_BUILD_TYPE:STRING=RELEASE //Enable/Disable color output during build. CMAKE_COLOR_MAKEFILE:BOOL=ON //CXX compiler. CMAKE_CXX_COMPILER:FILEPATH=/usr/bin/c++ //No help, variable specified on the command line. CMAKE_CXX_FLAGS:STRING=-fvisibility=hidden -fvisibility-inlines-hidden //Flags used by the compiler during debug builds. CMAKE_CXX_FLAGS_DEBUG:STRING=-g //Flags used by the compiler during release builds for minimum // size. CMAKE_CXX_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG //Flags used by the compiler during release builds. CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -DNDEBUG //Flags used by the compiler during release builds with debug info. CMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG //C compiler. CMAKE_C_COMPILER:FILEPATH=/usr/bin/cc //No help, variable specified on the command line. CMAKE_C_FLAGS:STRING=-fvisibility=hidden //Flags used by the compiler during debug builds. CMAKE_C_FLAGS_DEBUG:STRING=-g //Flags used by the compiler during release builds for minimum // size. CMAKE_C_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG //Flags used by the compiler during release builds. CMAKE_C_FLAGS_RELEASE:STRING=-O3 -DNDEBUG //Flags used by the compiler during release builds with debug info. CMAKE_C_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG //Flags used by the linker. CMAKE_EXE_LINKER_FLAGS:STRING=' ' //Flags used by the linker during debug builds. CMAKE_EXE_LINKER_FLAGS_DEBUG:STRING= //Flags used by the linker during release minsize builds. CMAKE_EXE_LINKER_FLAGS_MINSIZEREL:STRING= //Flags used by the linker during release builds. CMAKE_EXE_LINKER_FLAGS_RELEASE:STRING= //Flags used by the linker during Release with Debug Info builds. CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO:STRING= //Enable/Disable output of compile commands during generation. CMAKE_EXPORT_COMPILE_COMMANDS:BOOL=OFF //Where all the prerequisite libraries go CMAKE_INSTALL_PREFIX:PATH=/home/lemaitre/anaconda/conda-bld/work/build //No help, variable specified on the command line. CMAKE_INSTALL_PREFIX=:PATH=/home/lemaitre/anaconda/envs/_build //Path to a program. CMAKE_LINKER:FILEPATH=/usr/bin/ld //Path to a program. CMAKE_MAKE_PROGRAM:FILEPATH=/usr/bin/make //Flags used by the linker during the creation of modules. CMAKE_MODULE_LINKER_FLAGS:STRING=' ' //Flags used by the linker during debug builds. CMAKE_MODULE_LINKER_FLAGS_DEBUG:STRING= //Flags used by the linker during release minsize builds. CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL:STRING= //Flags used by the linker during release builds. CMAKE_MODULE_LINKER_FLAGS_RELEASE:STRING= //Flags used by the linker during Release with Debug Info builds. CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO:STRING= //Path to a program. CMAKE_NM:FILEPATH=/usr/bin/nm //Path to a program. CMAKE_OBJCOPY:FILEPATH=/usr/bin/objcopy //Path to a program. CMAKE_OBJDUMP:FILEPATH=/usr/bin/objdump //No help, variable specified on the command line. CMAKE_OSX_DEPLOYMENT_TARGET:STRING= //Value Computed by CMake CMAKE_PROJECT_NAME:STATIC=SuperBuildSimpleITK //Path to a program. CMAKE_RANLIB:FILEPATH=/usr/bin/ranlib //Flags used by the linker during the creation of dll's. CMAKE_SHARED_LINKER_FLAGS:STRING=' ' //Flags used by the linker during debug builds. CMAKE_SHARED_LINKER_FLAGS_DEBUG:STRING= //Flags used by the linker during release minsize builds. CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL:STRING= //Flags used by the linker during release builds. CMAKE_SHARED_LINKER_FLAGS_RELEASE:STRING= //Flags used by the linker during Release with Debug Info builds. CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO:STRING= //If set, runtime paths are not added when installing shared libraries, // but are added when building. CMAKE_SKIP_INSTALL_RPATH:BOOL=NO //If set, runtime paths are not added when using shared libraries. CMAKE_SKIP_RPATH:BOOL=NO //Flags used by the linker during the creation of static libraries. CMAKE_STATIC_LINKER_FLAGS:STRING= //Flags used by the linker during debug builds. CMAKE_STATIC_LINKER_FLAGS_DEBUG:STRING= //Flags used by the linker during release minsize builds. CMAKE_STATIC_LINKER_FLAGS_MINSIZEREL:STRING= //Flags used by the linker during release builds. CMAKE_STATIC_LINKER_FLAGS_RELEASE:STRING= //Flags used by the linker during Release with Debug Info builds. CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO:STRING= //Path to a program. CMAKE_STRIP:FILEPATH=/usr/bin/strip //If true, cmake will use relative paths in makefiles and projects. CMAKE_USE_RELATIVE_PATHS:BOOL=OFF //If this value is on, makefiles will be generated without the // .SILENT directive, and all commands will be echoed to the console // during the make. This is useful for debugging only. With Visual // Studio IDE projects all commands are done without /nologo. CMAKE_VERBOSE_MAKEFILE:BOOL=FALSE //C# target platform: x86, x64, anycpu, or itanium CSHARP_PLATFORM:STRING=anycpu //git command line client GIT_EXECUTABLE:FILEPATH=/usr/bin/git //No help, variable specified on the command line. ITK_USE_SYSTEM_JPEG:BOOL=ON //No help, variable specified on the command line. ITK_USE_SYSTEM_PNG:BOOL=ON //No help, variable specified on the command line. ITK_USE_SYSTEM_TIFF:BOOL=ON //No help, variable specified on the command line. ITK_USE_SYSTEM_ZLIB:BOOL=ON //Turn OFF wrapping ITK with WrapITK ITK_WRAPPING:BOOL=OFF //Path to a file. JAVA_AWT_INCLUDE_PATH:PATH=/usr/lib/jvm/default-java/include //Path to a library. 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PYTHON_INCLUDE_PATH:PATH=/home/lemaitre/anaconda/envs/_build/include/python2.7 //No help, variable specified on the command line. PYTHON_LIBRARY:FILEPATH=/home/lemaitre/anaconda/envs/_build/lib/libpython2.7.so //Path to a library. PYTHON_LIBRARY_DEBUG:FILEPATH=PYTHON_LIBRARY_DEBUG-NOTFOUND //Rscript executable. RSCRIPT_EXECUTABLE:FILEPATH=RSCRIPT_EXECUTABLE-NOTFOUND //The Ruby arch header dir (2.0+) RUBY_ARCHHDR_DIR:PATH= //The Ruby arch dir RUBY_ARCH_DIR:PATH=/usr/lib/ruby/1.9.1/x86_64-linux //Path to a file. RUBY_CONFIG_INCLUDE_DIR:PATH=RUBY_CONFIG_INCLUDE_DIR-NOTFOUND //Path to a program. RUBY_EXECUTABLE:FILEPATH=/usr/bin/ruby //Vendor Ruby is available RUBY_HAS_VENDOR_RUBY:BOOL= //The Ruby header dir (1.9+) RUBY_HDR_DIR:PATH=/usr/include/ruby-1.9.1 //Path to a file. RUBY_INCLUDE_DIR:PATH=RUBY_INCLUDE_DIR-NOTFOUND //Path to a library. 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TCL_INCLUDE_PATH-ADVANCED:INTERNAL=1 //ADVANCED property for variable: TCL_LIBRARY TCL_LIBRARY-ADVANCED:INTERNAL=1 //ADVANCED property for variable: TCL_TCLSH TCL_TCLSH-ADVANCED:INTERNAL=1 //ADVANCED property for variable: TK_INCLUDE_PATH TK_INCLUDE_PATH-ADVANCED:INTERNAL=1 //ADVANCED property for variable: TK_LIBRARY TK_LIBRARY-ADVANCED:INTERNAL=1 //ADVANCED property for variable: TK_WISH TK_WISH-ADVANCED:INTERNAL=1 //ADVANCED property for variable: USE_SYSTEM_ITK USE_SYSTEM_ITK-ADVANCED:INTERNAL=1 //ADVANCED property for variable: USE_SYSTEM_SWIG USE_SYSTEM_SWIG-ADVANCED:INTERNAL=1 -------------- 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 Oct 23 09:21:31 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 23 Oct 2014 09:21:31 -0400 Subject: [ITK] [ITK-users] Issue installing SimpleITK via conda-recipe In-Reply-To: References: <4129C8F3-7952-4104-94E4-A4407A40D41C@mail.nih.gov> Message-ID: Hello, Yes, Changing the problematic USE_SYSTEM cmake options to OFF should fix this issue. Unfortunately, the variables I was looking for were not in that CMakeCache.txt file. They would be in the CMakeCache.txt file in the ITK-buiild subdirectory. Could you please e-mail that one off list? Thanks, Brad On Oct 23, 2014, at 9:00 AM, Guillaume Lema?tre wrote: > Hi Brad, > > Find attached the CMakeCache.txt from ./anaconda/conda-bld/work/build > In this file it seems that, > ITK_USE_SYSTEM_TIFF:BOOL=ON > > Does it mean that the TIFF used is from the anaconda "system"? I assume that I have to try to put the boolean to OFF to use the one of ITK. > > Thanks, > > On 23 October 2014 14:52, Bradley Lowekamp wrote: > Hello, > > Can you please send me you CMakeCache.txt file from the build directory. > > The simplest thing to do may be to remote using the anaconda "system" tiff library and just use the one ITK has. This can be done by modifying the conda recipe build script here [1]. > > Most likely there is some confusion which occurs during the CMake configuration about which tiff library to use. > > Brad > > [1] https://github.com/conda/conda-recipes/blob/master/simpleitk/build.sh#L35 > > On Oct 23, 2014, at 4:43 AM, Guillaume Lema?tre wrote: > >> Hi all, >> >> First, I am a newbie in Python and anaconda and sorry in advance if things seems trivial >> I tried to install SimpleITK through conda-recipe. The installation by itself seems to be fined but the test is failling: >> >> ==== testing package: simpleitk-0.8.0.post29-py27_0 ===== >> import: u'SimpleITK' >> Traceback (most recent call last): >> File "/home/lemaitre/anaconda/conda-bld/test-tmp_dir/run_test.py", line 25, in >> import SimpleITK >> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/__init__.py", line 1, in >> from .SimpleITK import * >> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 28, in >> _SimpleITK = swig_import_helper() >> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 24, in swig_import_helper >> _mod = imp.load_module('_SimpleITK', fp, pathname, description) >> ImportError: /home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: symbol TIFFFieldDataType, version LIBTIFF_4.0 not defined in file libtiff.so.5 with link time reference >> TESTS FAILED: simpleitk-0.8.0.post29-py27_0 >> >> I got that the issue is linked with the libtiff but I believed that anaconda would manage the installation of the dependencies needed. >> >> My system is: >> Ubuntu 14.04 >> Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21) >> [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 >> >> Cheers, >> >> -- >> LEMA?TRE Guillaume >> PhD Candiate >> MSc Erasmus Mundus ViBOT (Vision-roBOTic) >> MSc Business Innovation and Technology Management >> >> g.lemaitre58 at gmail.com >> >> >> ViCOROB - Computer Vision and Robotic Team >> Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona >> Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 >> http://vicorob.udg.es/ >> LE2I - Le Creusot >> IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot >> Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 >> http://le2i.cnrs.fr >> >> https://sites.google.com/site/glemaitre58/ >> Vice - Chairman of A.S.C. Fours UFOLEP >> Chairman of A.S.C. Fours FFC >> Webmaster of http://ascfours.free.fr >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > > > > > -- > LEMA?TRE Guillaume > PhD Candiate > MSc Erasmus Mundus ViBOT (Vision-roBOTic) > MSc Business Innovation and Technology Management > > g.lemaitre58 at gmail.com > > > ViCOROB - Computer Vision and Robotic Team > Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona > Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 > http://vicorob.udg.es/ > LE2I - Le Creusot > IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot > Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 > http://le2i.cnrs.fr > > https://sites.google.com/site/glemaitre58/ > Vice - Chairman of A.S.C. Fours UFOLEP > Chairman of A.S.C. Fours FFC > Webmaster of http://ascfours.free.fr > -------------- 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 Oct 23 09:57:01 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Thu, 23 Oct 2014 09:57:01 -0400 Subject: [ITK] [ITK-users] Issue installing SimpleITK via conda-recipe In-Reply-To: References: <4129C8F3-7952-4104-94E4-A4407A40D41C@mail.nih.gov> Message-ID: <3CA52435-26B7-46DA-B0CD-3ADF369F23F6@mail.nih.gov> Hello, Thank you for sending me the file off list. I asked that just because of the potential size of the file. It's best to keep the conversation on the list so that all can benefit. It does appear that there is a problem with the SimpleITK using system libraries not picking up the anaconda dependencies but instead the system ones. For example here in the ITK CMakeCache.txt file we have: TIFF_INCLUDE_DIR:PATH=/usr/include/x86_64-linux-gnu TIFF_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libtiff.so PNG_PNG_INCLUDE_DIR:PATH=/usr/include and simular things for jpeg and zlib. I'd recommend turning them all off until a better solution is found. I have a pull request for this change here: https://github.com/conda/conda-recipes/pull/201 Thanks, Brad On Oct 23, 2014, at 9:21 AM, Bradley Lowekamp wrote: > Hello, > > Yes, Changing the problematic USE_SYSTEM cmake options to OFF should fix this issue. > > Unfortunately, the variables I was looking for were not in that CMakeCache.txt file. They would be in the CMakeCache.txt file in the ITK-buiild subdirectory. Could you please e-mail that one off list? > > Thanks, > Brad > > On Oct 23, 2014, at 9:00 AM, Guillaume Lema?tre wrote: > >> Hi Brad, >> >> Find attached the CMakeCache.txt from ./anaconda/conda-bld/work/build >> In this file it seems that, >> ITK_USE_SYSTEM_TIFF:BOOL=ON >> >> Does it mean that the TIFF used is from the anaconda "system"? I assume that I have to try to put the boolean to OFF to use the one of ITK. >> >> Thanks, >> >> On 23 October 2014 14:52, Bradley Lowekamp wrote: >> Hello, >> >> Can you please send me you CMakeCache.txt file from the build directory. >> >> The simplest thing to do may be to remote using the anaconda "system" tiff library and just use the one ITK has. This can be done by modifying the conda recipe build script here [1]. >> >> Most likely there is some confusion which occurs during the CMake configuration about which tiff library to use. >> >> Brad >> >> [1] https://github.com/conda/conda-recipes/blob/master/simpleitk/build.sh#L35 >> >> On Oct 23, 2014, at 4:43 AM, Guillaume Lema?tre wrote: >> >>> Hi all, >>> >>> First, I am a newbie in Python and anaconda and sorry in advance if things seems trivial >>> I tried to install SimpleITK through conda-recipe. The installation by itself seems to be fined but the test is failling: >>> >>> ==== testing package: simpleitk-0.8.0.post29-py27_0 ===== >>> import: u'SimpleITK' >>> Traceback (most recent call last): >>> File "/home/lemaitre/anaconda/conda-bld/test-tmp_dir/run_test.py", line 25, in >>> import SimpleITK >>> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/__init__.py", line 1, in >>> from .SimpleITK import * >>> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 28, in >>> _SimpleITK = swig_import_helper() >>> File "/home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 24, in swig_import_helper >>> _mod = imp.load_module('_SimpleITK', fp, pathname, description) >>> ImportError: /home/lemaitre/anaconda/envs/_test/lib/python2.7/site-packages/SimpleITK/_SimpleITK.so: symbol TIFFFieldDataType, version LIBTIFF_4.0 not defined in file libtiff.so.5 with link time reference >>> TESTS FAILED: simpleitk-0.8.0.post29-py27_0 >>> >>> I got that the issue is linked with the libtiff but I believed that anaconda would manage the installation of the dependencies needed. >>> >>> My system is: >>> Ubuntu 14.04 >>> Python 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Aug 21 2014, 18:22:21) >>> [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2 >>> >>> Cheers, >>> >>> -- >>> LEMA?TRE Guillaume >>> PhD Candiate >>> MSc Erasmus Mundus ViBOT (Vision-roBOTic) >>> MSc Business Innovation and Technology Management >>> >>> g.lemaitre58 at gmail.com >>> >>> >>> ViCOROB - Computer Vision and Robotic Team >>> Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona >>> Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 >>> http://vicorob.udg.es/ >>> LE2I - Le Creusot >>> IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot >>> Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 >>> http://le2i.cnrs.fr >>> >>> https://sites.google.com/site/glemaitre58/ >>> Vice - Chairman of A.S.C. Fours UFOLEP >>> Chairman of A.S.C. Fours FFC >>> Webmaster of http://ascfours.free.fr >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >> >> >> >> >> -- >> LEMA?TRE Guillaume >> PhD Candiate >> MSc Erasmus Mundus ViBOT (Vision-roBOTic) >> MSc Business Innovation and Technology Management >> >> g.lemaitre58 at gmail.com >> >> >> ViCOROB - Computer Vision and Robotic Team >> Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona >> Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 >> http://vicorob.udg.es/ >> LE2I - Le Creusot >> IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot >> Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 >> http://le2i.cnrs.fr >> >> https://sites.google.com/site/glemaitre58/ >> Vice - Chairman of A.S.C. Fours UFOLEP >> Chairman of A.S.C. Fours FFC >> Webmaster of http://ascfours.free.fr >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 lefebvre at imnc.in2p3.fr Thu Oct 23 12:20:03 2014 From: lefebvre at imnc.in2p3.fr (=?ISO-8859-1?Q?Fran=E7oise_Lefebvre?=) Date: Thu, 23 Oct 2014 18:20:03 +0200 Subject: [ITK] [ITK-users] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: <54475B84.5020906@imnc.in2p3.fr> References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> <54475B84.5020906@imnc.in2p3.fr> Message-ID: <54492AB3.2030006@imnc.in2p3.fr> Hi, I also tried on Windows 8,msvc2012_opengl and Qt5.3. I get exactly the same link error. FL Le 22/10/2014 09:23, Fran?oise Lefebvre a ?crit : > Yes I did. > > Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : >> Did you try the latest 4.6.1 release? >> >> Brad >> >> On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre >> wrote: >> >>> Hi, >>> >>> ITK 4.6 was succesfully build using cmake2.8.10.2, the default >>> parameters and the Module_ITKReview on. >>> >>> I am now trying to compile a program developed in C++ using Qt5.1.1 >>> and Microsoft Visual C++ express 2010 on Windows 7. >>> >>> I get the following link error : >>> >>> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe >>> non r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction >>> "public: static class itksys::Encoding::CommandLineArguments __cdecl >>> itksys::Encoding::CommandLineArguments::Main(int,char const * const >>> *)" (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) >>> >>> I didn't get this error when compiling with itk4.3 . >>> >>> Any hint ? >>> >>> Thank you for your help, >>> >>> F. Lefebvre >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the 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 norman-k-williams at uiowa.edu Thu Oct 23 13:32:05 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Thu, 23 Oct 2014 17:32:05 +0000 Subject: [ITK] [ITK-dev] Can't build using NINJA with ITKDCMTK/ITKIODCMTK turned on. Message-ID: A couple of years ago, with massive help from Brad King, I managed to get an embedded ExternalProject build of DCMTK embedded into ITK/Modules/ThirdParty. This was workable, because the CMake dependencies were explicitly set up such that the DCMTK libraries depended on the ExternalProject DCMTK target, and the DCMTKImageIO module depended on the libraries. When using the CMake with the Makefile generator, this hangs together, because the sub-make in Modules/IO/DCMTK won?t happen until the ExternalProject build in Modules/ThirdParty/DCMTK is complete. Ninja, on the other hand, makes one flat megamake at the top level of ITK, and if you try and build with Module_ITKDCMTK/Module_ITKIODCMTK/Module_IOTransformDCMTK turned on, it fails immediately because the targets in Modules/IO/DCMTK depend on non-existent DCMTK libraries. It?s a problem if we support all CMake generators except Ninja. I like using Ninja because it shaves several seconds off build times, which is great when you?re in an edit/compile/test workflow. I have no idea how this could be resolved, except to remove the internal DCMTK build and require USE_SYSTEM_DCMTK=ON. Does anyone have a better idea. ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- 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 bill.hoffman at kitware.com Thu Oct 23 13:57:08 2014 From: bill.hoffman at kitware.com (Bill Hoffman) Date: Thu, 23 Oct 2014 13:57:08 -0400 Subject: [ITK] [ITK-dev] Can't build using NINJA with ITKDCMTK/ITKIODCMTK turned on. In-Reply-To: References: Message-ID: <54494174.1080602@kitware.com> On 10/23/2014 1:32 PM, Williams, Norman K wrote: > I have no idea how this could be resolved, except to remove the internal > DCMTK build and require USE_SYSTEM_DCMTK=ON. Does anyone have a better > idea. > The other option is to build this without external project and use add_subdirectory like we do with other 3rd party stuff (png, etc). Using ExternalProject does not work unless you build everything with external project as this case shows. How hard would that be to do? -Bill _______________________________________________ Powered by www.kitware.com 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 Oct 23 14:03:21 2014 From: brad.king at kitware.com (Brad King) Date: Thu, 23 Oct 2014 14:03:21 -0400 Subject: [ITK] [ITK-dev] Can't build using NINJA with ITKDCMTK/ITKIODCMTK turned on. In-Reply-To: References: Message-ID: <544942E9.40805@kitware.com> On 10/23/2014 01:32 PM, Williams, Norman K wrote: > it fails immediately because the targets in Modules/IO/DCMTK depend > on non-existent DCMTK libraries. This cannot be solved cleanly without addressing these issues: https://github.com/martine/ninja/issues/760#issuecomment-46540858 http://www.cmake.org/Bug/view.php?id=14963#c36130 Currently the only way to build an ExternalProject cleanly with Ninja is if the outer project contains nothing except custom commands/targets, i.e. a superbuild that does both DCMTK and ITK as external projects. -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 norman-k-williams at uiowa.edu Thu Oct 23 15:04:14 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Thu, 23 Oct 2014 19:04:14 +0000 Subject: [ITK] [ITK-dev] Can't build using NINJA with ITKDCMTK/ITKIODCMTK turned on. In-Reply-To: <544942E9.40805@kitware.com> References: <544942E9.40805@kitware.com> Message-ID: Yeah that?s the problem right there. I would have no problem with including DCMTK in the distro. On 10/23/14, 1:03 PM, "Brad King" wrote: >On 10/23/2014 01:32 PM, Williams, Norman K wrote: >> it fails immediately because the targets in Modules/IO/DCMTK depend >> on non-existent DCMTK libraries. > >This cannot be solved cleanly without addressing these issues: > > https://github.com/martine/ninja/issues/760#issuecomment-46540858 > http://www.cmake.org/Bug/view.php?id=14963#c36130 > >Currently the only way to build an ExternalProject cleanly >with Ninja is if the outer project contains nothing except >custom commands/targets, i.e. a superbuild that does both >DCMTK and ITK as external projects. > >-Brad > ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Thu Oct 23 17:37:02 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 23 Oct 2014 17:37:02 -0400 Subject: [ITK] [ITK-users] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: <54492AB3.2030006@imnc.in2p3.fr> References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> <54475B84.5020906@imnc.in2p3.fr> <54492AB3.2030006@imnc.in2p3.fr> Message-ID: Hi, Are you using CMake to configure your project? Matt On Thu, Oct 23, 2014 at 12:20 PM, Fran?oise Lefebvre wrote: > Hi, > > I also tried on Windows 8,msvc2012_opengl and Qt5.3. I get exactly the same > link error. > > FL > > > Le 22/10/2014 09:23, Fran?oise Lefebvre a ?crit : > >> Yes I did. >> >> Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : >>> >>> Did you try the latest 4.6.1 release? >>> >>> Brad >>> >>> On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre >>> wrote: >>> >>>> Hi, >>>> >>>> ITK 4.6 was succesfully build using cmake2.8.10.2, the default >>>> parameters and the Module_ITKReview on. >>>> >>>> I am now trying to compile a program developed in C++ using Qt5.1.1 and >>>> Microsoft Visual C++ express 2010 on Windows 7. >>>> >>>> I get the following link error : >>>> >>>> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non >>>> r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: >>>> static class itksys::Encoding::CommandLineArguments __cdecl >>>> itksys::Encoding::CommandLineArguments::Main(int,char const * const *)" >>>> (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) >>>> >>>> I didn't get this error when compiling with itk4.3 . >>>> >>>> Any hint ? >>>> >>>> Thank you for your help, >>>> >>>> F. Lefebvre >>>> >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the 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 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 JCerrola at childrensnational.org Thu Oct 23 17:53:24 2014 From: JCerrola at childrensnational.org (Cerrolaza, Juan) Date: Thu, 23 Oct 2014 21:53:24 +0000 Subject: [ITK] Question about the use of LevelSetsv4 Message-ID: <9560AC300206F04C862B7A34B9BC37A902DC69AA@PVTH-EXMBX2.cnmc.org> Dear ITK community, I recently started to use the new framework ITK provides for Level Sets (LevelSetsv4). It seems to be a pretty nice framework and an ideal way to combine different terms from Level Sets theory (advection terms, curvature-based terms, propagation terms, etc). However, I'm still a bit confused about how to use and configure it. I would really appreciate if anyone of you could help me to clarify any of these questions. i) Looking into the description of these terms, for instance the curvature term: 'LevelSetEquationCurvatureTerm' (though this is this is also valid for any other term such as the advection term 'LevelSetEquationAdvectionTerm', or the propagation term 'LevelSetEquationPropagationTerm'), it seems like the user has the option to define a specific curvature image (according to the literature, this terms is typically defined as an the result of using any edge detector to the image we are trying to segment. If no curvature image is set, it casts the input image and uses it in the term contribution calculation. My question is how does ITK calculate this term actually. Does it use any edge detector over the input image (such as 1/(1 + G(I)), where I is the input image, and G(.) is the Gaussian filter)? What happened if both, the input image and the curvature image are defined? Does ITK ignore the first one? ii) The second question is about how to control the propagation direction of the level set. In the example, the level set is initialized as a big square area that contains all the elements to segment. In this scenario, the evolution of the level set should be inward. What if we initialize the level set inside the target structure? In this case the evolution of the level set should be outward. How can we control it? My guess was that the sign of the coefficients that define the weight of each term would control it, but after making different test, I'm not completely sure about it. Thank you very much in advance. Juan Juan J. Cerrolaza PhD Sheikh Zayed Institute for Pediatric Surgical Innovation Children's National Health System 111 Michigan Avenue, NW Washington, DC 20010 E-mail: JCerrola at cnmc.org, jjcerromar at gmail.com Phone: +1 (202) 476-1272 We stand for children. www.ChildrensNational.org ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lefebvre at imnc.in2p3.fr Fri Oct 24 04:00:59 2014 From: lefebvre at imnc.in2p3.fr (=?UTF-8?B?RnJhbsOnb2lzZSBMZWZlYnZyZQ==?=) Date: Fri, 24 Oct 2014 10:00:59 +0200 Subject: [ITK] [ITK-users] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> <54475B84.5020906@imnc.in2p3.fr> <54492AB3.2030006@imnc.in2p3.fr> Message-ID: <544A073B.4080905@imnc.in2p3.fr> No, I'm not. I have always used a .pro file and qmake. Le 23/10/2014 23:37, Matt McCormick a ?crit : > Hi, > > Are you using CMake to configure your project? > > Matt > > On Thu, Oct 23, 2014 at 12:20 PM, Fran?oise Lefebvre > wrote: >> Hi, >> >> I also tried on Windows 8,msvc2012_opengl and Qt5.3. I get exactly the same >> link error. >> >> FL >> >> >> Le 22/10/2014 09:23, Fran?oise Lefebvre a ?crit : >> >>> Yes I did. >>> >>> Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : >>>> Did you try the latest 4.6.1 release? >>>> >>>> Brad >>>> >>>> On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre >>>> wrote: >>>> >>>>> Hi, >>>>> >>>>> ITK 4.6 was succesfully build using cmake2.8.10.2, the default >>>>> parameters and the Module_ITKReview on. >>>>> >>>>> I am now trying to compile a program developed in C++ using Qt5.1.1 and >>>>> Microsoft Visual C++ express 2010 on Windows 7. >>>>> >>>>> I get the following link error : >>>>> >>>>> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non >>>>> r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: >>>>> static class itksys::Encoding::CommandLineArguments __cdecl >>>>> itksys::Encoding::CommandLineArguments::Main(int,char const * const *)" >>>>> (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) >>>>> >>>>> I didn't get this error when compiling with itk4.3 . >>>>> >>>>> Any hint ? >>>>> >>>>> Thank you for your help, >>>>> >>>>> F. Lefebvre >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the 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 -- Fran?oise LEFEBVRE IMNC (Imagerie et Mod?lisation en Neurobiologie et Canc?rologie) Campus d'Orsay - B?t 440 91405 ORSAY Cedex 01 69 15 51 87 _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 abdul.sw84 at gmail.com Fri Oct 24 04:30:29 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 10:30:29 +0200 Subject: [ITK] [ITK-users] ImageFileReader Update() Message-ID: Hello, I'm new to ITK, and just want to ask about what "Update()" means when used with ImageFileReader. For instance: typedef itk::ImageFileReader ReaderType; ReaderType::Pointer imageReader = ReaderType::New(); imageReader->SetFileName( argv[1] ); * imageReader->Update();* Thanks. -------------- 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 abdul.sw84 at gmail.com Fri Oct 24 04:32:33 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 10:32:33 +0200 Subject: [ITK] [ITK-users] Numeric traits Message-ID: Hello, I came across the following statement: PixelType label = itk::NumericTraits::One; It seems to be related to numric traits, which I have visited its documentation website, here , but, yet, didn't get the idea of the statement. Can you kindly just describe to me what the statement means? Thanks. -------------- 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 abdul.sw84 at gmail.com Fri Oct 24 05:00:42 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 11:00:42 +0200 Subject: [ITK] [ITK-users] ImageRegionIteratorWithIndex Message-ID: Hello, What is the purpose of ImageRegionIteratorWithIndex ? I didn't get the whole point from the documentation. Can you kindly just clarify it a bit? Thanks. -------------- 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 abdul.sw84 at gmail.com Fri Oct 24 05:04:01 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 11:04:01 +0200 Subject: [ITK] [ITK-users] ItI in itk Message-ID: Hello, I came across this code: itk::ImageRegionIteratorWithIndex *ItI*( imageReader->GetOutput(), imageReader->GetOutput()->GetLargestPossibleRegion() ); What does "ItI" mean? Thanks. -------------- 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 abdul.sw84 at gmail.com Fri Oct 24 05:11:02 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 11:11:02 +0200 Subject: [ITK] [ITK-users] Shouldn't they be swapped? Message-ID: Hello, I came across the following code: PixelType maxValue = itk::NumericTraits::NonpositiveMin(); PixelType minValue = itk::NumericTraits::max(); Shouldn't the above statements be swapped? That is, minValue for the first, and ,maxValue for the second? Thanks. -------------- 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 arnaudgelas at gmail.com Fri Oct 24 05:16:40 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Fri, 24 Oct 2014 11:16:40 +0200 Subject: [ITK] [ITK-users] ImageFileReader Update() In-Reply-To: References: Message-ID: Hi Abdul, A good starting point is the software guide: http://www.itk.org/ItkSoftwareGuide.pdf Best Arnaud On Oct 24, 2014, at 10:30 AM, Abdul Abdul wrote: > Hello, > > I'm new to ITK, and just want to ask about what "Update()" means when used with ImageFileReader. > > For instance: > > typedef itk::ImageFileReader ReaderType; > ReaderType::Pointer imageReader = ReaderType::New(); > imageReader->SetFileName( argv[1] ); > imageReader->Update(); > > Thanks. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 abdul.sw84 at gmail.com Fri Oct 24 05:54:53 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 11:54:53 +0200 Subject: [ITK] [ITK-users] Pointers and New() Message-ID: Hello, I noticed that when we want to use "New()" in itk with some type, we use "Pointer" with that type. Like for instance: SomeType::Pointer st = SomeType::New(); In "itk", is this always the case? Is it because in order to access the "functions" with a a type in itk, this can only be done through pointers? Thanks. -------------- 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 abdul.sw84 at gmail.com Fri Oct 24 06:10:45 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 24 Oct 2014 12:10:45 +0200 Subject: [ITK] [ITK-users] ImageFileReader Update() In-Reply-To: References: Message-ID: Hi Arnaud, Thanks for your kind reply. That is very helpful. I got the following from the guide regarding "Update()": *The pipeline update mechanism ensures that the reader only executes when a data request is made to the reader and the reader has not read any data.* But, it is yet not very clear. Can you kindly describe it a bit? Thanks. On Fri, Oct 24, 2014 at 11:16 AM, Arnaud Gelas wrote: > Hi Abdul, > > A good starting point is the software guide: > > http://www.itk.org/ItkSoftwareGuide.pdf > > Best > Arnaud > > On Oct 24, 2014, at 10:30 AM, Abdul Abdul wrote: > > Hello, > > I'm new to ITK, and just want to ask about what "Update()" means when used > with ImageFileReader. > > For instance: > > typedef itk::ImageFileReader ReaderType; > ReaderType::Pointer imageReader = ReaderType::New(); > imageReader->SetFileName( argv[1] ); > * imageReader->Update();* > > Thanks. > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 arnaudgelas at gmail.com Fri Oct 24 07:03:46 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Fri, 24 Oct 2014 13:03:46 +0200 Subject: [ITK] [ITK-users] ImageFileReader Update() In-Reply-To: References: Message-ID: <8261ECB7-BEFC-4841-9A95-E9F3BD9C612F@gmail.com> please read section 3.5 Data Processing Pipeline On Oct 24, 2014, at 12:10 PM, Abdul Abdul wrote: > Hi Arnaud, > > Thanks for your kind reply. That is very helpful. I got the following from the guide regarding "Update()": > > The pipeline update mechanism ensures that the reader only executes when a data request is made to the reader and the reader has not read any data. > > But, it is yet not very clear. > > Can you kindly describe it a bit? > > Thanks. > > On Fri, Oct 24, 2014 at 11:16 AM, Arnaud Gelas wrote: > Hi Abdul, > > A good starting point is the software guide: > > http://www.itk.org/ItkSoftwareGuide.pdf > > Best > Arnaud > > On Oct 24, 2014, at 10:30 AM, Abdul Abdul wrote: > >> Hello, >> >> I'm new to ITK, and just want to ask about what "Update()" means when used with ImageFileReader. >> >> For instance: >> >> typedef itk::ImageFileReader ReaderType; >> ReaderType::Pointer imageReader = ReaderType::New(); >> imageReader->SetFileName( argv[1] ); >> imageReader->Update(); >> >> Thanks. >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 millerjv at gmail.com Fri Oct 24 07:31:24 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 24 Oct 2014 07:31:24 -0400 Subject: [ITK] [ITK-users] Numeric traits In-Reply-To: References: Message-ID: This statement assigns the value of 1 to variable "label". The value of NumericTraits::One is specific to the datatype PixelType. For instance, For an integer type, NumericTraits::One will be 1. For a floating point type, it will be 1.0. Techniques like this are used in Generic Programming to initialize or assign a variable a value of the appropriate type (and avoid compiler warnings and performance associated with casting between types). On Fri, Oct 24, 2014 at 4:32 AM, Abdul Abdul wrote: > Hello, > > I came across the following statement: > > PixelType label = itk::NumericTraits::One; > > It seems to be related to numric traits, which I have visited its > documentation website, here > , but, > yet, didn't get the idea of the statement. > > Can you kindly just describe to me what the statement means? > > Thanks. > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 millerjv at gmail.com Fri Oct 24 07:33:26 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 24 Oct 2014 07:33:26 -0400 Subject: [ITK] [ITK-users] ImageRegionIteratorWithIndex In-Reply-To: References: Message-ID: Image Iterators allow you to visit every pixel in an image (or image region) with a prescribed pattern of access. We use Image Iterators to write generic code that can operate on 1D, 2D, 3D, and 4D images without requiring the algorithm code to understand the dimension of the image. The WithIndex variants of the Image Iterators are optimized to be able to report the pixel position (Index) of the iterator. On Fri, Oct 24, 2014 at 5:00 AM, Abdul Abdul wrote: > Hello, > > What is the purpose of ImageRegionIteratorWithIndex > ? > I didn't get the whole point from the documentation. Can you kindly just > clarify it a bit? > > Thanks. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 millerjv at gmail.com Fri Oct 24 07:34:54 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 24 Oct 2014 07:34:54 -0400 Subject: [ITK] [ITK-users] ItI in itk In-Reply-To: References: Message-ID: Itl is this case is a variable of type ImageRegionIteratorWithIndex. Its constructor is being called with the output of the ImageReader and the iterator will walk the LargestPossibleRegion of the ImageReader's output. On Fri, Oct 24, 2014 at 5:04 AM, Abdul Abdul wrote: > Hello, > > I came across this code: > > itk::ImageRegionIteratorWithIndex *ItI*( > imageReader->GetOutput(), > imageReader->GetOutput()->GetLargestPossibleRegion() ); > > What does "ItI" mean? > > Thanks. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 millerjv at gmail.com Fri Oct 24 07:36:52 2014 From: millerjv at gmail.com (Jim Miller) Date: Fri, 24 Oct 2014 07:36:52 -0400 Subject: [ITK] [ITK-users] Shouldn't they be swapped? In-Reply-To: References: Message-ID: Most likely you are looking at code that is just before a loop that is searching to find the min and max values within an image. It is common practice to initialize the current values of min and max in this manner so that you can write code like if (value > maxValue) { value = maxValue; } On Fri, Oct 24, 2014 at 5:11 AM, Abdul Abdul wrote: > Hello, > > I came across the following code: > > PixelType maxValue = itk::NumericTraits::NonpositiveMin(); > PixelType minValue = itk::NumericTraits::max(); > > Shouldn't the above statements be swapped? That is, minValue for the > first, and ,maxValue for the second? > > Thanks. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 anton.delehony at gmail.com Fri Oct 24 09:56:56 2014 From: anton.delehony at gmail.com (Anton Delehony) Date: Fri, 24 Oct 2014 09:56:56 -0400 Subject: [ITK] [ITK-users] Liver lobes atlas Message-ID: Hi All, I'm looking for a liver atlas that I can use to segment the different lobes of the liver from MR images. Does something like this exist? Anton -------------- 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 norman-k-williams at uiowa.edu Fri Oct 24 10:06:41 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Fri, 24 Oct 2014 14:06:41 +0000 Subject: [ITK] [ITK-users] ImageRegionIteratorWithIndex In-Reply-To: References: Message-ID: Normally, to visit every pixel in an Image, you?d use an ImageRegionIterator, or ImageRegionConstIterator. The latter you?d use when you don?t want to or cannot modify the image. ImageRegionIteratorWithIndex (and ImageRegionConstIteratorWithIndex) are, as Jim Miller said, optimized for reporting the index of the voxel currently referenced by the iterator. A very common use would be to iterate through an image, but use the index to access another image?s voxels as well. Generally, you?d use an iterator for each image but there are cases ? like when you only occasionally use the index to access another image ? where it makes sense not to bother with the second iterator. From: Abdul Abdul > Date: Friday, October 24, 2014 at 4:00 AM To: Insight > Subject: [ITK-users] ImageRegionIteratorWithIndex Hello, What is the purpose of ImageRegionIteratorWithIndex? I didn't get the whole point from the documentation. Can you kindly just clarify it a bit? Thanks. ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- 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 sami.koho at gmail.com Fri Oct 24 10:36:01 2014 From: sami.koho at gmail.com (Sami Koho) Date: Fri, 24 Oct 2014 17:36:01 +0300 Subject: [ITK] [ITK-users] Example medical images for teaching Image Segmentation Message-ID: Hello, This is not directly related to ITK, but I will ask anyway, out of curiosity. This fall I have been teaching Digital Image Processing to Biomedical imaging students. The next subject will be Image Segmentation (Edge detection models, / thresholding). Would any of you have some favorite medical images to demonstrate these subjects? I can of course use any pictures, but having examples relevant to the students would be nice. I have my own libraries as well, but they are mostly of cells and their internals (microscopy lab). Feel free to send any links/files, if something comes to mind. Best, Sami -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Fri Oct 24 10:56:17 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 24 Oct 2014 10:56:17 -0400 Subject: [ITK] [ITK-users] Pointers and New() In-Reply-To: References: Message-ID: Hi Abdul, Welcome to ITK! Yes, we always want to use ::New(), which returns ITK SmartPointer's [1] since this is used by the reference count kept in all ITK Object's [2]. This is described in more detail in the ITK Software Guide [3]. Hope this helps, Matt [1] http://www.itk.org/Doxygen/html/classitk_1_1SmartPointer.html [2] http://www.itk.org/Doxygen/html/classitk_1_1Object.html [3] http://itk.org/ItkSoftwareGuide.pdf On Fri, Oct 24, 2014 at 5:54 AM, Abdul Abdul wrote: > Hello, > > I noticed that when we want to use "New()" in itk with some type, we use > "Pointer" with that type. Like for instance: > > SomeType::Pointer st = SomeType::New(); > > In "itk", is this always the case? Is it because in order to access the > "functions" with a a type in itk, this can only be done through pointers? > > Thanks. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 Fri Oct 24 10:57:29 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 24 Oct 2014 10:57:29 -0400 Subject: [ITK] [ITK-users] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: <544A073B.4080905@imnc.in2p3.fr> References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> <54475B84.5020906@imnc.in2p3.fr> <54492AB3.2030006@imnc.in2p3.fr> <544A073B.4080905@imnc.in2p3.fr> Message-ID: Hi Fran?oise, CMake is recommended -- it will avoid this problem and others. It works well with Qt. Thanks, Matt On Fri, Oct 24, 2014 at 4:00 AM, Fran?oise Lefebvre wrote: > > No, I'm not. I have always used a .pro file and qmake. > > Le 23/10/2014 23:37, Matt McCormick a ?crit : > >> Hi, >> >> Are you using CMake to configure your project? >> >> Matt >> >> On Thu, Oct 23, 2014 at 12:20 PM, Fran?oise Lefebvre >> wrote: >>> >>> Hi, >>> >>> I also tried on Windows 8,msvc2012_opengl and Qt5.3. I get exactly the >>> same >>> link error. >>> >>> FL >>> >>> >>> Le 22/10/2014 09:23, Fran?oise Lefebvre a ?crit : >>> >>>> Yes I did. >>>> >>>> Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : >>>>> >>>>> Did you try the latest 4.6.1 release? >>>>> >>>>> Brad >>>>> >>>>> On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre >>>>> >>>>> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> ITK 4.6 was succesfully build using cmake2.8.10.2, the default >>>>>> parameters and the Module_ITKReview on. >>>>>> >>>>>> I am now trying to compile a program developed in C++ using Qt5.1.1 >>>>>> and >>>>>> Microsoft Visual C++ express 2010 on Windows 7. >>>>>> >>>>>> I get the following link error : >>>>>> >>>>>> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe non >>>>>> r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction "public: >>>>>> static class itksys::Encoding::CommandLineArguments __cdecl >>>>>> itksys::Encoding::CommandLineArguments::Main(int,char const * const >>>>>> *)" >>>>>> (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) >>>>>> >>>>>> I didn't get this error when compiling with itk4.3 . >>>>>> >>>>>> Any hint ? >>>>>> >>>>>> Thank you for your help, >>>>>> >>>>>> F. Lefebvre >>>>>> >>>>>> _____________________________________ >>>>>> Powered by www.kitware.com >>>>>> >>>>>> Visit other Kitware open-source projects at >>>>>> http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>> http://www.kitware.com/products/protraining.php >>>>>> >>>>>> Please keep messages on-topic and check the 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 > > > -- > Fran?oise LEFEBVRE > IMNC (Imagerie et Mod?lisation en Neurobiologie et Canc?rologie) > Campus d'Orsay - B?t 440 > 91405 ORSAY Cedex > 01 69 15 51 87 > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From matt.mccormick at kitware.com Fri Oct 24 12:33:41 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 24 Oct 2014 12:33:41 -0400 Subject: [ITK] [ITK-users] Example medical images for teaching Image Segmentation In-Reply-To: References: Message-ID: Hi Sami, Thanks for helping to educate the next generation on medical computing :-). If you happen to use ITK/SimpleITK in your course, please add a link to the materials in this wiki page [1]. The data used in the examples can be a good resource. Some very nice examples that illustrate level sets segmentation can be found here [2] [3] [4] [5] [6]. Thanks, Matt [1] http://www.itk.org/Wiki/ITK/Documentation [2] http://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization/VisualizeStaticDense2DLevelSetAsElevationMap/Documentation.html [3] http://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization/VisualizeStaticDense2DLevelSetZeroSet/Documentation.html [4] http://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization/VisualizeStaticShi2DLevelSetLayers/Documentation.html [5] http://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization/VisualizeEvolvingDense2DLevelSetAsElevationMap/Documentation.html [6] http://itk.org/ITKExamples/src/Segmentation/LevelSetsv4Visualization/VisualizeEvolvingDense2DLevelSetZeroSet/Documentation.html On Fri, Oct 24, 2014 at 10:36 AM, Sami Koho wrote: > Hello, > > This is not directly related to ITK, but I will ask anyway, out of > curiosity. This fall I have been teaching Digital Image Processing to > Biomedical imaging students. The next subject will be Image Segmentation > (Edge detection models, / thresholding). Would any of you have some > favorite medical images to demonstrate these subjects? I can of course use > any pictures, but having examples relevant to the students would be nice. > I have my own libraries as well, but they are mostly of cells and their > internals (microscopy lab). Feel free to send any links/files, if > something comes to mind. > > Best, > > Sami > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 bill.lorensen at gmail.com Fri Oct 24 12:40:06 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Fri, 24 Oct 2014 12:40:06 -0400 Subject: [ITK] [ITK-users] Example medical images for teaching Image Segmentation In-Reply-To: References: Message-ID: You might contact John Galeotti at CMU. He has taught image processing courses using ITK. http://www.cs.cmu.edu/~galeotti/methods_course/books_references.html On Fri, Oct 24, 2014 at 10:36 AM, Sami Koho wrote: > Hello, > > This is not directly related to ITK, but I will ask anyway, out of > curiosity. This fall I have been teaching Digital Image Processing to > Biomedical imaging students. The next subject will be Image Segmentation > (Edge detection models, / thresholding). Would any of you have some > favorite medical images to demonstrate these subjects? I can of course use > any pictures, but having examples relevant to the students would be nice. > I have my own libraries as well, but they are mostly of cells and their > internals (microscopy lab). Feel free to send any links/files, if > something comes to mind. > > Best, > > Sami > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 norman-k-williams at uiowa.edu Fri Oct 24 12:45:17 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Fri, 24 Oct 2014 16:45:17 +0000 Subject: [ITK] [ITK-dev] MatrixOffsetTransformBase::GetFixedParameters not ThreadSafe -- regression test? Message-ID: I was going to address this bug that I just logged: https://issues.itk.org/jira/browse/ITK-3324 Basically, if GetFixedParameters is called from multiple threads, it introduces a race to resize the internal fixed parameter array. This was never a problem before Hans Johnson?s recent patch to propagate fixed parameters int Transform::GetInverse() methods. He added: inverse->SetFixedParameters(this->GetFixedParameters()); which makes perfect sense. I have a decent idea of how to make this better: Set the fixed parameters? size in the constructor for MatrixOffsetTransformBase, and set the fixed parameters in SetCenter. I will review the other instances of GetFixedParameters and GetParameters to see if they?re similarly thread-unsafe. But how do you write a regression test for this? ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- 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 norman-k-williams at uiowa.edu Fri Oct 24 12:59:41 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Fri, 24 Oct 2014 16:59:41 +0000 Subject: [ITK] [ITK-dev] MatrixOffsetTransformBase::GetFixedParameters not ThreadSafe -- regression test? Message-ID: The problem is worse than I thought. CompositeTransform::GetFixedParameters() dynamically resizes the FixedParameters array, and then does a bunch of std::copy to copy fixed parameters out of its list of sub-transforms. The only way to make that thread safe is to use a Mutex lock to guard where it changes the member variable. From: , Mushly McMushmaster > Date: Friday, October 24, 2014 at 11:45 AM To: ITK > Subject: [ITK-dev] MatrixOffsetTransformBase::GetFixedParameters not ThreadSafe -- regression test? I was going to address this bug that I just logged: https://issues.itk.org/jira/browse/ITK-3324 Basically, if GetFixedParameters is called from multiple threads, it introduces a race to resize the internal fixed parameter array. This was never a problem before Hans Johnson?s recent patch to propagate fixed parameters int Transform::GetInverse() methods. He added: inverse->SetFixedParameters(this->GetFixedParameters()); which makes perfect sense. I have a decent idea of how to make this better: Set the fixed parameters? size in the constructor for MatrixOffsetTransformBase, and set the fixed parameters in SetCenter. I will review the other instances of GetFixedParameters and GetParameters to see if they?re similarly thread-unsafe. But how do you write a regression test for this? ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- 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 llliu at umich.edu Fri Oct 24 13:08:54 2014 From: llliu at umich.edu (Lianli Liu) Date: Fri, 24 Oct 2014 13:08:54 -0400 Subject: [ITK] [ITK-users] Jacobian in translation transform Message-ID: Hi all, I am quiet new to registration and I am having difficulty understanding the Jacobian matrix calculated in translation transform. From my understanding, the ComputeJacobianWithRespectToParameters should calculate the shift of EACH voxel with respect to parameters, thus the matrix size should be related with number of voxels? But the Jacobian matrix here is only related with image dimensions? (3 by 3 for 3D image). Can anyone help me understand this? And I am confused for other transformation methods such as rigid, where is the Jacobian calculated? Thanks! Best, Lianli -------------- 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 Fri Oct 24 13:25:42 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Fri, 24 Oct 2014 13:25:42 -0400 Subject: [ITK] [ITK-dev] MatrixOffsetTransformBase::GetFixedParameters not ThreadSafe -- regression test? In-Reply-To: References: Message-ID: Kent, Mutable member are evil. Would it be possible to have the m_Center and the m_FixedArray point to the same block of data? Brad On Oct 24, 2014, at 12:59 PM, Williams, Norman K wrote: > The problem is worse than I thought. > > CompositeTransform::GetFixedParameters() dynamically resizes the FixedParameters array, and then does a bunch of std::copy to copy fixed parameters out of its list of sub-transforms. > > The only way to make that thread safe is to use a Mutex lock to guard where it changes the member variable. > > From: , Mushly McMushmaster > Date: Friday, October 24, 2014 at 11:45 AM > To: ITK > Subject: [ITK-dev] MatrixOffsetTransformBase::GetFixedParameters not ThreadSafe -- regression test? > > I was going to address this bug that I just logged: > > https://issues.itk.org/jira/browse/ITK-3324 > > Basically, if GetFixedParameters is called from multiple threads, it introduces a race to resize the internal fixed parameter array. > > This was never a problem before Hans Johnson?s recent patch to propagate fixed parameters int Transform::GetInverse() methods. He added: > > inverse->SetFixedParameters(this->GetFixedParameters()); > > which makes perfect sense. > > I have a decent idea of how to make this better: Set the fixed parameters? size in the constructor for MatrixOffsetTransformBase, and set the fixed parameters in SetCenter. I will review the other instances of GetFixedParameters and GetParameters to see if they?re similarly thread-unsafe. > > But how do you write a regression test for this? > > > > > Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. > > > Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers -------------- 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 norman-k-williams at uiowa.edu Fri Oct 24 13:41:31 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Fri, 24 Oct 2014 17:41:31 +0000 Subject: [ITK] [ITK-dev] MatrixOffsetTransformBase::GetFixedParameters not ThreadSafe -- regression test? In-Reply-To: References: Message-ID: If the API says const bool GetInverse(Self *inverse) const; If that changes the internal state of the class, isn?t that false advertising? Actually, I tried just fixing that one problem in MatrixOffsetTransformBase, and it just kicked the problem slightly down the road. ImageMaskSpatialObject::IsInside also advertises as being a const method; yet it calls SetInternalInverseTransformToWorldToIndexTransform() which is ALSO marked as const, and yet modifies an instance variable. From: Bradley Lowekamp > Date: Friday, October 24, 2014 at 12:25 PM To: Mushly McMushmaster > Cc: ITK > Subject: Re: [ITK-dev] MatrixOffsetTransformBase::GetFixedParameters not ThreadSafe -- regression test? Kent, Mutable member are evil. Would it be possible to have the m_Center and the m_FixedArray point to the same block of data? Brad On Oct 24, 2014, at 12:59 PM, Williams, Norman K > wrote: The problem is worse than I thought. CompositeTransform::GetFixedParameters() dynamically resizes the FixedParameters array, and then does a bunch of std::copy to copy fixed parameters out of its list of sub-transforms. The only way to make that thread safe is to use a Mutex lock to guard where it changes the member variable. From: , Mushly McMushmaster > Date: Friday, October 24, 2014 at 11:45 AM To: ITK > Subject: [ITK-dev] MatrixOffsetTransformBase::GetFixedParameters not ThreadSafe -- regression test? I was going to address this bug that I just logged: https://issues.itk.org/jira/browse/ITK-3324 Basically, if GetFixedParameters is called from multiple threads, it introduces a race to resize the internal fixed parameter array. This was never a problem before Hans Johnson?s recent patch to propagate fixed parameters int Transform::GetInverse() methods. He added: inverse->SetFixedParameters(this->GetFixedParameters()); which makes perfect sense. I have a decent idea of how to make this better: Set the fixed parameters? size in the constructor for MatrixOffsetTransformBase, and set the fixed parameters in SetCenter. I will review the other instances of GetFixedParameters and GetParameters to see if they?re similarly thread-unsafe. But how do you write a regression test for this? ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Fri Oct 24 14:33:25 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Fri, 24 Oct 2014 14:33:25 -0400 Subject: [ITK] [ITK-users] Jacobian in translation transform In-Reply-To: References: Message-ID: Hi Lianli, The ComputeJacobianWithRespectToParameters takes an input parameter the position in space that the jacobian is to be computed, so it returns the value at that point in space. For the TranslationTransform, it is not that interesting since the jacobian is a uniform identity matrix. Hope this helps, Matt On Fri, Oct 24, 2014 at 1:08 PM, Lianli Liu wrote: > Hi all, > > I am quiet new to registration and I am having difficulty understanding the > Jacobian matrix calculated in translation transform. From my understanding, > the ComputeJacobianWithRespectToParameters should calculate the shift of > EACH voxel with respect to parameters, thus the matrix size should be > related with number of voxels? But the Jacobian matrix here is only related > with image dimensions? (3 by 3 for 3D image). Can anyone help me understand > this? > > And I am confused for other transformation methods such as rigid, where is > the Jacobian calculated? Thanks! > > Best, > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 noreply at insightsoftwareconsortium.org Sat Oct 25 15:45:58 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Sat, 25 Oct 2014 15:45:58 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Brain Tumor Progression Modeling - A Data Driven Approach Message-ID: <20141025194558.AB0B13D6C4DD@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Brain Tumor Progression Modeling - A Data Driven Approach Authors: Weber C., G??tz M., Stieltjes B., Polanska J., Binczyk F., Tarnawski R., Bobek-Billewicz B., Maier-Hein K. Abstract: Malignant gliomas are highly heterogeneous brain tumors with complex an- isotropic growth patterns and occult invasion. Computational modeling of cell migration and proliferation has been subject of intensive research aiming at a deeper understanding of the tumor biology and the ability to predict growth and thus improve therapy. However, current modeling techniques follow a generative approach and make strong assumptions about underlying mechanisms. The tumor is so far treated as homogeneous entity with behavioral parameters extrapolated from previous longitudinal image information. We present a novel way of approaching this problem by employing data driven, discrim- inative modeling techniques that learn relevant features from observed growth patterns and are able to make meaningful predictions solely on basis of local and regional tissue characteristics at one given point in time. We demonstrate superior performance of the proposed discriminative method (DICE score 83) compared to the state of the art generative approach (DICE score 72) on six patients and a total of nine different time intervals. Our approach can help estimating occult invasion as well as it can advance our understanding of the tumor biology and lead to valuable predictions of tumor growth patterns that could guide and improve radio therapy. Download and review this publication at: http://hdl.handle.net/10380/3474 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Sat Oct 25 15:47:33 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Sat, 25 Oct 2014 15:47:33 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Visualization of 4D-PET/CT, Target Volumes and Dose Distribution: Applications in Radiotherapy Planning Message-ID: <20141025194733.151A33D6C492@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Visualization of 4D-PET/CT, Target Volumes and Dose Distribution: Applications in Radiotherapy Planning Authors: Schlachter M., Fechter T., Nestle U., B??hler K. Abstract: In radiation treatment (RT) planning medical doctors need to consider a variety of information sources for anatomical and functional target volume delineation. The validation and inspection of the defined target volumes and the resulting RT plan is a complex task, especially in the presence of moving target areas as it is the case for tumors of the chest and the upper abdomen. A 4D-PET/CT visualization system may become a helpful tool for validating RT plans. We define major requirements such a visualization system should fulfill to provide medical doctors with the necessary visual information to validate tumor delineations, and review the dose distribution of a RT plan. We present an implementation of such a system, and present qualitative results of its applications for a lung cancer patient. Download and review this publication at: http://hdl.handle.net/10380/3491 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Sat Oct 25 15:48:24 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Sat, 25 Oct 2014 15:48:24 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Improvements in SlicerRT, the radiation therapy research toolkit for 3D Slicer Message-ID: <20141025194824.224513D6C411@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Improvements in SlicerRT, the radiation therapy research toolkit for 3D Slicer Authors: Pinter C., Lasso A., Wang A., Sharp G.C., Jaffray D., Fichtinger G. Abstract: Purpose: Recent years have seen growing interest in adaptive radiation therapy (RT), but the existing software tools are not ideal for research use, as they are either expensive and closed proprietary applications or free open-source packages with limited scope, extensibility, reliability, or user support. To address these limitations, we have developed SlicerRT, an open-source toolkit for RT research, providing fast computations and user-friendly interface for researchers. It is a medium for RT researchers to integrate their workflows in, assists clinical translation of experimental approaches, and enables comparative testing. Methods: SlicerRT builds on the widely used medical image visualization and analysis platform, 3D Slicer (www.slicer.org). In addition to the tools that 3D Slicer offers for visualization, registration and segmentation, the toolkit provides functions specifically designed for RT research. Established development processes as well as testing and validation environment ensure software quality. Standardized software development mechanisms of 3D Slicer were applied for documentation, distribution, and user support. The design and architecture of the toolkit was outlined in [1]. SlicerRT has evolved to contain the most widely used features in the field (see www.slicerrt.org), which have been defined through consensus discussions with a large pool of RT researchers. Results: Numerous modules have been developed for RT-specific features such as DICOM-RT data import and export, as well as dose analysis tools including dose volume histogram, dose accumulation, dose comparison, and isodose line and surface generation. The toolkit also includes contour analysis modules for handling various contour representations, contour morphology, and contour comparison. Advanced registration tools are provided by the included Plastimatch library [2]. The main new features developed in the last year are RT plan and RT image import and the subject hierarchy module, which arranges the loaded data to a structure familiar to clinicians, while providing advanced automation features through the underlying extendible mechanism. The toolkit is being used by several research groups to support and evaluate adaptive radiation therapy workflows. SlicerRT is available for download through the Extension Manager component of 3D Slicer 4.3 or later (see instructions on our websit e). Future work: As SlicerRT has matured to contain most of the planned functions, our focus has shifted from feature development to usability and stability. The subject hierarchy module, and its features such as bulk deformation of studies embodies our efforts toward usability, while the integration of the subject hierarchy and the advanced contour handling mechanism into the 3D Slicer core points towards stability, also benefiting the whole 3D Slicer community. There is ongoing work to evaluate and potentially standardize the way the 2D contours are rasterized into 3D volumes, thus mitigating the great variability between the different solutions for this problem. Current funding ensures continuous development for several years, so SlicerRT is expected to develop further. Acknowledgement: This work was in part funded by Cancer Care Ontario through Applied Cancer Research Unit and Research Chair in Cancer Imaging grants, and the Ontario Consortium for Adaptive Invention in Radiation Oncology (OCAIRO). Download and review this publication at: http://hdl.handle.net/10380/3494 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Sat Oct 25 15:48:55 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Sat, 25 Oct 2014 15:48:55 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Automatic accuracy measurement for multi-modal rigid registration using feature descriptors Message-ID: <20141025194855.F0C933D6C609@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Automatic accuracy measurement for multi-modal rigid registration using feature descriptors Authors: Hauler F., Jurisic M., Furtado H., Sabatini U., Laprie A., Nestle U., Birkfellner W. Abstract: In radiotherapy (RT) for tumor delineation and diagnostics, complementary information of multi-modal images is used. Using high ionizing radiation, the accuracy of registered volume data is crucial; therefore a reliable and robust evaluation method for registered images is needed in clinical practice. Multi-modal image registration aligns images from different modalities like computed tomography (CT) and magnetic resonance imaging (MRI) or cone beam computed tomography (CBCT) into one common frame of reference. The gold standard validation methods are visual inspection by radiation oncology experts and fiducial-based evaluation. However, visual inspection is a qualitative measure with a range of 2-6 mm inaccuracy, it is time consuming and prone to errors. The fiducial-based evaluation is an invasive method when fiducial markers are fixated to bone or implanted in organs. Therefore, in clinical practice a robust non-invasive automated method is needed to validate registratio n of multi-modal images. The aim of this study is to introduce and validate an automatic landmark-based accuracy measure for multi-modal image rigid registration using feature descriptors. A porcine dataset with fixed fiducial markers was used to compare our accuracy measure with the target registration error of fiducial markers.In addition, the robustness of our evaluation method was tested on multi-vendor database consisted of 10 brain and 20 lung cases comparing the automatic landmark accuracy measure based on feature descriptors with manual landmark based evaluation. An automatic, non-invasive method based on feature descriptors for accuracy evaluation of multi-modal rigid registration was introduced. The method can be used to provide accuracy information slice-by slice on CT, CBCT and CT, MR-T1, -T2 weighted, MR-T1 contrast enhanced (ce) multi-modal images. Download and review this publication at: http://hdl.handle.net/10380/3490 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Sat Oct 25 15:49:31 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Sat, 25 Oct 2014 15:49:31 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Gauss-Newton Method for Segmentation assisted Deformable Registration Message-ID: <20141025194931.E2EA03D6C4F0@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Gauss-Newton Method for Segmentation assisted Deformable Registration Authors: Jurisic M., Fechter T., Hauler F., Furtado H., Nestle U., Birkfellner W. Abstract: In this work, we try to develop a fast converging method for segmentation assisted deformable registration. The segmentation step consists of a piece-wise constant Mumford-Shah energy model while reg- istration is driven by the sum of squared distances of both initial images and segmented mask with a diffusion regularization. In order to solve this energy minimization problem, a second order Gauss-Newton opti- mization method is used. For the numerical experiments we used CT data sets from the EMPIRE10 challenge. In this preliminary study, we show high accuracy of our algorithm. Download and review this publication at: http://hdl.handle.net/10380/3492 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Sat Oct 25 15:50:51 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Sat, 25 Oct 2014 15:50:51 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Dose Painting with a Variable Collimator for the Small Animal Radiation Research Platform (SARRP) Message-ID: <20141025195051.C908F3D6C768@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Dose Painting with a Variable Collimator for the Small Animal Radiation Research Platform (SARRP) Authors: Cho N., Wong J., Kazanzides P. Abstract: The goal of radiation treatment is to irradiate cancer cells (i.e., a target region) without destroying adjacent healthy tissue. Thus, it is advantageous to form the beam so that it best approximates the target, thereby reducing the amount of dose absorbed in critical regions outside the target area. While multi-leaf collimators are common in human clinical systems, small animal radiotherapy systems are typically limited to a set of fixed-size collimators. For these systems, dose painting can be used for conformal dose delivery, but is significantly slower than a multi-leaf collimator. As a compromise solution, a variable rectangular collimator has been developed for the Small Animal Radiation Research Platform (SARRP). This enables more efficient dose painting via the decomposition of a 2D target region into a minimum number of rectangles of variable size, which is the topic of this paper. The proposed method consists of several distinct steps and was implemented on the SA RRP Treatment Planning System (TPS). Download and review this publication at: http://hdl.handle.net/10380/3476 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From noreply at insightsoftwareconsortium.org Sat Oct 25 15:51:31 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Sat, 25 Oct 2014 15:51:31 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Deformable Registration with Discontinuity Preservation using Multi-Scale MRF Message-ID: <20141025195131.607C23D6C820@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Deformable Registration with Discontinuity Preservation using Multi-Scale MRF Authors: Seo D., Van Baar J. Abstract: Deformable (2D or 3D) medical image registration is a challenging problem. Existing approaches assume that the underlying deformation is smooth. This smoothness assumption allows for solving the deformable registration at a coarse resolution and interpolate for finer resolutions. However, sliding of organs and breathing motion, exhibit discontinuities. We propose a discrete optimization approach to preserve these discontinuities. Solving continuous deformations using discrete optimization requires a fine distribution of the discrete labels. Coupled with the typical size of medical image datasets, this poses challenges to compute solutions efficiently. In this paper we present a practical, multi-scale formulation. We describe how discontinuities can be preserved, and how the optimization problem is solved. Results on synthetic 2D, and real 3D data show that we can well approximate the smoothness of continuous optimization, while accurately maintaining discontinuities. Download and review this publication at: http://hdl.handle.net/10380/3496 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From Helen.Gustafsson at act.gov.au Sun Oct 26 21:28:48 2014 From: Helen.Gustafsson at act.gov.au (Gustafsson, Helen (Health)) Date: Mon, 27 Oct 2014 01:28:48 +0000 Subject: [ITK] Edit .mha header Message-ID: <8D3BE075AEDCB74589161A162E904FC721F744EE@PRDEXM004.act.gov.au> Hello all, We are working on a project where we are reconstructing cone beam CT data using the ITK software, creating an .mha file which we then need to convert to DICOM - I was hoping to use 3Dslicer for this. Our problem is that the image orientation in the mha header seems to be incorrect (?), so 3D slicer is trying to make axial slices from what it thinks is a coronal slice. I have been googling ways to edit the mha header but I can't find anything that works. Any ideas about how to solve this? Thanks, Helen ----------------------------------------------------------------------- This email, and any attachments, may be confidential and also privileged. If you are not the intended recipient, please notify the sender and delete all copies of this transmission along with any attachments immediately. You should not copy or use it for any purpose, nor disclose its contents to any other person. ----------------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at insightsoftwareconsortium.org Mon Oct 27 06:38:02 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Mon, 27 Oct 2014 06:38:02 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Deformable Registration with Discontinuity Preservation using Multi-Scale MRF Message-ID: <20141027103802.E13403D6C6A9@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Deformable Registration with Discontinuity Preservation using Multi-Scale MRF Authors: Seo D., Van Baar J. Abstract: Deformable (2D or 3D) medical image registration is a challenging problem. Existing approaches assume that the underlying deformation is smooth. This smoothness assumption allows for solving the deformable registration at a coarse resolution and interpolate for finer resolutions. However, sliding of organs and breathing motion, exhibit discontinuities. We propose a discrete optimization approach to preserve these discontinuities. Solving continuous deformations using discrete optimization requires a fine distribution of the discrete labels. Coupled with the typical size of medical image datasets, this poses challenges to compute solutions efficiently. In this paper we present a practical, multi-scale formulation. We describe how discontinuities can be preserved, and how the optimization problem is solved. Results on synthetic 2D, and real 3D data show that we can well approximate the smoothness of continuous optimization, while accurately maintaining discontinuities. Download and review this publication at: http://hdl.handle.net/10380/3475 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From zeinsalah at gmail.com Mon Oct 27 08:17:37 2014 From: zeinsalah at gmail.com (Zein Salah) Date: Mon, 27 Oct 2014 13:17:37 +0100 Subject: [ITK] (no subject) Message-ID: Hi, I am doing something with histograms and want to write a function for saving a histogram into a text file, i.e. something like this: typedef itk::Statistics::ScalarImageToHistogramGenerator< InputImageType > ScalarImageToHistogramGeneratorType; typedef ScalarImageToHistogramGeneratorType::HistogramType HistogramType; In the implementation of the function SaveHistogram, the compilter is giving an error error C2248::itk::Statistics::Histogram::~Histogram": that there is no access to protected members that are defined in the class itk::Statistics::Histogram Am I missing something? Is it not possible to pass a histogram as parameter? Thanks, Zein -------------- next part -------------- An HTML attachment was scrubbed... URL: From assil-king at hotmail.fr Mon Oct 27 08:21:31 2014 From: assil-king at hotmail.fr (assil) Date: Mon, 27 Oct 2014 05:21:31 -0700 (PDT) Subject: [ITK] [ITK-users] ITK Importing Image Data from a Buffer Message-ID: <1414412491137-7586419.post@n2.nabble.com> I have coded a method to create an Itk image from a buffer (in my case it's a Cimg image type). This is the algorithme : void Cimg_To_ITK (CImg img) { const unsigned int Dimension = 2; typedef itk::RGBPixel< unsigned char > RGBPixelType; typedef itk::Image< RGBPixelType, Dimension > RGBImageType; typedef itk::ImportImageFilter< RGBPixelType, Dimension > ImportFilterType; ImportFilterType::Pointer importFilter = ImportFilterType::New(); typedef itk::ImageFileWriter< RGBImageType > WriterType; WriterType::Pointer writer = WriterType::New(); RGBImageType::SizeType imsize; imsize[0] = img.width(); imsize[1] = img.height(); ImportFilterType::IndexType start; start.Fill( 0 ); ImportFilterType::RegionType region; region.SetIndex( start ); region.SetSize( imsize ); importFilter->SetRegion( region ); const itk::SpacePrecisionType origin[ Dimension ] = { 0.0, 0.0 }; importFilter->SetOrigin( origin ); const itk::SpacePrecisionType spacing[ Dimension ] = { 1.0, 1.0 }; importFilter->SetSpacing( spacing ); const unsigned int numberOfPixels = imsize[0] * imsize[1]; const bool importImageFilterWillOwnTheBuffer = true; RGBPixelType * localBuffer = new RGBPixelType[ numberOfPixels ]; memcpy(localBuffer->GetDataPointer(), img.data(), numberOfPixels); importFilter->SetImportPointer( localBuffer, numberOfPixels,importImageFilterWillOwnTheBuffer ); writer->SetInput( importFilter->GetOutput() ); writer->SetFileName( "output.png" ); writer->Update(); } I dont have what i want as a output : input : output : -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Importing-Image-Data-from-a-Buffer-tp7586419.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 blowekamp at mail.nih.gov Mon Oct 27 09:11:47 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 27 Oct 2014 09:11:47 -0400 Subject: [ITK] (no subject) In-Reply-To: References: Message-ID: <44E1359C-6F21-47DF-A132-92FA203F5829@mail.nih.gov> Hello, The Histogram class is derived from the itk::Object class. Just about all ITK Object must manage by smart pointers, and must be dynamically created. The typical usage of an object type is: HistogramType::Pointer histogramPointer = HistogramType::New(); This dynamically creates an Histogram, and uses the correct smart pointer type. This particular error message: On Oct 27, 2014, at 8:17 AM, Zein Salah wrote: > > error C2248::itk::Statistics::Histogram::~Histogram": is an indication that you are passing the type by value an not by a pointer. You should pass the histogram as PointerType of the class or as a raw pointer if there is not an issue of ownership that the smart pointe need to preserve. Brad p.s. You didn't include any of you code that was causing the problem. This is quite a luck case where I new the cause of the error message with out even seeing the code. It's best practice to include some code so that other can see what's causing the problem. From zeinsalah at gmail.com Mon Oct 27 10:48:49 2014 From: zeinsalah at gmail.com (Zein Salah) Date: Mon, 27 Oct 2014 15:48:49 +0100 Subject: [ITK] (no subject) In-Reply-To: <44E1359C-6F21-47DF-A132-92FA203F5829@mail.nih.gov> References: <44E1359C-6F21-47DF-A132-92FA203F5829@mail.nih.gov> Message-ID: well, thanks first for the feedback. I now wrote this code: typedef itk::Statistics::ScalarImageToHistogramGenerator< InputImageType > ScalarImageToHistogramGeneratorType; typedef ScalarImageToHistogramGeneratorType::HistogramType HistogramType; ScalarImageToHistogramGeneratorType::Pointer scalarImageToHistogramGenerator = ScalarImageToHistogramGeneratorType::New(); scalarImageToHistogramGenerator->SetNumberOfBins(128); scalarImageToHistogramGenerator->SetInput( m_ShiftedImage ); scalarImageToHistogramGenerator->Compute(); HistogramType::Pointer hist = scalarImageToHistogramGenerator->GetOutput(); // This statement causes the error SaveHistogram(hist, "c:/Hist.txt"); Now: the compiler gives an error error C2440: 'Initialisierung': 'const itk::Statistics::Histogram *' kann nicht in 'itk::SmartPointer' konvertiert werden 1> with 1> [ 1> TMeasurement=double, 1> VMeasurementVectorSize=1, 1> TFrequencyContainer=itk::Statistics::DenseFrequencyContainer 1> ] 1> and 1> [ 1> TObjectType=itk::Statistics::Histogram 1> ] Translation: 'const itk::Statistics::Histogram *' cannot be converted to 'itk::SmartPointer' On Mon, Oct 27, 2014 at 2:11 PM, Bradley Lowekamp wrote: > Hello, > > The Histogram class is derived from the itk::Object class. Just about all > ITK Object must manage by smart pointers, and must be dynamically created. > The typical usage of an object type is: > > HistogramType::Pointer histogramPointer = HistogramType::New(); > > This dynamically creates an Histogram, and uses the correct smart pointer > type. > > > This particular error message: > > On Oct 27, 2014, at 8:17 AM, Zein Salah wrote: > > > > error > C2248::itk::Statistics::Histogram::~Histogram": > > > is an indication that you are passing the type by value an not by a > pointer. You should pass the histogram as PointerType of the class or as a > raw pointer if there is not an issue of ownership that the smart pointe > need to preserve. > > Brad > > p.s. You didn't include any of you code that was causing the problem. This > is quite a luck case where I new the cause of the error message with out > even seeing the code. It's best practice to include some code so that other > can see what's causing the problem. > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From blowekamp at mail.nih.gov Mon Oct 27 10:54:32 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 27 Oct 2014 10:54:32 -0400 Subject: [ITK] (no subject) In-Reply-To: References: <44E1359C-6F21-47DF-A132-92FA203F5829@mail.nih.gov> Message-ID: <0C884559-F109-45B4-88E8-80823E83A2F6@mail.nih.gov> Hello, This error message indicates there is a constant qualifier for the result of the GetOutput method, and that there is no conversion to the non-const SmartPointer. You need to use a ConstPointer type. On Oct 27, 2014, at 10:48 AM, Zein Salah wrote: > error C2440: 'Initialisierung': 'const itk::Statistics::Histogram *' kann nicht in 'itk::SmartPointer' konvertiert werden -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Mon Oct 27 10:57:57 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 27 Oct 2014 10:57:57 -0400 Subject: [ITK] Edit .mha header In-Reply-To: <8D3BE075AEDCB74589161A162E904FC721F744EE@PRDEXM004.act.gov.au> References: <8D3BE075AEDCB74589161A162E904FC721F744EE@PRDEXM004.act.gov.au> Message-ID: Hi Helen, Before writing the image to file, the Direction matrix [1] can be populated with appropriate 1's and -1's. This will modify the TransformMatrix in the MetaImage header. Or a FlipImageFilter could be applied [2]. HTH, Matt [1] http://www.itk.org/Doxygen/html/classitk_1_1Image.html#a07c7c68338cee5537f997d68591a1214 [2] http://www.itk.org/Doxygen/html/classitk_1_1FlipImageFilter.html On Sun, Oct 26, 2014 at 9:28 PM, Gustafsson, Helen (Health) wrote: > Hello all, > > > > We are working on a project where we are reconstructing cone beam CT data > using the ITK software, creating an .mha file which we then need to convert > to DICOM ? I was hoping to use 3Dslicer for this. Our problem is that the > image orientation in the mha header seems to be incorrect (?), so 3D slicer > is trying to make axial slices from what it thinks is a coronal slice. I > have been googling ways to edit the mha header but I can?t find anything > that works. > > > > Any ideas about how to solve this? > > > > Thanks, > > Helen > > ----------------------------------------------------------------------- > This email, and any attachments, may be confidential and also privileged. If > you are not the intended recipient, please notify the sender and delete all > copies of this transmission along with any attachments immediately. You > should not copy or use it for any purpose, nor disclose its contents to any > other person. > ----------------------------------------------------------------------- > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From matt.mccormick at kitware.com Mon Oct 27 11:23:53 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 27 Oct 2014 11:23:53 -0400 Subject: [ITK] [ITK-users] ITK Importing Image Data from a Buffer In-Reply-To: <1414412491137-7586419.post@n2.nabble.com> References: <1414412491137-7586419.post@n2.nabble.com> Message-ID: Hi Assil, > > const unsigned int numberOfPixels = imsize[0] * imsize[1]; > const bool importImageFilterWillOwnTheBuffer = true; > > RGBPixelType * localBuffer = new RGBPixelType[ numberOfPixels ]; > memcpy(localBuffer->GetDataPointer(), img.data(), numberOfPixels); This should be numberOfPixels * 3, since there are three unsigned char bytes in for every RGB pixel. HTH, Matt _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From assil-king at hotmail.fr Mon Oct 27 11:48:40 2014 From: assil-king at hotmail.fr (assil) Date: Mon, 27 Oct 2014 08:48:40 -0700 (PDT) Subject: [ITK] [ITK-users] ITK Importing Image Data from a Buffer In-Reply-To: References: <1414412491137-7586419.post@n2.nabble.com> Message-ID: <1414424920694-7586421.post@n2.nabble.com> Hi Matt, I already did that. my mistake i have plaste the wrong version of the code. Her is what i have : void Cimg_To_ITK (CImg img) { typedef unsigned char PixelType; typedef itk::RGBPixel< PixelType > RGBPixelType; typedef itk::Image< RGBPixelType, 2 > RGBImageType; typedef itk::ImportImageFilter< RGBPixelType, 2 > ImportFilterType; ImportFilterType::Pointer importFilter = ImportFilterType::New(); typedef itk::ImageFileWriter< RGBImageType > WriterType; WriterType::Pointer writer = WriterType::New(); RGBImageType::SizeType imsize; imsize[0] = img.width(); imsize[1] = img.height(); ImportFilterType::IndexType start; start.Fill( 0 ); ImportFilterType::RegionType region; region.SetIndex( start ); region.SetSize( imsize ); importFilter->SetRegion( region ); double origin[ 2 ]; origin[0] = 0.0; // X coordinate origin[1] = 0.0; // Y coordinate importFilter->SetOrigin( origin ); double spacing[ 2 ]; spacing[0] = 1.0; // along X direction spacing[1] = 1.0; // along Y direction importFilter->SetSpacing( spacing ); const unsigned int numberOfPixels = imsize[0] * imsize[1] * 3; const unsigned int numberOfBytes = numberOfPixels * sizeof( PixelType ); const bool importImageFilterWillOwnTheBuffer = true; unsigned char * localBuffer = new unsigned char[ numberOfPixels ]; memcpy(localBuffer, img.data(), numberOfBytes); importFilter->SetImportPointer( localBuffer, numberOfPixels,importImageFilterWillOwnTheBuffer ); importFilter->Update(); writer->SetInput( importFilter->GetOutput() ); writer->SetFileName( "output.png" ); writer->Update(); } the out image is in the same. -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Importing-Image-Data-from-a-Buffer-tp7586419p7586421.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 bill.lorensen at gmail.com Mon Oct 27 11:58:25 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Mon, 27 Oct 2014 11:58:25 -0400 Subject: [ITK] [ITK-users] ITK Importing Image Data from a Buffer In-Reply-To: <1414424920694-7586421.post@n2.nabble.com> References: <1414412491137-7586419.post@n2.nabble.com> <1414424920694-7586421.post@n2.nabble.com> Message-ID: What is the layout of the CImg. 1) RGBRGBRGB... 2) RRRRRRRRRRRR...GGGGGGGGGGGGGGGG....BBBBBBBBBBBBBBBBB... On Mon, Oct 27, 2014 at 11:48 AM, assil wrote: > Hi Matt, > > I already did that. my mistake i have plaste the wrong version of the code. > Her is what i have : > > > void Cimg_To_ITK (CImg img) > { > typedef unsigned char PixelType; > typedef itk::RGBPixel< PixelType > RGBPixelType; > typedef itk::Image< RGBPixelType, 2 > RGBImageType; > typedef itk::ImportImageFilter< RGBPixelType, 2 > ImportFilterType; > ImportFilterType::Pointer importFilter = ImportFilterType::New(); > typedef itk::ImageFileWriter< RGBImageType > WriterType; > WriterType::Pointer writer = WriterType::New(); > > > RGBImageType::SizeType imsize; > imsize[0] = img.width(); > imsize[1] = img.height(); > > ImportFilterType::IndexType start; > start.Fill( 0 ); > ImportFilterType::RegionType region; > region.SetIndex( start ); > region.SetSize( imsize ); > importFilter->SetRegion( region ); > > double origin[ 2 ]; > origin[0] = 0.0; // X coordinate > origin[1] = 0.0; // Y coordinate > importFilter->SetOrigin( origin ); > > double spacing[ 2 ]; > spacing[0] = 1.0; // along X direction > spacing[1] = 1.0; // along Y direction > importFilter->SetSpacing( spacing ); > > const unsigned int numberOfPixels = imsize[0] * imsize[1] * 3; > const unsigned int numberOfBytes = numberOfPixels * sizeof( PixelType ); > const bool importImageFilterWillOwnTheBuffer = true; > > unsigned char * localBuffer = new unsigned char[ numberOfPixels ]; > memcpy(localBuffer, img.data(), numberOfBytes); > importFilter->SetImportPointer( localBuffer, > numberOfPixels,importImageFilterWillOwnTheBuffer ); > importFilter->Update(); > writer->SetInput( importFilter->GetOutput() ); > writer->SetFileName( "output.png" ); > writer->Update(); > > } > > > the out image is in the same. > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Importing-Image-Data-from-a-Buffer-tp7586419p7586421.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 -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 assil-king at hotmail.fr Mon Oct 27 12:05:34 2014 From: assil-king at hotmail.fr (assil) Date: Mon, 27 Oct 2014 09:05:34 -0700 (PDT) Subject: [ITK] [ITK-users] ITK Importing Image Data from a Buffer In-Reply-To: References: <1414412491137-7586419.post@n2.nabble.com> <1414424920694-7586421.post@n2.nabble.com> Message-ID: <1414425934443-7586423.post@n2.nabble.com> Hi Bill, It's RRRRRRRRRRRR...GGGGGGGGGGGGGGGG....BBBBBBBBBBBBBBBBB... -- View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Importing-Image-Data-from-a-Buffer-tp7586419p7586423.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 blowekamp at mail.nih.gov Mon Oct 27 12:14:01 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Mon, 27 Oct 2014 12:14:01 -0400 Subject: [ITK] [ITK-users] ITK Importing Image Data from a Buffer In-Reply-To: <1414425934443-7586423.post@n2.nabble.com> References: <1414412491137-7586419.post@n2.nabble.com> <1414424920694-7586421.post@n2.nabble.com> <1414425934443-7586423.post@n2.nabble.com> Message-ID: Hello, I would create separate R, G and B images, with 3 different import filters then use the ComposeImageFilter to make an ITK RGB image. ITK image or RGBPixel, are stored in RGBRGBRGB format. A simular conversion was done here[1], when reading the VisibleHuman data set. You will need to use an ImportImageFilter in stead of the readers used in the example. Brad [1] http://www.itk.org/Doxygen/html/IO_2VisibleHumanStreamReadWrite_8cxx-example.html On Oct 27, 2014, at 12:05 PM, assil wrote: > Hi Bill, > > It's RRRRRRRRRRRR...GGGGGGGGGGGGGGGG....BBBBBBBBBBBBBBBBB... > > > > -- > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-Importing-Image-Data-from-a-Buffer-tp7586419p7586423.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 rsvpitt at gmail.com Mon Oct 27 13:06:29 2014 From: rsvpitt at gmail.com (Vikas) Date: Mon, 27 Oct 2014 13:06:29 -0400 Subject: [ITK] [ITK-users] Landmarks in FEM registration Message-ID: Hi, Has anyone used FEM registration with landmarks? I am having trouble specifying landmarks. Is this feature now supported? Thanks Vikas -------------- 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 rhaqx001 at odu.edu Mon Oct 27 13:28:51 2014 From: rhaqx001 at odu.edu (Rabia Haq) Date: Mon, 27 Oct 2014 13:28:51 -0400 Subject: [ITK] [ITK-users] how to connect components resulting from itkBinaryThinningImageFilter Message-ID: Hello ITK users, I am currently trying to extract the medial axis of a 3D image using itkBinaryThinningImageFilter. The resulting binary image contains a lot of unconnected components. Is there any filter in itk to connect these components and obtain a connected image, from which I can extract a contour? Thank you so much for your time and consideration, regards, Rabia Ph.D. Candidate, Research Assistant Department of Modeling, Simulation and Visualization Engineering, Old Dominion University, Norfolk, VA. -------------- 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 norman-k-williams at uiowa.edu Mon Oct 27 15:31:01 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Mon, 27 Oct 2014 19:31:01 +0000 Subject: [ITK] [ITK-dev] review.source.kitware.com down again Message-ID: Someone needs to go bang on the side of the server. ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-developers From matt.mccormick at kitware.com Mon Oct 27 16:06:02 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Mon, 27 Oct 2014 16:06:02 -0400 Subject: [ITK] [ITK-dev] review.source.kitware.com down again In-Reply-To: References: Message-ID: Thanks for the note. There was some unexpected downtime due to maintenance. It is back up again. On Mon, Oct 27, 2014 at 3:31 PM, Williams, Norman K wrote: > Someone needs to go bang on the side of the server. > > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the > Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential > and may be legally privileged. If you are not the intended recipient, you > are hereby notified that any retention, dissemination, distribution, or > copying of this communication is strictly prohibited. Please reply to the > sender that you have received the message in error, then delete it. Thank > you. > ________________________________ > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > _______________________________________________ > 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 From noreply at insightsoftwareconsortium.org Tue Oct 28 06:30:29 2014 From: noreply at insightsoftwareconsortium.org (MIDAS Journal) Date: Tue, 28 Oct 2014 06:30:29 -0400 (EDT) Subject: [ITK] [ITK-users] New Submission: Validation of real-time intensity based 2D/3D registration for image guided radiotherapy Message-ID: <20141028103029.4B4053D6C67C@insightsoftwareconsortium.org> Hello, A new submission has been added to the MIDAS Journal. Title: Validation of real-time intensity based 2D/3D registration for image guided radiotherapy Authors: Furtado H., Underwood T., Depuydt T., Stock M., Georg D., Birkfellner W. Abstract: Patient motion during radiotherapy or intra-fractional motion, is one of the major sources of uncertainty in dose application. 2D/3D registration is an intensity based method used successfully to track tumor motion with the potential to reduce uncertainty. Despite promising results, validation remains a problem due to the lack of a gold standard. In this paper, we demonstrate the use of clinical datasets acquired with the VERO LINAC to validate intensity based 2D/3D registration. The patient considered in this study had a gold marker implanted to enable live tumor tracking. We verify our results against the tracked gold marker position. Our results show that it is possible to accurately track the tumor using only intensity based 2D/3D registration. The mean error of our registration is of 1.6 ?? 0.3mm and as low as 1.1 ?? 0.5mm when looking only at the cranial-caudal direction. The results pave the way for a possible clinical application of the method. Download and review this publication at: http://hdl.handle.net/10380/3497 Generated by the MIDAS Journal You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ . -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.lemaitre58 at gmail.com Tue Oct 28 09:33:46 2014 From: g.lemaitre58 at gmail.com (=?UTF-8?Q?Guillaume_Lema=C3=AEtre?=) Date: Tue, 28 Oct 2014 14:33:46 +0100 Subject: [ITK] [ITK-users] Resample Message-ID: Hi all, I am currently working on resampling. I am using the code available: http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM I was wondering if with the version of ITK-4.7, it is still necessary to shift the data to undo the effect of the rescale intercept by the DICOM reader as coded in the section 4) Thanks, Best regards, -- *LEMA?TRE GuillaumePhD CandiateMSc Erasmus Mundus ViBOT (Vision-roBOTic)MSc Business Innovation and Technology Management* g.lemaitre58 at gmail.com *ViCOROB - Computer Vision and Robotic Team* Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 http://vicorob.udg.es/ *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 http://le2i.cnrs.fr https://sites.google.com/site/glemaitre58/ Vice - Chairman of A.S.C. Fours UFOLEP Chairman of A.S.C. Fours FFC Webmaster of http://ascfours.free.fr -------------- 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 Oct 28 09:54:17 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 28 Oct 2014 09:54:17 -0400 Subject: [ITK] [ITK-users] Resample In-Reply-To: References: Message-ID: <8CE5D58E-4AFE-4CFE-9E22-2137AA1A243F@mail.nih.gov> Hello, There was a recent Kitware blog post about this issue: http://www.kitware.com/blog/home/post/754 Although after reading it I am still not sure how to answer your question, but it may help. Brad On Oct 28, 2014, at 9:33 AM, Guillaume Lema?tre wrote: > Hi all, > > I am currently working on resampling. I am using the code available: > http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM > > I was wondering if with the version of ITK-4.7, it is still necessary to shift the data to undo the effect of the rescale intercept by the DICOM reader as coded in the section 4) > > Thanks, > Best regards, > -- > LEMA?TRE Guillaume > PhD Candiate > MSc Erasmus Mundus ViBOT (Vision-roBOTic) > MSc Business Innovation and Technology Management > > g.lemaitre58 at gmail.com > > > ViCOROB - Computer Vision and Robotic Team > Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona > Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 > http://vicorob.udg.es/ > LE2I - Le Creusot > IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot > Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 > http://le2i.cnrs.fr > > https://sites.google.com/site/glemaitre58/ > Vice - Chairman of A.S.C. Fours UFOLEP > Chairman of A.S.C. Fours FFC > Webmaster of http://ascfours.free.fr > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 bill.lorensen at gmail.com Tue Oct 28 10:31:32 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 28 Oct 2014 10:31:32 -0400 Subject: [ITK] [ITK-users] Resample In-Reply-To: <8CE5D58E-4AFE-4CFE-9E22-2137AA1A243F@mail.nih.gov> References: <8CE5D58E-4AFE-4CFE-9E22-2137AA1A243F@mail.nih.gov> Message-ID: The example contains #ifdef's that remove the slope/intercept recalling for ITK 4.6 and above. On Tue, Oct 28, 2014 at 9:54 AM, Bradley Lowekamp wrote: > Hello, > > There was a recent Kitware blog post about this issue: > http://www.kitware.com/blog/home/post/754 > > Although after reading it I am still not sure how to answer your question, > but it may help. > Brad > > On Oct 28, 2014, at 9:33 AM, Guillaume Lema?tre > wrote: > > Hi all, > > I am currently working on resampling. I am using the code available: > http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM > > I was wondering if with the version of ITK-4.7, it is still necessary to > shift the data to undo the effect of the rescale intercept by the DICOM > reader as coded in the section 4) > > Thanks, > Best regards, > -- > > > > > *LEMA?TRE GuillaumePhD CandiateMSc Erasmus Mundus ViBOT > (Vision-roBOTic)MSc Business Innovation and Technology Management* > g.lemaitre58 at gmail.com > > > *ViCOROB - Computer Vision and Robotic Team* > Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona > Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 > http://vicorob.udg.es/ > > *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la > Fonderie, 71200 Le Creusot > Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 > http://le2i.cnrs.fr > > https://sites.google.com/site/glemaitre58/ > Vice - Chairman of A.S.C. Fours UFOLEP > Chairman of A.S.C. Fours FFC > Webmaster of http://ascfours.free.fr > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 > > -- Unpaid intern in BillsBasement at noware dot 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 abdul.sw84 at gmail.com Tue Oct 28 11:12:26 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Tue, 28 Oct 2014 16:12:26 +0100 Subject: [ITK] [ITK-users] Running an ITK program Message-ID: Hi, I'm new to ITK. I have installed ITK, and want to run the example here: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader How can I do that? Should the files be in the same directory of ITK? Thanks. -------------- 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 daviddoria at gmail.com Tue Oct 28 11:17:57 2014 From: daviddoria at gmail.com (David Doria) Date: Tue, 28 Oct 2014 11:17:57 -0400 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: On Tue, Oct 28, 2014 at 11:12 AM, Abdul Abdul wrote: > Hi, > > I'm new to ITK. I have installed ITK, and want to run the example here: > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > How can I do that? Should the files be in the same directory of ITK? > > Thanks. > Please see this page to get started: http://www.itk.org/Wiki/ITK/Examples/Instructions/ForUsers Let us know if you have any questions. David -------------- 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 bill.lorensen at gmail.com Tue Oct 28 11:18:22 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 28 Oct 2014 11:18:22 -0400 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: Follow the instructions at the bottom of the example page: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#Download_and_Build_ImageFileReader On Tue, Oct 28, 2014 at 11:12 AM, Abdul Abdul wrote: > Hi, > > I'm new to ITK. I have installed ITK, and want to run the example here: > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > How can I do that? Should the files be in the same directory of ITK? > > Thanks. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 abdul.sw84 at gmail.com Tue Oct 28 11:37:49 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Tue, 28 Oct 2014 16:37:49 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: David, Thanks for your reply. I went to the following steps: Windows 1. Open CMake 2. Select your CMakeLists.txt file 3. Select your build system 4. Click "Generate" But, it is not clear. I opened CMake, and selected CMakeLists.txt as the source file, and the directory where my main program is in as the "build" directory, but get the following error: ? On Tue, Oct 28, 2014 at 4:17 PM, David Doria wrote: > On Tue, Oct 28, 2014 at 11:12 AM, Abdul Abdul > wrote: > >> Hi, >> >> I'm new to ITK. I have installed ITK, and want to run the example here: >> http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >> >> How can I do that? Should the files be in the same directory of ITK? >> >> Thanks. >> > > Please see this page to get started: > > http://www.itk.org/Wiki/ITK/Examples/Instructions/ForUsers > > Let us know if you have any questions. > > David > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 9923 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From abdul.sw84 at gmail.com Tue Oct 28 11:44:51 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Tue, 28 Oct 2014 16:44:51 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: I made a "src" and "bin" directories. When I configure using CMake, this is what I get in "red": CMake Error at CMakeLists.txt:11 (find_package): By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "ItkVtkGlue", but CMake did not find one. Could not find a package configuration file provided by "ItkVtkGlue" with any of the following names: ItkVtkGlueConfig.cmake itkvtkglue-config.cmake Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set "ItkVtkGlue_DIR" to a directory containing one of the above files. If "ItkVtkGlue" provides a separate development package or SDK, be sure it has been installed. On Tue, Oct 28, 2014 at 4:37 PM, Abdul Abdul wrote: > David, > > Thanks for your reply. > > I went to the following steps: > Windows > > 1. Open CMake > 2. Select your CMakeLists.txt file > 3. Select your build system > 4. Click "Generate" > > But, it is not clear. I opened CMake, and selected CMakeLists.txt as the > source file, and the directory where my main program is in as the "build" > directory, but get the following error: > > > ? > > > > > On Tue, Oct 28, 2014 at 4:17 PM, David Doria wrote: > >> On Tue, Oct 28, 2014 at 11:12 AM, Abdul Abdul >> wrote: >> >>> Hi, >>> >>> I'm new to ITK. I have installed ITK, and want to run the example here: >>> http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >>> >>> How can I do that? Should the files be in the same directory of ITK? >>> >>> Thanks. >>> >> >> Please see this page to get started: >> >> http://www.itk.org/Wiki/ITK/Examples/Instructions/ForUsers >> >> Let us know if you have any questions. >> >> David >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 9923 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From abdul.sw84 at gmail.com Tue Oct 28 11:46:51 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Tue, 28 Oct 2014 16:46:51 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: It seems it is to do with the package. I got the CMakeLists.txt from the link I showed in my question. What would be a suitable CMakeLists.txt to use here? On Tue, Oct 28, 2014 at 4:44 PM, Abdul Abdul wrote: > I made a "src" and "bin" directories. When I configure using CMake, this > is what I get in "red": > > CMake Error at CMakeLists.txt:11 (find_package): > By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project > has asked CMake to find a package configuration file provided by > "ItkVtkGlue", but CMake did not find one. > > Could not find a package configuration file provided by "ItkVtkGlue" with > any of the following names: > > ItkVtkGlueConfig.cmake > itkvtkglue-config.cmake > > Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set > "ItkVtkGlue_DIR" to a directory containing one of the above files. If > "ItkVtkGlue" provides a separate development package or SDK, be sure it has > been installed. > > On Tue, Oct 28, 2014 at 4:37 PM, Abdul Abdul wrote: > >> David, >> >> Thanks for your reply. >> >> I went to the following steps: >> Windows >> >> 1. Open CMake >> 2. Select your CMakeLists.txt file >> 3. Select your build system >> 4. Click "Generate" >> >> But, it is not clear. I opened CMake, and selected CMakeLists.txt as the >> source file, and the directory where my main program is in as the "build" >> directory, but get the following error: >> >> >> ? >> >> >> >> >> On Tue, Oct 28, 2014 at 4:17 PM, David Doria >> wrote: >> >>> On Tue, Oct 28, 2014 at 11:12 AM, Abdul Abdul >>> wrote: >>> >>>> Hi, >>>> >>>> I'm new to ITK. I have installed ITK, and want to run the example here: >>>> http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >>>> >>>> How can I do that? Should the files be in the same directory of ITK? >>>> >>>> Thanks. >>>> >>> >>> Please see this page to get started: >>> >>> http://www.itk.org/Wiki/ITK/Examples/Instructions/ForUsers >>> >>> Let us know if you have any questions. >>> >>> David >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 9923 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From bill.lorensen at gmail.com Tue Oct 28 12:24:54 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 28 Oct 2014 12:24:54 -0400 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: That particular examples requires VTK. Have you built VTK also? On Tue, Oct 28, 2014 at 11:46 AM, Abdul Abdul wrote: > It seems it is to do with the package. I got the CMakeLists.txt from the > link I showed in my question. What would be a suitable CMakeLists.txt to > use here? > > On Tue, Oct 28, 2014 at 4:44 PM, Abdul Abdul wrote: > >> I made a "src" and "bin" directories. When I configure using CMake, this >> is what I get in "red": >> >> CMake Error at CMakeLists.txt:11 (find_package): >> By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project >> has asked CMake to find a package configuration file provided by >> "ItkVtkGlue", but CMake did not find one. >> >> Could not find a package configuration file provided by "ItkVtkGlue" with >> any of the following names: >> >> ItkVtkGlueConfig.cmake >> itkvtkglue-config.cmake >> >> Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set >> "ItkVtkGlue_DIR" to a directory containing one of the above files. If >> "ItkVtkGlue" provides a separate development package or SDK, be sure it >> has >> been installed. >> >> On Tue, Oct 28, 2014 at 4:37 PM, Abdul Abdul >> wrote: >> >>> David, >>> >>> Thanks for your reply. >>> >>> I went to the following steps: >>> Windows >>> >>> 1. Open CMake >>> 2. Select your CMakeLists.txt file >>> 3. Select your build system >>> 4. Click "Generate" >>> >>> But, it is not clear. I opened CMake, and selected CMakeLists.txt as the >>> source file, and the directory where my main program is in as the "build" >>> directory, but get the following error: >>> >>> >>> ? >>> >>> >>> >>> >>> On Tue, Oct 28, 2014 at 4:17 PM, David Doria >>> wrote: >>> >>>> On Tue, Oct 28, 2014 at 11:12 AM, Abdul Abdul >>>> wrote: >>>> >>>>> Hi, >>>>> >>>>> I'm new to ITK. I have installed ITK, and want to run the example >>>>> here: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >>>>> >>>>> How can I do that? Should the files be in the same directory of ITK? >>>>> >>>>> Thanks. >>>>> >>>> >>>> Please see this page to get started: >>>> >>>> http://www.itk.org/Wiki/ITK/Examples/Instructions/ForUsers >>>> >>>> Let us know if you have any questions. >>>> >>>> David >>>> >>> >>> >> > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -- Unpaid intern in BillsBasement at noware dot com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 9923 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From norman-k-williams at uiowa.edu Tue Oct 28 13:21:31 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Tue, 28 Oct 2014 17:21:31 +0000 Subject: [ITK] [ITK-dev] Thread-unsafety of transform classes FOLLUWUP Message-ID: This is mostly for Bradley Lowenkamp and Matt McCormick, but at some point the wider developer community will be affected and input solicited. The MatrixOffsetTransformBase has 3 values in its FixedParameters, which is the values of the center of rotation. There was a mystery as to why MatrixOffsetTransformBase starts out with 12 fixed parameters, when it only really has 3. The reason is in the constructor for Transform, which initializes the FixedParameters to have the same number of values as the Parameters. This is a design flaw; it represents the Anti-Pattern ?Initialize a member/variable to a default that is almost always wrong.? This leads to most Transform classes resizing the FixedParameters when GetFixedParameters is called, and assigning their value based on the actual fixed parameters for that Transform class. This is thread-unsafe, since resizing m_FixedParameters involves a free/allocate pair. template Transform ::Transform(NumberOfParametersType numberOfParameters) : m_Parameters(numberOfParameters), m_FixedParameters(numberOfParameters) #ifdef ITKV3_COMPATIBILITY , m_SharedLocalJacobian(NOutputDimensions, numberOfParameters) #endif { } ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- 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 Tue Oct 28 13:41:07 2014 From: blowekamp at mail.nih.gov (Bradley Lowekamp) Date: Tue, 28 Oct 2014 13:41:07 -0400 Subject: [ITK] [ITK-dev] Thread-unsafety of transform classes FOLLUWUP In-Reply-To: References: Message-ID: <34B144F1-76BB-497B-914A-CAAE3F2A6893@mail.nih.gov> Perhaps the constructor needs another argument name numberOfFixedParameters, which defaults to the prior argument? Brad On Oct 28, 2014, at 1:21 PM, Williams, Norman K wrote: > This is mostly for Bradley Lowenkamp and Matt McCormick, but at some point the wider developer community will be affected and input solicited. > > The MatrixOffsetTransformBase has 3 values in its FixedParameters, which is the values of the center of rotation. > > There was a mystery as to why MatrixOffsetTransformBase starts out with 12 fixed parameters, when it only really has 3. > > The reason is in the constructor for Transform, which initializes the FixedParameters to have the same number of values as the Parameters. > > This is a design flaw; it represents the Anti-Pattern ?Initialize a member/variable to a default that is almost always wrong.? > > This leads to most Transform classes resizing the FixedParameters when GetFixedParameters is called, and assigning their value based on the actual fixed parameters for that Transform class. > > This is thread-unsafe, since resizing m_FixedParameters involves a free/allocate pair. > > template unsigned int NInputDimensions, > unsigned int NOutputDimensions> > Transform > ::Transform(NumberOfParametersType numberOfParameters) : > m_Parameters(numberOfParameters), > m_FixedParameters(numberOfParameters) > #ifdef ITKV3_COMPATIBILITY > , m_SharedLocalJacobian(NOutputDimensions, numberOfParameters) > #endif > { > } > > > > Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers -------------- 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 michael.meuli at gmail.com Tue Oct 28 15:49:09 2014 From: michael.meuli at gmail.com (Michael Meuli) Date: Tue, 28 Oct 2014 20:49:09 +0100 Subject: [ITK] SCIFIO Message-ID: Hi all If I modify the RunTest() function in itkSCIFIOImageIOTest.cxx just a little bit to get hold of the image for processing it, I get the following error which appears, depending on the file, after a certain number of series were processed with the following error: terminate called after throwing an instance of 'itk::InvalidRequestedRegionError' what(): /home/michael/bioimage/itk/itk-master/InsightToolkit/Modules/Core/Common/src/itkDataObject.cxx:393: Requested region is (at least partially) outside the largest possible region. Aborted (core dumped) In case of dead-A.ome.tiff after processing the first two series. Please find attached the runnable code. The file dead-A.ome.tiff can be found here: https://www.dropbox.com/sh/t2z0f4jttcnfh8s/AADq21HNR7EwH1JFxskhXXhea in the folder ome-tiff-files/5.0.5 Googling for the poblem I found the following about the Update() fuction: http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#a4041fb21e9105500eee311e265691bd5 I don't really understand it but I've tried UpdateLargestPossibleRegion() instead of Update() but the complier didn't eat it. Many thanks and best regards Michael -------------- next part -------------- A non-text attachment was scrubbed... Name: main.cxx Type: text/x-c++src Size: 3637 bytes Desc: not available URL: From matt.mccormick at kitware.com Tue Oct 28 18:20:02 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 28 Oct 2014 18:20:02 -0400 Subject: [ITK] Gerrit Downtime Message-ID: Hi, Gerrit will be down tonight for maintenance. Sorry for the inconvenience. Matt From matt.mccormick at kitware.com Tue Oct 28 22:14:49 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 28 Oct 2014 22:14:49 -0400 Subject: [ITK] [ITK-dev] Thread-unsafety of transform classes FOLLUWUP In-Reply-To: <34B144F1-76BB-497B-914A-CAAE3F2A6893@mail.nih.gov> References: <34B144F1-76BB-497B-914A-CAAE3F2A6893@mail.nih.gov> Message-ID: Thanks for the further investigations. I think it should default to zero fixed parameters. Here's a patch: http://review.source.kitware.com/#/c/17789/ Thanks, Matt On Tue, Oct 28, 2014 at 1:41 PM, Bradley Lowekamp wrote: > Perhaps the constructor needs another argument name numberOfFixedParameters, > which defaults to the prior argument? > > Brad > > On Oct 28, 2014, at 1:21 PM, Williams, Norman K > wrote: > > This is mostly for Bradley Lowenkamp and Matt McCormick, but at some point > the wider developer community will be affected and input solicited. > > The MatrixOffsetTransformBase has 3 values in its FixedParameters, which is > the values of the center of rotation. > > There was a mystery as to why MatrixOffsetTransformBase starts out with 12 > fixed parameters, when it only really has 3. > > The reason is in the constructor for Transform, which initializes the > FixedParameters to have the same number of values as the Parameters. > > This is a design flaw; it represents the Anti-Pattern ?Initialize a > member/variable to a default that is almost always wrong.? > > This leads to most Transform classes resizing the FixedParameters when > GetFixedParameters is called, and assigning their value based on the actual > fixed parameters for that Transform class. > > This is thread-unsafe, since resizing m_FixedParameters involves a > free/allocate pair. > > template unsigned int NInputDimensions, > unsigned int NOutputDimensions> > Transform > ::Transform(NumberOfParametersType numberOfParameters) : > m_Parameters(numberOfParameters), > m_FixedParameters(numberOfParameters) > #ifdef ITKV3_COMPATIBILITY > , m_SharedLocalJacobian(NOutputDimensions, numberOfParameters) > #endif > { > } > > > > ________________________________ > Notice: This UI Health Care e-mail (including attachments) is covered by the > Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential > and may be legally privileged. If you are not the intended recipient, you > are hereby notified that any retention, dissemination, distribution, or > copying of this communication is strictly prohibited. Please reply to the > sender that you have received the message in error, then delete it. Thank > you. > ________________________________ > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > _______________________________________________ > 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 From matt.mccormick at kitware.com Tue Oct 28 22:22:26 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Tue, 28 Oct 2014 22:22:26 -0400 Subject: [ITK] Opportunities to share, discuss, design, and learn with other ITK community members Message-ID: There are a couple of upcoming opportunities to share, discuss, design, and learn with your fellow ITK community members. On Thursday, 1:00 PM Eastern USA time, there will be a Google+ Hangout where we will be doing code reviews: https://plus.google.com/events/carevmgo0kpecsvrontn575i34g On Friday, 11:00 AM Eastern USA time, an ITK development conference, https://plus.google.com/events/c7hsglaqhvn0hdkkbmqki8bs580 For those that cannot join via Hangout, telephone call-in is also possible. Dial: 585-632-6296 Enter pin: 31423 To get regular invites to these events, join the ITK Bar Camp G+ Community: https://plus.google.com/u/0/communities/111375098792764998322 All are welcome. Hope to talk to you then! From abdul.sw84 at gmail.com Wed Oct 29 06:09:21 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 11:09:21 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: I will build VTK. But, the main issue is on the steps to follow to run an ITK program. Does that make sense? For instance, should I create "source" and "build" directories? When I run CMake, what should I do? ....etc Sorry I'm new to this. Thanks. On Tue, Oct 28, 2014 at 5:24 PM, Bill Lorensen wrote: > That particular examples requires VTK. Have you built VTK also? > > > On Tue, Oct 28, 2014 at 11:46 AM, Abdul Abdul > wrote: > >> It seems it is to do with the package. I got the CMakeLists.txt from the >> link I showed in my question. What would be a suitable CMakeLists.txt to >> use here? >> >> On Tue, Oct 28, 2014 at 4:44 PM, Abdul Abdul >> wrote: >> >>> I made a "src" and "bin" directories. When I configure using CMake, this >>> is what I get in "red": >>> >>> CMake Error at CMakeLists.txt:11 (find_package): >>> By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project >>> has asked CMake to find a package configuration file provided by >>> "ItkVtkGlue", but CMake did not find one. >>> >>> Could not find a package configuration file provided by "ItkVtkGlue" with >>> any of the following names: >>> >>> ItkVtkGlueConfig.cmake >>> itkvtkglue-config.cmake >>> >>> Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set >>> "ItkVtkGlue_DIR" to a directory containing one of the above files. If >>> "ItkVtkGlue" provides a separate development package or SDK, be sure it >>> has >>> been installed. >>> >>> On Tue, Oct 28, 2014 at 4:37 PM, Abdul Abdul >>> wrote: >>> >>>> David, >>>> >>>> Thanks for your reply. >>>> >>>> I went to the following steps: >>>> Windows >>>> >>>> 1. Open CMake >>>> 2. Select your CMakeLists.txt file >>>> 3. Select your build system >>>> 4. Click "Generate" >>>> >>>> But, it is not clear. I opened CMake, and selected CMakeLists.txt as >>>> the source file, and the directory where my main program is in as the >>>> "build" directory, but get the following error: >>>> >>>> >>>> ? >>>> >>>> >>>> >>>> >>>> On Tue, Oct 28, 2014 at 4:17 PM, David Doria >>>> wrote: >>>> >>>>> On Tue, Oct 28, 2014 at 11:12 AM, Abdul Abdul >>>>> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I'm new to ITK. I have installed ITK, and want to run the example >>>>>> here: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >>>>>> >>>>>> How can I do that? Should the files be in the same directory of ITK? >>>>>> >>>>>> Thanks. >>>>>> >>>>> >>>>> Please see this page to get started: >>>>> >>>>> http://www.itk.org/Wiki/ITK/Examples/Instructions/ForUsers >>>>> >>>>> Let us know if you have any questions. >>>>> >>>>> David >>>>> >>>> >>>> >>> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > > -- > Unpaid intern in BillsBasement at noware dot com > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 9923 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Wed Oct 29 06:26:31 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 11:26:31 +0100 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 Message-ID: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Hi all, I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 (built with Qt5). Note I use cmake 2.8.12... I get link 1 error: ld library not found for -lQt5::Widgets Any idea how to fix it? Thanks, Arnaud _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 drescherjm at gmail.com Wed Oct 29 08:03:11 2014 From: drescherjm at gmail.com (John Drescher) Date: Wed, 29 Oct 2014 08:03:11 -0400 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: On Wed, Oct 29, 2014 at 6:09 AM, Abdul Abdul wrote: > I will build VTK. But, the main issue is on the steps to follow to run an > ITK program. Does that make sense? > > For instance, should I create "source" and "build" directories? > You do not create a source folder. This folder is where your source exists. You do create a build folder. I put the build folder in a completely different tree from the source tree but you can if you want make the build folder a subfolder of the source. > When I run CMake, what should I do? ....etc > Usually in cmake-gui its set the source folder and the build folder. Then Configure. You will be asked what generator to use (Visual Studio 12 2013 Win64 ...) After this you Generate. John -------------- 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 bill.lorensen at gmail.com Wed Oct 29 08:15:15 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 08:15:15 -0400 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Arnaud, I build ITK with itkVtkGlue fine on my Mac, but I build against the nightly VTK. I'm not sure if that makes a difference. Bill On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas wrote: > Hi all, > > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 (built with Qt5). Note I use cmake 2.8.12... > > I get link 1 error: > ld library not found for -lQt5::Widgets > > Any idea how to fix it? > > Thanks, > Arnaud > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 arnaudgelas at gmail.com Wed Oct 29 08:23:12 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 13:23:12 +0100 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Bill, It seems builds fine as long as Qt5 is not involved in the process (?) I just wonder if there is not something missing in vtk's cmake installed files to help finding Qt5::Widgets (?), or if we could only use required libraries from vtk which should not depend on Qt5 (?) Thanks, Arnaud On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen wrote: > Arnaud, > > I build ITK with itkVtkGlue fine on my Mac, but I build against the > nightly VTK. I'm not sure if that makes a difference. > > Bill > > > On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas > wrote: > > Hi all, > > > > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 (built > with Qt5). Note I use cmake 2.8.12... > > > > I get link 1 error: > > ld library not found for -lQt5::Widgets > > > > Any idea how to fix it? > > > > Thanks, > > Arnaud > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/insight-users > > > > -- > Unpaid intern in BillsBasement at noware dot 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 bill.lorensen at gmail.com Wed Oct 29 08:32:46 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 08:32:46 -0400 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: I did not build against an installed VTK. On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas wrote: > Bill, > > It seems builds fine as long as Qt5 is not involved in the process (?) > > I just wonder if there is not something missing in vtk's cmake installed > files to help finding Qt5::Widgets (?), or if we could only use required > libraries from vtk which should not depend on Qt5 (?) > > Thanks, > Arnaud > > On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen > wrote: >> >> Arnaud, >> >> I build ITK with itkVtkGlue fine on my Mac, but I build against the >> nightly VTK. I'm not sure if that makes a difference. >> >> Bill >> >> >> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >> wrote: >> > Hi all, >> > >> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 (built >> > with Qt5). Note I use cmake 2.8.12... >> > >> > I get link 1 error: >> > ld library not found for -lQt5::Widgets >> > >> > Any idea how to fix it? >> > >> > Thanks, >> > Arnaud >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the ITK FAQ at: >> > http://www.itk.org/Wiki/ITK_FAQ >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/insight-users >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com > > -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 abdul.sw84 at gmail.com Wed Oct 29 09:56:47 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 14:56:47 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: I got the following error for CMakeLists.txt (attached): CMake Error at CMakeLists.txt:11 (find_package): By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "ItkVtkGlue", but CMake did not find one. Could not find a package configuration file provided by "ItkVtkGlue" with any of the following names: ItkVtkGlueConfig.cmake itkvtkglue-config.cmake Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set "ItkVtkGlue_DIR" to a directory containing one of the above files. If "ItkVtkGlue" provides a separate development package or SDK, be sure it has been installed. Do you know why is that? Should I look for "ItkVtkGlue"? Thanks. On Wed, Oct 29, 2014 at 1:03 PM, John Drescher wrote: > > > On Wed, Oct 29, 2014 at 6:09 AM, Abdul Abdul wrote: > >> I will build VTK. But, the main issue is on the steps to follow to run an >> ITK program. Does that make sense? >> >> For instance, should I create "source" and "build" directories? >> > > You do not create a source folder. This folder is where your source > exists. You do create a build folder. I put the build folder in a > completely different tree from the source tree but you can if you want make > the build folder a subfolder of the source. > > >> When I run CMake, what should I do? ....etc >> > > > Usually in cmake-gui its set the source folder and the build folder. Then > Configure. You will be asked what generator to use (Visual Studio 12 2013 > Win64 ...) After this you Generate. > > John > -------------- 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 abdul.sw84 at gmail.com Wed Oct 29 09:58:23 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 14:58:23 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: Sorry, forgot to attach CMakeLists.txt On Wed, Oct 29, 2014 at 2:56 PM, Abdul Abdul wrote: > I got the following error for CMakeLists.txt (attached): > > CMake Error at CMakeLists.txt:11 (find_package): > By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project > has asked CMake to find a package configuration file provided by > "ItkVtkGlue", but CMake did not find one. > > Could not find a package configuration file provided by "ItkVtkGlue" with > any of the following names: > > ItkVtkGlueConfig.cmake > itkvtkglue-config.cmake > > Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set > "ItkVtkGlue_DIR" to a directory containing one of the above files. If > "ItkVtkGlue" provides a separate development package or SDK, be sure it has > been installed. > > Do you know why is that? Should I look for "ItkVtkGlue"? > > Thanks. > > On Wed, Oct 29, 2014 at 1:03 PM, John Drescher > wrote: > >> >> >> On Wed, Oct 29, 2014 at 6:09 AM, Abdul Abdul >> wrote: >> >>> I will build VTK. But, the main issue is on the steps to follow to run >>> an ITK program. Does that make sense? >>> >>> For instance, should I create "source" and "build" directories? >>> >> >> You do not create a source folder. This folder is where your source >> exists. You do create a build folder. I put the build folder in a >> completely different tree from the source tree but you can if you want make >> the build folder a subfolder of the source. >> >> >>> When I run CMake, what should I do? ....etc >>> >> >> >> Usually in cmake-gui its set the source folder and the build folder. Then >> Configure. You will be asked what generator to use (Visual Studio 12 2013 >> Win64 ...) After this you Generate. >> >> John >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- cmake_minimum_required(VERSION 2.8) project(readDisplayImageInfo) find_package(ITK REQUIRED) include(${ITK_USE_FILE}) if (ITKVtkGlue_LOADED) find_package(VTK REQUIRED) include(${VTK_USE_FILE}) else() find_package(ItkVtkGlue REQUIRED) include(${ItkVtkGlue_USE_FILE}) set(Glue ItkVtkGlue) endif() add_executable(readDisplayImageInfo MACOSX_BUNDLE readDisplayImageInfo.cxx) target_link_libraries(readDisplayImageInfo ${Glue} ${VTK_LIBRARIES} ${ITK_LIBRARIES}) -------------- 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 abdul.sw84 at gmail.com Wed Oct 29 10:03:14 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 15:03:14 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: Sorry I'm really new to that. The example I'm trying to run is here: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader What would a basic CMakeLists.txt for this example be? Thanks. On Wed, Oct 29, 2014 at 3:00 PM, John Drescher wrote: > On Wed, Oct 29, 2014 at 9:56 AM, Abdul Abdul wrote: > > I got the following error for CMakeLists.txt (attached): > > > > CMake Error at CMakeLists.txt:11 (find_package): > > By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project > > has asked CMake to find a package configuration file provided by > > "ItkVtkGlue", but CMake did not find one. > > > > Could not find a package configuration file provided by "ItkVtkGlue" with > > any of the following names: > > > > ItkVtkGlueConfig.cmake > > itkvtkglue-config.cmake > > > > Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set > > "ItkVtkGlue_DIR" to a directory containing one of the above files. If > > "ItkVtkGlue" provides a separate development package or SDK, be sure it > has > > been installed. > > > > Do you know why is that? Should I look for "ItkVtkGlue"? > > > > This is part of ITK4 (which you have to configure to use ItkVtkGlue) > or a separate package in older versions of ITK. > > John > -------------- 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 drescherjm at gmail.com Wed Oct 29 10:07:38 2014 From: drescherjm at gmail.com (John Drescher) Date: Wed, 29 Oct 2014 10:07:38 -0400 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul wrote: > Sorry I'm really new to that. > > The example I'm trying to run is here: > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > What would a basic CMakeLists.txt for this example be? > You have the correct CMakeLists.txt you do not have the correct dependent librarys installed. You need to understand how to build and install software with CMake. John _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 abdul.sw84 at gmail.com Wed Oct 29 10:10:05 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 15:10:05 +0100 Subject: [ITK] [ITK-users] Where can I get ItKVtkGlue Message-ID: Hello, I'm trying to run this example: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader But, get the following when I "configure" in CMake: CMake Error at CMakeLists.txt:11 (find_package): By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "ItkVtkGlue", but CMake did not find one. Could not find a package configuration file provided by "ItkVtkGlue" with any of the following names: ItkVtkGlueConfig.cmake itkvtkglue-config.cmake Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set "ItkVtkGlue_DIR" to a directory containing one of the above files. If "ItkVtkGlue" provides a separate development package or SDK, be sure it has been installed. It seems I need "ItkVtkGlue"? Where can I download it? And, what should I do to combine it with the program? Thanks. -------------- 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 abdul.sw84 at gmail.com Wed Oct 29 10:10:50 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 15:10:50 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: I know how to use CMake already. But, seems something to do with the paths or libraries. On Wed, Oct 29, 2014 at 3:07 PM, John Drescher wrote: > On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul > wrote: > > Sorry I'm really new to that. > > > > The example I'm trying to run is here: > > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > > > What would a basic CMakeLists.txt for this example be? > > > > You have the correct CMakeLists.txt you do not have the correct > dependent librarys installed. You need to understand how to build and > install software with CMake. > > John > -------------- 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 abdul.sw84 at gmail.com Wed Oct 29 10:11:21 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 15:11:21 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: The question is thus, where to get those libraries? On Wed, Oct 29, 2014 at 3:10 PM, Abdul Abdul wrote: > I know how to use CMake already. But, seems something to do with the paths > or libraries. > > On Wed, Oct 29, 2014 at 3:07 PM, John Drescher > wrote: > >> On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul >> wrote: >> > Sorry I'm really new to that. >> > >> > The example I'm trying to run is here: >> > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >> > >> > What would a basic CMakeLists.txt for this example be? >> > >> >> You have the correct CMakeLists.txt you do not have the correct >> dependent librarys installed. You need to understand how to build and >> install software with CMake. >> >> John >> > > -------------- 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 drescherjm at gmail.com Wed Oct 29 10:17:42 2014 From: drescherjm at gmail.com (John Drescher) Date: Wed, 29 Oct 2014 10:17:42 -0400 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: On Wed, Oct 29, 2014 at 10:11 AM, Abdul Abdul wrote: > The question is thus, where to get those libraries? You need to build them with CMake. John _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 drescherjm at gmail.com Wed Oct 29 10:19:53 2014 From: drescherjm at gmail.com (John Drescher) Date: Wed, 29 Oct 2014 10:19:53 -0400 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: On Wed, Oct 29, 2014 at 10:17 AM, John Drescher wrote: > On Wed, Oct 29, 2014 at 10:11 AM, Abdul Abdul wrote: >> The question is thus, where to get those libraries? > > You need to build them with CMake. What I mean is when you build ITK from source you need to enable the ItkVtkGlue module using cmake. John _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 cr at neuro.ma.uni-heidelberg.de Wed Oct 29 10:15:17 2014 From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith) Date: Wed, 29 Oct 2014 15:15:17 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: Message-ID: <5450F675.5010404@neuro.ma.uni-heidelberg.de> Did you build ITK with Module_ITKVtkGlue=ON? (c.f. http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue) Christina On 29.10.2014 15:10, Abdul Abdul wrote: > I know how to use CMake already. But, seems something to do with the > paths or libraries. > > On Wed, Oct 29, 2014 at 3:07 PM, John Drescher > wrote: > > On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul > > wrote: > > Sorry I'm really new to that. > > > > The example I'm trying to run is here: > > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > > > What would a basic CMakeLists.txt for this example be? > > > > You have the correct CMakeLists.txt you do not have the correct > dependent librarys installed. You need to understand how to build and > install software with CMake. > > John > > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 bill.lorensen at gmail.com Wed Oct 29 10:37:20 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 10:37:20 -0400 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Arnaud, I just tried an ITK build against an installed VTK and it built just fine. Bill On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen wrote: > I did not build against an installed VTK. > > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas wrote: >> Bill, >> >> It seems builds fine as long as Qt5 is not involved in the process (?) >> >> I just wonder if there is not something missing in vtk's cmake installed >> files to help finding Qt5::Widgets (?), or if we could only use required >> libraries from vtk which should not depend on Qt5 (?) >> >> Thanks, >> Arnaud >> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >> wrote: >>> >>> Arnaud, >>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against the >>> nightly VTK. I'm not sure if that makes a difference. >>> >>> Bill >>> >>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >>> wrote: >>> > Hi all, >>> > >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 (built >>> > with Qt5). Note I use cmake 2.8.12... >>> > >>> > I get link 1 error: >>> > ld library not found for -lQt5::Widgets >>> > >>> > Any idea how to fix it? >>> > >>> > Thanks, >>> > Arnaud >>> > _____________________________________ >>> > Powered by www.kitware.com >>> > >>> > Visit other Kitware open-source projects at >>> > http://www.kitware.com/opensource/opensource.html >>> > >>> > Kitware offers ITK Training Courses, for more information visit: >>> > http://www.kitware.com/products/protraining.php >>> > >>> > Please keep messages on-topic and check the ITK FAQ at: >>> > http://www.itk.org/Wiki/ITK_FAQ >>> > >>> > Follow this link to subscribe/unsubscribe: >>> > http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>> >>> -- >>> Unpaid intern in BillsBasement at noware dot com >> >> > > > > -- > Unpaid intern in BillsBasement at noware dot com -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 deu439 at gmail.com Wed Oct 29 10:47:22 2014 From: deu439 at gmail.com (Jan Dorazil) Date: Wed, 29 Oct 2014 15:47:22 +0100 Subject: [ITK] Segfault while running Examples/IO/ImageFileReader Message-ID: <5450FDFA.1000500@gmail.com> Hello, after successfully building the example ImageFileReader I have encountered segmentation fault error while running the built binary. back trace: #0 0xb0c88175 in __GI__IO_default_xsputn () from /lib/libc.so.6 #1 0xb0c58e73 in vfprintf () from /lib/libc.so.6 #2 0xb0c82dc1 in vasprintf () from /lib/libc.so.6 #3 0xb6614704 in vtk__H5E_printf_stack () from /usr/lib/libvtkhdf5-6.1.so.1 #4 0xb67c7711 in vtk__H5I_inc_ref () from /usr/lib/libvtkhdf5-6.1.so.1 #5 0xb66145ac in vtk__H5E_push_stack () from /usr/lib/libvtkhdf5-6.1.so.1 #6 0xb661474c in vtk__H5E_printf_stack () from /usr/lib/libvtkhdf5-6.1.so.1 #7 0xb67c7711 in vtk__H5I_inc_ref () from /usr/lib/libvtkhdf5-6.1.so.1 #8 0xb66145ac in vtk__H5E_push_stack () from /usr/lib/libvtkhdf5-6.1.so.1 #9 0xb661474c in vtk__H5E_printf_stack () from /usr/lib/libvtkhdf5-6.1.so.1 #10 0xb67c7711 in vtk__H5I_inc_ref () from /usr/lib/libvtkhdf5-6.1.so.1 #11 0xb66145ac in vtk__H5E_push_stack () from /usr/lib/libvtkhdf5-6.1.so.1 #12 0xb661474c in vtk__H5E_printf_stack () from /usr/lib/libvtkhdf5-6.1.so.1 #13 0xb67c7711 in vtk__H5I_inc_ref () from /usr/lib/libvtkhdf5-6.1.so.1 #14 0xb66145ac in vtk__H5E_push_stack () from /usr/lib/libvtkhdf5-6.1.so.1 #15 0xb661474c in vtk__H5E_printf_stack () from /usr/lib/libvtkhdf5-6.1.so.1 .... ITK version 4.6.1 built with: -DBUILD_SHARED_LIBS=ON \ -DBUILD_DOCUMENTATION=ON \ -DITK_DOXYGEN_HTML=ON \ -DITK_DOXYGEN_ECLIPSEHELP=OFF \ -DModule_ITKVtkGlue=ON \ -DModule_ITKVideoBridgeOpenCV=ON \ -DITK_USE_SYSTEM_ZLIB=ON \ -DITK_USE_SYSTEM_JPEG=ON \ -DITK_USE_SYSTEM_TIFF=ON \ -DITK_USE_SYSTEM_PNG=ON \ -DITK_USE_SYSTEM_FFTW=ON \ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_BUILD_TYPE=Release .. VTK version: 6.1.0 built with: -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_BUILD_TYPE=Release \ -DVTK_Group_Qt=ON \ -DBUILD_SHARED_LIBS=ON .. Could anybody help me please? From arnaudgelas at gmail.com Wed Oct 29 10:48:46 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 15:48:46 +0100 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Bill, I can also confirm everything builds fine if VTK is not compiled with Qt5 (which is part of my requirements...) On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen wrote: > Arnaud, > > I just tried an ITK build against an installed VTK and it built just fine. > > Bill > > > On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen > wrote: > > I did not build against an installed VTK. > > > > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas > wrote: > >> Bill, > >> > >> It seems builds fine as long as Qt5 is not involved in the process (?) > >> > >> I just wonder if there is not something missing in vtk's cmake installed > >> files to help finding Qt5::Widgets (?), or if we could only use required > >> libraries from vtk which should not depend on Qt5 (?) > >> > >> Thanks, > >> Arnaud > >> > >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen > > >> wrote: > >>> > >>> Arnaud, > >>> > >>> I build ITK with itkVtkGlue fine on my Mac, but I build against the > >>> nightly VTK. I'm not sure if that makes a difference. > >>> > >>> Bill > >>> > >>> > >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas > >>> wrote: > >>> > Hi all, > >>> > > >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 > (built > >>> > with Qt5). Note I use cmake 2.8.12... > >>> > > >>> > I get link 1 error: > >>> > ld library not found for -lQt5::Widgets > >>> > > >>> > Any idea how to fix it? > >>> > > >>> > Thanks, > >>> > Arnaud > >>> > _____________________________________ > >>> > Powered by www.kitware.com > >>> > > >>> > Visit other Kitware open-source projects at > >>> > http://www.kitware.com/opensource/opensource.html > >>> > > >>> > Kitware offers ITK Training Courses, for more information visit: > >>> > http://www.kitware.com/products/protraining.php > >>> > > >>> > Please keep messages on-topic and check the ITK FAQ at: > >>> > http://www.itk.org/Wiki/ITK_FAQ > >>> > > >>> > Follow this link to subscribe/unsubscribe: > >>> > http://public.kitware.com/mailman/listinfo/insight-users > >>> > >>> > >>> > >>> -- > >>> Unpaid intern in BillsBasement at noware dot com > >> > >> > > > > > > > > -- > > Unpaid intern in BillsBasement at noware dot com > > > > -- > Unpaid intern in BillsBasement at noware dot 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 emmasaunders123 at gmail.com Wed Oct 29 10:56:31 2014 From: emmasaunders123 at gmail.com (Emma Saunders) Date: Wed, 29 Oct 2014 14:56:31 +0000 Subject: [ITK] [ITK-users] amount of smoothing ITK pyramid scheme Message-ID: Hello all, It is common to smooth images with a Gaussain with particular variance. I have read that the extent of smoothing should depend upon the amount of noise pattern in the images. It's also common to have higher smoothing values with higher shrink values. I am wondering how users first determine the amount of smoothing, do they make any actual measurements which represent the noise pattern in the images? Also is there a mechanism to determine how this level of noise varies dependent upon the shrink factor in a multi pyramid scheme? Thanks for any help Emma -------------- 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 bill.lorensen at gmail.com Wed Oct 29 11:01:57 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 11:01:57 -0400 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: I have qt enabled for my vtk build, but I am using qt4.7.4. On Wed, Oct 29, 2014 at 10:50 AM, Sam Raby wrote: > I thought Arnaud means that if Qt5 is enabled in VTK, then ITK compilation > with itkVtkGlue-enabled will fail. I had this issue about 3-4 month ago and > I was not able to resolve it. > > -S > > On Wed, Oct 29, 2014 at 9:37 AM, Bill Lorensen > wrote: >> >> Arnaud, >> >> I just tried an ITK build against an installed VTK and it built just fine. >> >> Bill >> >> >> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >> wrote: >> > I did not build against an installed VTK. >> > >> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >> > wrote: >> >> Bill, >> >> >> >> It seems builds fine as long as Qt5 is not involved in the process (?) >> >> >> >> I just wonder if there is not something missing in vtk's cmake >> >> installed >> >> files to help finding Qt5::Widgets (?), or if we could only use >> >> required >> >> libraries from vtk which should not depend on Qt5 (?) >> >> >> >> Thanks, >> >> Arnaud >> >> >> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >> >> >> >> wrote: >> >>> >> >>> Arnaud, >> >>> >> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against the >> >>> nightly VTK. I'm not sure if that makes a difference. >> >>> >> >>> Bill >> >>> >> >>> >> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >> >>> wrote: >> >>> > Hi all, >> >>> > >> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 >> >>> > (built >> >>> > with Qt5). Note I use cmake 2.8.12... >> >>> > >> >>> > I get link 1 error: >> >>> > ld library not found for -lQt5::Widgets >> >>> > >> >>> > Any idea how to fix it? >> >>> > >> >>> > Thanks, >> >>> > Arnaud >> >>> > _____________________________________ >> >>> > Powered by www.kitware.com >> >>> > >> >>> > Visit other Kitware open-source projects at >> >>> > http://www.kitware.com/opensource/opensource.html >> >>> > >> >>> > Kitware offers ITK Training Courses, for more information visit: >> >>> > http://www.kitware.com/products/protraining.php >> >>> > >> >>> > Please keep messages on-topic and check the ITK FAQ at: >> >>> > http://www.itk.org/Wiki/ITK_FAQ >> >>> > >> >>> > Follow this link to subscribe/unsubscribe: >> >>> > http://public.kitware.com/mailman/listinfo/insight-users >> >>> >> >>> >> >>> >> >>> -- >> >>> Unpaid intern in BillsBasement at noware dot com >> >> >> >> >> > >> > >> > >> > -- >> > Unpaid intern in BillsBasement at noware dot com >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 > > -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 Oct 29 11:03:26 2014 From: chinander at gmail.com (Mike Chinander) Date: Wed, 29 Oct 2014 10:03:26 -0500 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Can you share your CMakeLists.txt file? Are you using something like the following commands: ADD_EXECUTABLE(myexe ${MYSRCS}) TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} ${VTK_LIBRARIES}) On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas wrote: > Bill, > > I can also confirm everything builds fine if VTK is not compiled with Qt5 > (which is part of my requirements...) > > > > On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen > wrote: > >> Arnaud, >> >> I just tried an ITK build against an installed VTK and it built just fine. >> >> Bill >> >> >> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >> wrote: >> > I did not build against an installed VTK. >> > >> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >> wrote: >> >> Bill, >> >> >> >> It seems builds fine as long as Qt5 is not involved in the process (?) >> >> >> >> I just wonder if there is not something missing in vtk's cmake >> installed >> >> files to help finding Qt5::Widgets (?), or if we could only use >> required >> >> libraries from vtk which should not depend on Qt5 (?) >> >> >> >> Thanks, >> >> Arnaud >> >> >> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen < >> bill.lorensen at gmail.com> >> >> wrote: >> >>> >> >>> Arnaud, >> >>> >> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against the >> >>> nightly VTK. I'm not sure if that makes a difference. >> >>> >> >>> Bill >> >>> >> >>> >> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >> >>> wrote: >> >>> > Hi all, >> >>> > >> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 >> (built >> >>> > with Qt5). Note I use cmake 2.8.12... >> >>> > >> >>> > I get link 1 error: >> >>> > ld library not found for -lQt5::Widgets >> >>> > >> >>> > Any idea how to fix it? >> >>> > >> >>> > Thanks, >> >>> > Arnaud >> >>> > _____________________________________ >> >>> > Powered by www.kitware.com >> >>> > >> >>> > Visit other Kitware open-source projects at >> >>> > http://www.kitware.com/opensource/opensource.html >> >>> > >> >>> > Kitware offers ITK Training Courses, for more information visit: >> >>> > http://www.kitware.com/products/protraining.php >> >>> > >> >>> > Please keep messages on-topic and check the ITK FAQ at: >> >>> > http://www.itk.org/Wiki/ITK_FAQ >> >>> > >> >>> > Follow this link to subscribe/unsubscribe: >> >>> > http://public.kitware.com/mailman/listinfo/insight-users >> >>> >> >>> >> >>> >> >>> -- >> >>> Unpaid intern in BillsBasement at noware dot com >> >> >> >> >> > >> > >> > >> > -- >> > Unpaid intern in BillsBasement at noware dot com >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 abdul.sw84 at gmail.com Wed Oct 29 11:06:52 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 16:06:52 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: <5450F675.5010404@neuro.ma.uni-heidelberg.de> References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> Message-ID: Yes, I now downloaded ItkVtkGlue, and configured and generated it using CMake. Now, when I try to configure the program mentioned, I get the following: CMake Error at CMakeLists.txt:12 (include): include could not find load file: C:/Users/Abdul/Desktop/itk I'm using the same CMakeLists.txt as in the example (attached). Do you know why I'm getting this error? Thanks. On Wed, Oct 29, 2014 at 3:15 PM, Chr. Rossmanith < cr at neuro.ma.uni-heidelberg.de> wrote: > Did you build ITK with Module_ITKVtkGlue=ON? (c.f. > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue) > > Christina > > > > On 29.10.2014 15:10, Abdul Abdul wrote: > > I know how to use CMake already. But, seems something to do with the paths > or libraries. > > On Wed, Oct 29, 2014 at 3:07 PM, John Drescher > wrote: > >> On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul >> wrote: >> > Sorry I'm really new to that. >> > >> > The example I'm trying to run is here: >> > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >> > >> > What would a basic CMakeLists.txt for this example be? >> > >> >> You have the correct CMakeLists.txt you do not have the correct >> dependent librarys installed. You need to understand how to build and >> install software with CMake. >> >> John >> > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects athttp://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit:http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 -------------- cmake_minimum_required(VERSION 2.8) project(ImageFileReader) find_package(ITK REQUIRED) include(${ITK_USE_FILE}) if (ITKVtkGlue_LOADED) find_package(VTK REQUIRED) include(${VTK_USE_FILE}) else() find_package(ItkVtkGlue REQUIRED) include(${ItkVtkGlue_USE_FILE}) set(Glue ItkVtkGlue) endif() add_executable(ImageFileReader MACOSX_BUNDLE ImageFileReader.cxx) target_link_libraries(ImageFileReader ${Glue} ${VTK_LIBRARIES} ${ITK_LIBRARIES}) -------------- 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 arnaudgelas at gmail.com Wed Oct 29 11:09:21 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 16:09:21 +0100 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Bill, Until now, I have been using Qt4; and I can confirm it was working fine! It seems that Qt5 paths are not propagated in exported vtk cmake folder!? I see 2 ways of fixing it: * fixing exported cmake files in VTK to write proper information. Although I am not sure what needs to be exported? * reduce the libraries contained in VTK_LIBRARIES to the minimum set for ITKVtkGlue and hope there is no propagated link to Qt5 (actually I don't see why there should be) ? What do you think? Thanks, Arnaud On Wed, Oct 29, 2014 at 4:01 PM, Bill Lorensen wrote: > I have qt enabled for my vtk build, but I am using qt4.7.4. > > > On Wed, Oct 29, 2014 at 10:50 AM, Sam Raby wrote: > > I thought Arnaud means that if Qt5 is enabled in VTK, then ITK > compilation > > with itkVtkGlue-enabled will fail. I had this issue about 3-4 month ago > and > > I was not able to resolve it. > > > > -S > > > > On Wed, Oct 29, 2014 at 9:37 AM, Bill Lorensen > > wrote: > >> > >> Arnaud, > >> > >> I just tried an ITK build against an installed VTK and it built just > fine. > >> > >> Bill > >> > >> > >> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen > > >> wrote: > >> > I did not build against an installed VTK. > >> > > >> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas > >> > wrote: > >> >> Bill, > >> >> > >> >> It seems builds fine as long as Qt5 is not involved in the process > (?) > >> >> > >> >> I just wonder if there is not something missing in vtk's cmake > >> >> installed > >> >> files to help finding Qt5::Widgets (?), or if we could only use > >> >> required > >> >> libraries from vtk which should not depend on Qt5 (?) > >> >> > >> >> Thanks, > >> >> Arnaud > >> >> > >> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen > >> >> > >> >> wrote: > >> >>> > >> >>> Arnaud, > >> >>> > >> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against the > >> >>> nightly VTK. I'm not sure if that makes a difference. > >> >>> > >> >>> Bill > >> >>> > >> >>> > >> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas < > arnaudgelas at gmail.com> > >> >>> wrote: > >> >>> > Hi all, > >> >>> > > >> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 > >> >>> > (built > >> >>> > with Qt5). Note I use cmake 2.8.12... > >> >>> > > >> >>> > I get link 1 error: > >> >>> > ld library not found for -lQt5::Widgets > >> >>> > > >> >>> > Any idea how to fix it? > >> >>> > > >> >>> > Thanks, > >> >>> > Arnaud > >> >>> > _____________________________________ > >> >>> > Powered by www.kitware.com > >> >>> > > >> >>> > Visit other Kitware open-source projects at > >> >>> > http://www.kitware.com/opensource/opensource.html > >> >>> > > >> >>> > Kitware offers ITK Training Courses, for more information visit: > >> >>> > http://www.kitware.com/products/protraining.php > >> >>> > > >> >>> > Please keep messages on-topic and check the ITK FAQ at: > >> >>> > http://www.itk.org/Wiki/ITK_FAQ > >> >>> > > >> >>> > Follow this link to subscribe/unsubscribe: > >> >>> > http://public.kitware.com/mailman/listinfo/insight-users > >> >>> > >> >>> > >> >>> > >> >>> -- > >> >>> Unpaid intern in BillsBasement at noware dot com > >> >> > >> >> > >> > > >> > > >> > > >> > -- > >> > Unpaid intern in BillsBasement at noware dot com > >> > >> > >> > >> -- > >> Unpaid intern in BillsBasement at noware dot com > >> _____________________________________ > >> Powered by www.kitware.com > >> > >> Visit other Kitware open-source projects at > >> http://www.kitware.com/opensource/opensource.html > >> > >> Kitware offers ITK Training Courses, for more information visit: > >> http://www.kitware.com/products/protraining.php > >> > >> Please keep messages on-topic and check the 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 > > > > > > > > -- > Unpaid intern in BillsBasement at noware dot 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 abdul.sw84 at gmail.com Wed Oct 29 11:10:35 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 16:10:35 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> Message-ID: Those are the settings I'm having: ? On Wed, Oct 29, 2014 at 4:06 PM, Abdul Abdul wrote: > Yes, I now downloaded ItkVtkGlue, and configured and generated it using > CMake. > > Now, when I try to configure the program mentioned, I get the following: > > CMake Error at CMakeLists.txt:12 (include): > include could not find load file: > > C:/Users/Abdul/Desktop/itk > > I'm using the same CMakeLists.txt as in the example (attached). > > Do you know why I'm getting this error? > > Thanks. > > On Wed, Oct 29, 2014 at 3:15 PM, Chr. Rossmanith < > cr at neuro.ma.uni-heidelberg.de> wrote: > >> Did you build ITK with Module_ITKVtkGlue=ON? (c.f. >> http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue) >> >> Christina >> >> >> >> On 29.10.2014 15:10, Abdul Abdul wrote: >> >> I know how to use CMake already. But, seems something to do with the >> paths or libraries. >> >> On Wed, Oct 29, 2014 at 3:07 PM, John Drescher >> wrote: >> >>> On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul >>> wrote: >>> > Sorry I'm really new to that. >>> > >>> > The example I'm trying to run is here: >>> > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >>> > >>> > What would a basic CMakeLists.txt for this example be? >>> > >>> >>> You have the correct CMakeLists.txt you do not have the correct >>> dependent librarys installed. You need to understand how to build and >>> install software with CMake. >>> >>> John >>> >> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects athttp://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit:http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 21131 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From arnaudgelas at gmail.com Wed Oct 29 11:11:58 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 16:11:58 +0100 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Mike, It is difficult to refer to one single CMakeLists.txt, since it is tied up to ITK's modularization. But here are the files to look at: https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake Best Arnaud On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander wrote: > Can you share your CMakeLists.txt file? Are you using something like the > following commands: > > ADD_EXECUTABLE(myexe ${MYSRCS}) > TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} ${VTK_LIBRARIES}) > > On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas > wrote: > >> Bill, >> >> I can also confirm everything builds fine if VTK is not compiled with Qt5 >> (which is part of my requirements...) >> >> >> >> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen >> wrote: >> >>> Arnaud, >>> >>> I just tried an ITK build against an installed VTK and it built just >>> fine. >>> >>> Bill >>> >>> >>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >>> wrote: >>> > I did not build against an installed VTK. >>> > >>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >>> wrote: >>> >> Bill, >>> >> >>> >> It seems builds fine as long as Qt5 is not involved in the process (?) >>> >> >>> >> I just wonder if there is not something missing in vtk's cmake >>> installed >>> >> files to help finding Qt5::Widgets (?), or if we could only use >>> required >>> >> libraries from vtk which should not depend on Qt5 (?) >>> >> >>> >> Thanks, >>> >> Arnaud >>> >> >>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen < >>> bill.lorensen at gmail.com> >>> >> wrote: >>> >>> >>> >>> Arnaud, >>> >>> >>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against the >>> >>> nightly VTK. I'm not sure if that makes a difference. >>> >>> >>> >>> Bill >>> >>> >>> >>> >>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >> > >>> >>> wrote: >>> >>> > Hi all, >>> >>> > >>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 >>> (built >>> >>> > with Qt5). Note I use cmake 2.8.12... >>> >>> > >>> >>> > I get link 1 error: >>> >>> > ld library not found for -lQt5::Widgets >>> >>> > >>> >>> > Any idea how to fix it? >>> >>> > >>> >>> > Thanks, >>> >>> > Arnaud >>> >>> > _____________________________________ >>> >>> > Powered by www.kitware.com >>> >>> > >>> >>> > Visit other Kitware open-source projects at >>> >>> > http://www.kitware.com/opensource/opensource.html >>> >>> > >>> >>> > Kitware offers ITK Training Courses, for more information visit: >>> >>> > http://www.kitware.com/products/protraining.php >>> >>> > >>> >>> > Please keep messages on-topic and check the ITK FAQ at: >>> >>> > http://www.itk.org/Wiki/ITK_FAQ >>> >>> > >>> >>> > Follow this link to subscribe/unsubscribe: >>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>> >>> >>> >>> >>> >>> -- >>> >>> Unpaid intern in BillsBasement at noware dot com >>> >> >>> >> >>> > >>> > >>> > >>> > -- >>> > Unpaid intern in BillsBasement at noware dot com >>> >>> >>> >>> -- >>> Unpaid intern in BillsBasement at noware dot com >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 bill.lorensen at gmail.com Wed Oct 29 11:12:25 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 11:12:25 -0400 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> Message-ID: Try building your ITK with Module_ITKVtkGlue=ON It has been a while since I checked building against a separately downloaded ItkVtkGlue. It is possible that it no longer works. Bill On Wed, Oct 29, 2014 at 11:06 AM, Abdul Abdul wrote: > Yes, I now downloaded ItkVtkGlue, and configured and generated it using > CMake. > > Now, when I try to configure the program mentioned, I get the following: > > CMake Error at CMakeLists.txt:12 (include): > include could not find load file: > > C:/Users/Abdul/Desktop/itk > > I'm using the same CMakeLists.txt as in the example (attached). > > Do you know why I'm getting this error? > > Thanks. > > On Wed, Oct 29, 2014 at 3:15 PM, Chr. Rossmanith > wrote: >> >> Did you build ITK with Module_ITKVtkGlue=ON? (c.f. >> http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue) >> >> Christina >> >> >> >> On 29.10.2014 15:10, Abdul Abdul wrote: >> >> I know how to use CMake already. But, seems something to do with the paths >> or libraries. >> >> On Wed, Oct 29, 2014 at 3:07 PM, John Drescher >> wrote: >>> >>> On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul >>> wrote: >>> > Sorry I'm really new to that. >>> > >>> > The example I'm trying to run is here: >>> > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >>> > >>> > What would a basic CMakeLists.txt for this example be? >>> > >>> >>> You have the correct CMakeLists.txt you do not have the correct >>> dependent librarys installed. You need to understand how to build and >>> install software with CMake. >>> >>> John >> >> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 > -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 cr at neuro.ma.uni-heidelberg.de Wed Oct 29 11:13:47 2014 From: cr at neuro.ma.uni-heidelberg.de (Chr. Rossmanith) Date: Wed, 29 Oct 2014 16:13:47 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> Message-ID: <5451042B.9060102@neuro.ma.uni-heidelberg.de> On 29.10.2014 16:10, Abdul Abdul wrote: > Those are the settings I'm having: > > Probably I need new glasses but I can't read anything. Toggle to advanced settings and look for Module_ITKVtkGlue and make sure it is set to On - no need to download additional software - it is all there already. Christina > ? > > On Wed, Oct 29, 2014 at 4:06 PM, Abdul Abdul > wrote: > > Yes, I now downloaded ItkVtkGlue, and configured and generated it > using CMake. > > Now, when I try to configure the program mentioned, I get the > following: > > CMake Error at CMakeLists.txt:12 (include): > include could not find load file: > > C:/Users/Abdul/Desktop/itk > > I'm using the same CMakeLists.txt as in the example (attached). > > Do you know why I'm getting this error? > > Thanks. > > On Wed, Oct 29, 2014 at 3:15 PM, Chr. Rossmanith > > wrote: > > Did you build ITK with Module_ITKVtkGlue=ON? (c.f. > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue) > > Christina > > > > On 29.10.2014 15:10, Abdul Abdul wrote: >> I know how to use CMake already. But, seems something to do >> with the paths or libraries. >> >> On Wed, Oct 29, 2014 at 3:07 PM, John Drescher >> > wrote: >> >> On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul >> > wrote: >> > Sorry I'm really new to that. >> > >> > The example I'm trying to run is here: >> > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >> > >> > What would a basic CMakeLists.txt for this example be? >> > >> >> You have the correct CMakeLists.txt you do not have the >> correct >> dependent librarys installed. You need to understand how >> to build and >> install software with CMake. >> >> John >> >> >> >> >> _____________________________________ >> Powered bywww.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 21131 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From hiner at wisc.edu Wed Oct 29 11:23:13 2014 From: hiner at wisc.edu (Mark Hiner) Date: Wed, 29 Oct 2014 10:23:13 -0500 Subject: [ITK] SCIFIO In-Reply-To: References: Message-ID: Hi Michael, When you get InvalidRequestedRegionError on a series after the first, it strongly suggests series skew. In the dead-A.ome.tiff, series 2 is larger (more planes) than series 1, and series 3 is smaller than series 2. So it seems that at some point in the workflow the requested region is not matching the current series... which doesn't cause any errors until the region size decreases from one series to the next. Note that without the intermediate Update() call on the Image, the program will iterate successfully through the entire dataset. So it's the intermediate Update() that's exposing this problem. I assume you do not actually need it, since calling Update() on the writer will trigger the whole pipeline and you can then extract the intermediate image. On the other hand, I also assume you should be able to do incremental Update() calls, but I have no idea why it's not working with the SCIFIOImageIO. Perhaps someone else in the ITK community sees an error in usage of the ITK API? Otherwise I would suggest inspecting the requested region of various components at each series. A quick check of the Writer's region shows it changing at each series appropriately. However, the region of your image with intermediate updates never changes... but I don't really understand why (since it's also downstream of the reader). Sorry I can't be of more help, Mark On Tue, Oct 28, 2014 at 2:49 PM, Michael Meuli wrote: > Hi all > > If I modify the RunTest() function in itkSCIFIOImageIOTest.cxx just a > little bit to > get hold of the image for processing it, I get the following error > which appears, depending on the file, after a > certain number of series were processed with the following error: > > terminate called after throwing an instance of > 'itk::InvalidRequestedRegionError' > what(): > /home/michael/bioimage/itk/itk-master/InsightToolkit/Modules/Core/Common/src/itkDataObject.cxx:393: > Requested region is (at least partially) outside the largest possible > region. > Aborted (core dumped) > > In case of dead-A.ome.tiff after processing the first two series. > > Please find attached the runnable code. > The file dead-A.ome.tiff can be found here: > https://www.dropbox.com/sh/t2z0f4jttcnfh8s/AADq21HNR7EwH1JFxskhXXhea > in the folder ome-tiff-files/5.0.5 > > Googling for the poblem I found the following about the Update() fuction: > > http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html#a4041fb21e9105500eee311e265691bd5 > I don't really understand it but I've tried > UpdateLargestPossibleRegion() instead of Update() but the complier > didn't eat it. > > Many thanks and best regards > > Michael > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From abdul.sw84 at gmail.com Wed Oct 29 11:26:52 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 16:26:52 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: <5451042B.9060102@neuro.ma.uni-heidelberg.de> References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: Sorry for the small image. I attach it here. For the "advanced settings", I couldn't find such option in CMake. Should I be looking for that somewhere else? Thanks. On Wed, Oct 29, 2014 at 4:13 PM, Chr. Rossmanith < cr at neuro.ma.uni-heidelberg.de> wrote: > On 29.10.2014 16:10, Abdul Abdul wrote: > > Those are the settings I'm having: > > > Probably I need new glasses but I can't read anything. > > Toggle to advanced settings and look for Module_ITKVtkGlue and make sure > it is set to On - no need to download additional software - it is all there > already. > > Christina > > ? > > On Wed, Oct 29, 2014 at 4:06 PM, Abdul Abdul wrote: > >> Yes, I now downloaded ItkVtkGlue, and configured and generated it using >> CMake. >> >> Now, when I try to configure the program mentioned, I get the following: >> >> CMake Error at CMakeLists.txt:12 (include): >> include could not find load file: >> >> C:/Users/Abdul/Desktop/itk >> >> I'm using the same CMakeLists.txt as in the example (attached). >> >> Do you know why I'm getting this error? >> >> Thanks. >> >> On Wed, Oct 29, 2014 at 3:15 PM, Chr. Rossmanith < >> cr at neuro.ma.uni-heidelberg.de> wrote: >> >>> Did you build ITK with Module_ITKVtkGlue=ON? (c.f. >>> http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue) >>> >>> Christina >>> >>> >>> >>> On 29.10.2014 15:10, Abdul Abdul wrote: >>> >>> I know how to use CMake already. But, seems something to do with the >>> paths or libraries. >>> >>> On Wed, Oct 29, 2014 at 3:07 PM, John Drescher >>> wrote: >>> >>>> On Wed, Oct 29, 2014 at 10:03 AM, Abdul Abdul >>>> wrote: >>>> > Sorry I'm really new to that. >>>> > >>>> > The example I'm trying to run is here: >>>> > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >>>> > >>>> > What would a basic CMakeLists.txt for this example be? >>>> > >>>> >>>> You have the correct CMakeLists.txt you do not have the correct >>>> dependent librarys installed. You need to understand how to build and >>>> install software with CMake. >>>> >>>> John >>>> >>> >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects athttp://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit:http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the 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 -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 21131 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 21131 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From drescherjm at gmail.com Wed Oct 29 11:29:21 2014 From: drescherjm at gmail.com (John Drescher) Date: Wed, 29 Oct 2014 11:29:21 -0400 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: On Wed, Oct 29, 2014 at 11:26 AM, Abdul Abdul wrote: > Sorry for the small image. I attach it here. > > For the "advanced settings", I couldn't find such option in CMake. Should > I be looking for that somewhere else? > > Thanks. > > Is this a picture of you configuring ITK or the example. We are all telling you to configure and build ITK before you move on to the example. John -------------- 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 Oct 29 11:29:44 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 29 Oct 2014 11:29:44 -0400 Subject: [ITK] [ITK-users] Where can I get ItKVtkGlue In-Reply-To: References: Message-ID: Hi Abdul, ITKVtkGlue used to be a separate project, but it is now integrated into ITK as the module ITKVtkGlue. You can enable in your ITK CMake configuration by setting Module_ITKVtkGlue to ON. It requires a build of VTK. Hope this helps, Matt On Wed, Oct 29, 2014 at 10:10 AM, Abdul Abdul wrote: > Hello, > > I'm trying to run this example: > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > But, get the following when I "configure" in CMake: > > CMake Error at CMakeLists.txt:11 (find_package): > By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project > has asked CMake to find a package configuration file provided by > "ItkVtkGlue", but CMake did not find one. > > Could not find a package configuration file provided by "ItkVtkGlue" with > any of the following names: > > ItkVtkGlueConfig.cmake > itkvtkglue-config.cmake > > Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set > "ItkVtkGlue_DIR" to a directory containing one of the above files. If > "ItkVtkGlue" provides a separate development package or SDK, be sure it has > been installed. > > It seems I need "ItkVtkGlue"? Where can I download it? And, what should I do > to combine it with the program? > > Thanks. > > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 Oct 29 11:31:05 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 29 Oct 2014 11:31:05 -0400 Subject: [ITK] Segfault while running Examples/IO/ImageFileReader In-Reply-To: <5450FDFA.1000500@gmail.com> References: <5450FDFA.1000500@gmail.com> Message-ID: Hi Jan, Does it help to configure both your ITK and your VTK to use the system HDF5? Thanks, Matt On Wed, Oct 29, 2014 at 10:47 AM, Jan Dorazil wrote: > Hello, > after successfully building the example ImageFileReader I have encountered > segmentation fault error while running the built binary. > back trace: > #0 0xb0c88175 in __GI__IO_default_xsputn () from /lib/libc.so.6 > #1 0xb0c58e73 in vfprintf () from /lib/libc.so.6 > #2 0xb0c82dc1 in vasprintf () from /lib/libc.so.6 > #3 0xb6614704 in vtk__H5E_printf_stack () from /usr/lib/libvtkhdf5-6.1.so.1 > #4 0xb67c7711 in vtk__H5I_inc_ref () from /usr/lib/libvtkhdf5-6.1.so.1 > #5 0xb66145ac in vtk__H5E_push_stack () from /usr/lib/libvtkhdf5-6.1.so.1 > #6 0xb661474c in vtk__H5E_printf_stack () from /usr/lib/libvtkhdf5-6.1.so.1 > #7 0xb67c7711 in vtk__H5I_inc_ref () from /usr/lib/libvtkhdf5-6.1.so.1 > #8 0xb66145ac in vtk__H5E_push_stack () from /usr/lib/libvtkhdf5-6.1.so.1 > #9 0xb661474c in vtk__H5E_printf_stack () from /usr/lib/libvtkhdf5-6.1.so.1 > #10 0xb67c7711 in vtk__H5I_inc_ref () from /usr/lib/libvtkhdf5-6.1.so.1 > #11 0xb66145ac in vtk__H5E_push_stack () from /usr/lib/libvtkhdf5-6.1.so.1 > #12 0xb661474c in vtk__H5E_printf_stack () from /usr/lib/libvtkhdf5-6.1.so.1 > #13 0xb67c7711 in vtk__H5I_inc_ref () from /usr/lib/libvtkhdf5-6.1.so.1 > #14 0xb66145ac in vtk__H5E_push_stack () from /usr/lib/libvtkhdf5-6.1.so.1 > #15 0xb661474c in vtk__H5E_printf_stack () from /usr/lib/libvtkhdf5-6.1.so.1 > .... > ITK version 4.6.1 > built with: > -DBUILD_SHARED_LIBS=ON \ > -DBUILD_DOCUMENTATION=ON \ > -DITK_DOXYGEN_HTML=ON \ > -DITK_DOXYGEN_ECLIPSEHELP=OFF \ > -DModule_ITKVtkGlue=ON \ > -DModule_ITKVideoBridgeOpenCV=ON \ > -DITK_USE_SYSTEM_ZLIB=ON \ > -DITK_USE_SYSTEM_JPEG=ON \ > -DITK_USE_SYSTEM_TIFF=ON \ > -DITK_USE_SYSTEM_PNG=ON \ > -DITK_USE_SYSTEM_FFTW=ON \ > -DCMAKE_INSTALL_PREFIX=/usr \ > -DCMAKE_BUILD_TYPE=Release .. > > > VTK version: 6.1.0 > built with: > -DCMAKE_INSTALL_PREFIX=/usr \ > -DCMAKE_BUILD_TYPE=Release \ > -DVTK_Group_Qt=ON \ > -DBUILD_SHARED_LIBS=ON .. > > Could anybody help me please? > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community From bill.lorensen at gmail.com Wed Oct 29 11:31:42 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 11:31:42 -0400 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Arnaud, Can you try to build one of the ITK wiki examples against your installed VTK? This might help narrow down the problem. Whether it is a VTK of ITK issue. http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow Bill On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas wrote: > Mike, > > It is difficult to refer to one single CMakeLists.txt, since it is tied up > to ITK's modularization. > > But here are the files to look at: > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake > > Best > Arnaud > > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander wrote: >> >> Can you share your CMakeLists.txt file? Are you using something like the >> following commands: >> >> ADD_EXECUTABLE(myexe ${MYSRCS}) >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} >> ${VTK_LIBRARIES}) >> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas >> wrote: >>> >>> Bill, >>> >>> I can also confirm everything builds fine if VTK is not compiled with Qt5 >>> (which is part of my requirements...) >>> >>> >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen >>> wrote: >>>> >>>> Arnaud, >>>> >>>> I just tried an ITK build against an installed VTK and it built just >>>> fine. >>>> >>>> Bill >>>> >>>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >>>> wrote: >>>> > I did not build against an installed VTK. >>>> > >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >>>> > wrote: >>>> >> Bill, >>>> >> >>>> >> It seems builds fine as long as Qt5 is not involved in the process >>>> >> (?) >>>> >> >>>> >> I just wonder if there is not something missing in vtk's cmake >>>> >> installed >>>> >> files to help finding Qt5::Widgets (?), or if we could only use >>>> >> required >>>> >> libraries from vtk which should not depend on Qt5 (?) >>>> >> >>>> >> Thanks, >>>> >> Arnaud >>>> >> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >>>> >> >>>> >> wrote: >>>> >>> >>>> >>> Arnaud, >>>> >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against the >>>> >>> nightly VTK. I'm not sure if that makes a difference. >>>> >>> >>>> >>> Bill >>>> >>> >>>> >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >>>> >>> >>>> >>> wrote: >>>> >>> > Hi all, >>>> >>> > >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 >>>> >>> > (built >>>> >>> > with Qt5). Note I use cmake 2.8.12... >>>> >>> > >>>> >>> > I get link 1 error: >>>> >>> > ld library not found for -lQt5::Widgets >>>> >>> > >>>> >>> > Any idea how to fix it? >>>> >>> > >>>> >>> > Thanks, >>>> >>> > Arnaud >>>> >>> > _____________________________________ >>>> >>> > Powered by www.kitware.com >>>> >>> > >>>> >>> > Visit other Kitware open-source projects at >>>> >>> > http://www.kitware.com/opensource/opensource.html >>>> >>> > >>>> >>> > Kitware offers ITK Training Courses, for more information visit: >>>> >>> > http://www.kitware.com/products/protraining.php >>>> >>> > >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ >>>> >>> > >>>> >>> > Follow this link to subscribe/unsubscribe: >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> Unpaid intern in BillsBasement at noware dot com >>>> >> >>>> >> >>>> > >>>> > >>>> > >>>> > -- >>>> > Unpaid intern in BillsBasement at noware dot com >>>> >>>> >>>> >>>> -- >>>> Unpaid intern in BillsBasement at noware dot com >>> >>> >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the 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 > -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 abdul.sw84 at gmail.com Wed Oct 29 11:31:45 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 16:31:45 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: ITK is already being built. The picture is for the example. On Wed, Oct 29, 2014 at 4:29 PM, John Drescher wrote: > > > On Wed, Oct 29, 2014 at 11:26 AM, Abdul Abdul > wrote: > >> Sorry for the small image. I attach it here. >> >> For the "advanced settings", I couldn't find such option in CMake. Should >> I be looking for that somewhere else? >> >> Thanks. >> >> > Is this a picture of you configuring ITK or the example. We are all > telling you to configure and build ITK before you move on to the example. > > John > -------------- 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 drescherjm at gmail.com Wed Oct 29 11:33:51 2014 From: drescherjm at gmail.com (John Drescher) Date: Wed, 29 Oct 2014 11:33:51 -0400 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: On Wed, Oct 29, 2014 at 11:31 AM, Abdul Abdul wrote: > ITK is already being built. The picture is for the example. Then go back and build ITK. While you configure ITK4 make sure you enable the itkvtkglue module. You do not get this by default or in a binary download. This also requires that you have or build VTK. if this is on windows I highly recommend that you build all of these from source. John _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 arnaudgelas at gmail.com Wed Oct 29 11:46:13 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 16:46:13 +0100 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Bill, Same link error with this example... On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen wrote: > Arnaud, > > Can you try to build one of the ITK wiki examples against your > installed VTK? This might help narrow down the problem. Whether it is > a VTK of ITK issue. > http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow > > Bill > > On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas > wrote: > > Mike, > > > > It is difficult to refer to one single CMakeLists.txt, since it is tied > up > > to ITK's modularization. > > > > But here are the files to look at: > > > > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt > > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake > > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake > > > > Best > > Arnaud > > > > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander > wrote: > >> > >> Can you share your CMakeLists.txt file? Are you using something like the > >> following commands: > >> > >> ADD_EXECUTABLE(myexe ${MYSRCS}) > >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} > >> ${VTK_LIBRARIES}) > >> > >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas > >> wrote: > >>> > >>> Bill, > >>> > >>> I can also confirm everything builds fine if VTK is not compiled with > Qt5 > >>> (which is part of my requirements...) > >>> > >>> > >>> > >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen < > bill.lorensen at gmail.com> > >>> wrote: > >>>> > >>>> Arnaud, > >>>> > >>>> I just tried an ITK build against an installed VTK and it built just > >>>> fine. > >>>> > >>>> Bill > >>>> > >>>> > >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen < > bill.lorensen at gmail.com> > >>>> wrote: > >>>> > I did not build against an installed VTK. > >>>> > > >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas < > arnaudgelas at gmail.com> > >>>> > wrote: > >>>> >> Bill, > >>>> >> > >>>> >> It seems builds fine as long as Qt5 is not involved in the process > >>>> >> (?) > >>>> >> > >>>> >> I just wonder if there is not something missing in vtk's cmake > >>>> >> installed > >>>> >> files to help finding Qt5::Widgets (?), or if we could only use > >>>> >> required > >>>> >> libraries from vtk which should not depend on Qt5 (?) > >>>> >> > >>>> >> Thanks, > >>>> >> Arnaud > >>>> >> > >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen > >>>> >> > >>>> >> wrote: > >>>> >>> > >>>> >>> Arnaud, > >>>> >>> > >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against > the > >>>> >>> nightly VTK. I'm not sure if that makes a difference. > >>>> >>> > >>>> >>> Bill > >>>> >>> > >>>> >>> > >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas > >>>> >>> > >>>> >>> wrote: > >>>> >>> > Hi all, > >>>> >>> > > >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk 6.1.0 > >>>> >>> > (built > >>>> >>> > with Qt5). Note I use cmake 2.8.12... > >>>> >>> > > >>>> >>> > I get link 1 error: > >>>> >>> > ld library not found for -lQt5::Widgets > >>>> >>> > > >>>> >>> > Any idea how to fix it? > >>>> >>> > > >>>> >>> > Thanks, > >>>> >>> > Arnaud > >>>> >>> > _____________________________________ > >>>> >>> > Powered by www.kitware.com > >>>> >>> > > >>>> >>> > Visit other Kitware open-source projects at > >>>> >>> > http://www.kitware.com/opensource/opensource.html > >>>> >>> > > >>>> >>> > Kitware offers ITK Training Courses, for more information visit: > >>>> >>> > http://www.kitware.com/products/protraining.php > >>>> >>> > > >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: > >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ > >>>> >>> > > >>>> >>> > Follow this link to subscribe/unsubscribe: > >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users > >>>> >>> > >>>> >>> > >>>> >>> > >>>> >>> -- > >>>> >>> Unpaid intern in BillsBasement at noware dot com > >>>> >> > >>>> >> > >>>> > > >>>> > > >>>> > > >>>> > -- > >>>> > Unpaid intern in BillsBasement at noware dot com > >>>> > >>>> > >>>> > >>>> -- > >>>> Unpaid intern in BillsBasement at noware dot com > >>> > >>> > >>> > >>> _____________________________________ > >>> Powered by www.kitware.com > >>> > >>> Visit other Kitware open-source projects at > >>> http://www.kitware.com/opensource/opensource.html > >>> > >>> Kitware offers ITK Training Courses, for more information visit: > >>> http://www.kitware.com/products/protraining.php > >>> > >>> Please keep messages on-topic and check the 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 > > > > > > -- > Unpaid intern in BillsBasement at noware dot 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 bill.lorensen at gmail.com Wed Oct 29 11:50:25 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 11:50:25 -0400 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Great. That means it is a VTK issue. I'm downloading qt5 on my fedora system. I'll see if I can reproduce there. On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas wrote: > Bill, > > Same link error with this example... > > > On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen > wrote: >> >> Arnaud, >> >> Can you try to build one of the ITK wiki examples against your >> installed VTK? This might help narrow down the problem. Whether it is >> a VTK of ITK issue. >> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow >> >> Bill >> >> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas >> wrote: >> > Mike, >> > >> > It is difficult to refer to one single CMakeLists.txt, since it is tied >> > up >> > to ITK's modularization. >> > >> > But here are the files to look at: >> > >> > >> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt >> > >> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake >> > >> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake >> > >> > Best >> > Arnaud >> > >> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander >> > wrote: >> >> >> >> Can you share your CMakeLists.txt file? Are you using something like >> >> the >> >> following commands: >> >> >> >> ADD_EXECUTABLE(myexe ${MYSRCS}) >> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} >> >> ${VTK_LIBRARIES}) >> >> >> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas >> >> wrote: >> >>> >> >>> Bill, >> >>> >> >>> I can also confirm everything builds fine if VTK is not compiled with >> >>> Qt5 >> >>> (which is part of my requirements...) >> >>> >> >>> >> >>> >> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen >> >>> >> >>> wrote: >> >>>> >> >>>> Arnaud, >> >>>> >> >>>> I just tried an ITK build against an installed VTK and it built just >> >>>> fine. >> >>>> >> >>>> Bill >> >>>> >> >>>> >> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >> >>>> >> >>>> wrote: >> >>>> > I did not build against an installed VTK. >> >>>> > >> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >> >>>> > >> >>>> > wrote: >> >>>> >> Bill, >> >>>> >> >> >>>> >> It seems builds fine as long as Qt5 is not involved in the process >> >>>> >> (?) >> >>>> >> >> >>>> >> I just wonder if there is not something missing in vtk's cmake >> >>>> >> installed >> >>>> >> files to help finding Qt5::Widgets (?), or if we could only use >> >>>> >> required >> >>>> >> libraries from vtk which should not depend on Qt5 (?) >> >>>> >> >> >>>> >> Thanks, >> >>>> >> Arnaud >> >>>> >> >> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >> >>>> >> >> >>>> >> wrote: >> >>>> >>> >> >>>> >>> Arnaud, >> >>>> >>> >> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against >> >>>> >>> the >> >>>> >>> nightly VTK. I'm not sure if that makes a difference. >> >>>> >>> >> >>>> >>> Bill >> >>>> >>> >> >>>> >>> >> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >> >>>> >>> >> >>>> >>> wrote: >> >>>> >>> > Hi all, >> >>>> >>> > >> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk >> >>>> >>> > 6.1.0 >> >>>> >>> > (built >> >>>> >>> > with Qt5). Note I use cmake 2.8.12... >> >>>> >>> > >> >>>> >>> > I get link 1 error: >> >>>> >>> > ld library not found for -lQt5::Widgets >> >>>> >>> > >> >>>> >>> > Any idea how to fix it? >> >>>> >>> > >> >>>> >>> > Thanks, >> >>>> >>> > Arnaud >> >>>> >>> > _____________________________________ >> >>>> >>> > Powered by www.kitware.com >> >>>> >>> > >> >>>> >>> > Visit other Kitware open-source projects at >> >>>> >>> > http://www.kitware.com/opensource/opensource.html >> >>>> >>> > >> >>>> >>> > Kitware offers ITK Training Courses, for more information >> >>>> >>> > visit: >> >>>> >>> > http://www.kitware.com/products/protraining.php >> >>>> >>> > >> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: >> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ >> >>>> >>> > >> >>>> >>> > Follow this link to subscribe/unsubscribe: >> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >> >>>> >>> >> >>>> >>> >> >>>> >>> >> >>>> >>> -- >> >>>> >>> Unpaid intern in BillsBasement at noware dot com >> >>>> >> >> >>>> >> >> >>>> > >> >>>> > >> >>>> > >> >>>> > -- >> >>>> > Unpaid intern in BillsBasement at noware dot com >> >>>> >> >>>> >> >>>> >> >>>> -- >> >>>> Unpaid intern in BillsBasement at noware dot com >> >>> >> >>> >> >>> >> >>> _____________________________________ >> >>> Powered by www.kitware.com >> >>> >> >>> Visit other Kitware open-source projects at >> >>> http://www.kitware.com/opensource/opensource.html >> >>> >> >>> Kitware offers ITK Training Courses, for more information visit: >> >>> http://www.kitware.com/products/protraining.php >> >>> >> >>> Please keep messages on-topic and check the 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 >> > >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com > > -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 bill.lorensen at gmail.com Wed Oct 29 12:13:34 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 12:13:34 -0400 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Built the arrow example against an installed ITK with Qt5 on fedora. Arnaud, Can you provide the link.txt file in the Arrow bin tree? Bill On Wed, Oct 29, 2014 at 11:50 AM, Bill Lorensen wrote: > Great. That means it is a VTK issue. I'm downloading qt5 on my fedora > system. I'll see if I can reproduce there. > > > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas wrote: >> Bill, >> >> Same link error with this example... >> >> >> On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen >> wrote: >>> >>> Arnaud, >>> >>> Can you try to build one of the ITK wiki examples against your >>> installed VTK? This might help narrow down the problem. Whether it is >>> a VTK of ITK issue. >>> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow >>> >>> Bill >>> >>> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas >>> wrote: >>> > Mike, >>> > >>> > It is difficult to refer to one single CMakeLists.txt, since it is tied >>> > up >>> > to ITK's modularization. >>> > >>> > But here are the files to look at: >>> > >>> > >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt >>> > >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake >>> > >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake >>> > >>> > Best >>> > Arnaud >>> > >>> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander >>> > wrote: >>> >> >>> >> Can you share your CMakeLists.txt file? Are you using something like >>> >> the >>> >> following commands: >>> >> >>> >> ADD_EXECUTABLE(myexe ${MYSRCS}) >>> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} >>> >> ${VTK_LIBRARIES}) >>> >> >>> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas >>> >> wrote: >>> >>> >>> >>> Bill, >>> >>> >>> >>> I can also confirm everything builds fine if VTK is not compiled with >>> >>> Qt5 >>> >>> (which is part of my requirements...) >>> >>> >>> >>> >>> >>> >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen >>> >>> >>> >>> wrote: >>> >>>> >>> >>>> Arnaud, >>> >>>> >>> >>>> I just tried an ITK build against an installed VTK and it built just >>> >>>> fine. >>> >>>> >>> >>>> Bill >>> >>>> >>> >>>> >>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >>> >>>> >>> >>>> wrote: >>> >>>> > I did not build against an installed VTK. >>> >>>> > >>> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >>> >>>> > >>> >>>> > wrote: >>> >>>> >> Bill, >>> >>>> >> >>> >>>> >> It seems builds fine as long as Qt5 is not involved in the process >>> >>>> >> (?) >>> >>>> >> >>> >>>> >> I just wonder if there is not something missing in vtk's cmake >>> >>>> >> installed >>> >>>> >> files to help finding Qt5::Widgets (?), or if we could only use >>> >>>> >> required >>> >>>> >> libraries from vtk which should not depend on Qt5 (?) >>> >>>> >> >>> >>>> >> Thanks, >>> >>>> >> Arnaud >>> >>>> >> >>> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >>> >>>> >> >>> >>>> >> wrote: >>> >>>> >>> >>> >>>> >>> Arnaud, >>> >>>> >>> >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against >>> >>>> >>> the >>> >>>> >>> nightly VTK. I'm not sure if that makes a difference. >>> >>>> >>> >>> >>>> >>> Bill >>> >>>> >>> >>> >>>> >>> >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >>> >>>> >>> >>> >>>> >>> wrote: >>> >>>> >>> > Hi all, >>> >>>> >>> > >>> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk >>> >>>> >>> > 6.1.0 >>> >>>> >>> > (built >>> >>>> >>> > with Qt5). Note I use cmake 2.8.12... >>> >>>> >>> > >>> >>>> >>> > I get link 1 error: >>> >>>> >>> > ld library not found for -lQt5::Widgets >>> >>>> >>> > >>> >>>> >>> > Any idea how to fix it? >>> >>>> >>> > >>> >>>> >>> > Thanks, >>> >>>> >>> > Arnaud >>> >>>> >>> > _____________________________________ >>> >>>> >>> > Powered by www.kitware.com >>> >>>> >>> > >>> >>>> >>> > Visit other Kitware open-source projects at >>> >>>> >>> > http://www.kitware.com/opensource/opensource.html >>> >>>> >>> > >>> >>>> >>> > Kitware offers ITK Training Courses, for more information >>> >>>> >>> > visit: >>> >>>> >>> > http://www.kitware.com/products/protraining.php >>> >>>> >>> > >>> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: >>> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ >>> >>>> >>> > >>> >>>> >>> > Follow this link to subscribe/unsubscribe: >>> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >>> >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> >>>> >>> -- >>> >>>> >>> Unpaid intern in BillsBasement at noware dot com >>> >>>> >> >>> >>>> >> >>> >>>> > >>> >>>> > >>> >>>> > >>> >>>> > -- >>> >>>> > Unpaid intern in BillsBasement at noware dot com >>> >>>> >>> >>>> >>> >>>> >>> >>>> -- >>> >>>> Unpaid intern in BillsBasement at noware dot com >>> >>> >>> >>> >>> >>> >>> >>> _____________________________________ >>> >>> Powered by www.kitware.com >>> >>> >>> >>> Visit other Kitware open-source projects at >>> >>> http://www.kitware.com/opensource/opensource.html >>> >>> >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> >>> http://www.kitware.com/products/protraining.php >>> >>> >>> >>> Please keep messages on-topic and check the 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 >>> > >>> >>> >>> >>> -- >>> Unpaid intern in BillsBasement at noware dot com >> >> > > > > -- > Unpaid intern in BillsBasement at noware dot com -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 arnaudgelas at gmail.com Wed Oct 29 12:18:00 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 17:18:00 +0100 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Thank you very much for looking into it! I am also digging on my side. It seems to me that the problems come from ${vtk-module}_EXPORT_CODE_INSTALL which is not exported into corresponding installed ${vtk-module} cmake file. Normally this cmake variable should contain "find_package( Qt5Widgets QUIET)" given the path corresponding dir. But it seems it is not present in the install tree for all module dependent on Qt5... On Wed, Oct 29, 2014 at 4:50 PM, Bill Lorensen wrote: > Great. That means it is a VTK issue. I'm downloading qt5 on my fedora > system. I'll see if I can reproduce there. > > > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas > wrote: > > Bill, > > > > Same link error with this example... > > > > > > On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen > > wrote: > >> > >> Arnaud, > >> > >> Can you try to build one of the ITK wiki examples against your > >> installed VTK? This might help narrow down the problem. Whether it is > >> a VTK of ITK issue. > >> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow > >> > >> Bill > >> > >> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas > >> wrote: > >> > Mike, > >> > > >> > It is difficult to refer to one single CMakeLists.txt, since it is > tied > >> > up > >> > to ITK's modularization. > >> > > >> > But here are the files to look at: > >> > > >> > > >> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt > >> > > >> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake > >> > > >> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake > >> > > >> > Best > >> > Arnaud > >> > > >> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander > >> > wrote: > >> >> > >> >> Can you share your CMakeLists.txt file? Are you using something like > >> >> the > >> >> following commands: > >> >> > >> >> ADD_EXECUTABLE(myexe ${MYSRCS}) > >> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} > >> >> ${VTK_LIBRARIES}) > >> >> > >> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas > > >> >> wrote: > >> >>> > >> >>> Bill, > >> >>> > >> >>> I can also confirm everything builds fine if VTK is not compiled > with > >> >>> Qt5 > >> >>> (which is part of my requirements...) > >> >>> > >> >>> > >> >>> > >> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen > >> >>> > >> >>> wrote: > >> >>>> > >> >>>> Arnaud, > >> >>>> > >> >>>> I just tried an ITK build against an installed VTK and it built > just > >> >>>> fine. > >> >>>> > >> >>>> Bill > >> >>>> > >> >>>> > >> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen > >> >>>> > >> >>>> wrote: > >> >>>> > I did not build against an installed VTK. > >> >>>> > > >> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas > >> >>>> > > >> >>>> > wrote: > >> >>>> >> Bill, > >> >>>> >> > >> >>>> >> It seems builds fine as long as Qt5 is not involved in the > process > >> >>>> >> (?) > >> >>>> >> > >> >>>> >> I just wonder if there is not something missing in vtk's cmake > >> >>>> >> installed > >> >>>> >> files to help finding Qt5::Widgets (?), or if we could only use > >> >>>> >> required > >> >>>> >> libraries from vtk which should not depend on Qt5 (?) > >> >>>> >> > >> >>>> >> Thanks, > >> >>>> >> Arnaud > >> >>>> >> > >> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen > >> >>>> >> > >> >>>> >> wrote: > >> >>>> >>> > >> >>>> >>> Arnaud, > >> >>>> >>> > >> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build against > >> >>>> >>> the > >> >>>> >>> nightly VTK. I'm not sure if that makes a difference. > >> >>>> >>> > >> >>>> >>> Bill > >> >>>> >>> > >> >>>> >>> > >> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas > >> >>>> >>> > >> >>>> >>> wrote: > >> >>>> >>> > Hi all, > >> >>>> >>> > > >> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk > >> >>>> >>> > 6.1.0 > >> >>>> >>> > (built > >> >>>> >>> > with Qt5). Note I use cmake 2.8.12... > >> >>>> >>> > > >> >>>> >>> > I get link 1 error: > >> >>>> >>> > ld library not found for -lQt5::Widgets > >> >>>> >>> > > >> >>>> >>> > Any idea how to fix it? > >> >>>> >>> > > >> >>>> >>> > Thanks, > >> >>>> >>> > Arnaud > >> >>>> >>> > _____________________________________ > >> >>>> >>> > Powered by www.kitware.com > >> >>>> >>> > > >> >>>> >>> > Visit other Kitware open-source projects at > >> >>>> >>> > http://www.kitware.com/opensource/opensource.html > >> >>>> >>> > > >> >>>> >>> > Kitware offers ITK Training Courses, for more information > >> >>>> >>> > visit: > >> >>>> >>> > http://www.kitware.com/products/protraining.php > >> >>>> >>> > > >> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: > >> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ > >> >>>> >>> > > >> >>>> >>> > Follow this link to subscribe/unsubscribe: > >> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users > >> >>>> >>> > >> >>>> >>> > >> >>>> >>> > >> >>>> >>> -- > >> >>>> >>> Unpaid intern in BillsBasement at noware dot com > >> >>>> >> > >> >>>> >> > >> >>>> > > >> >>>> > > >> >>>> > > >> >>>> > -- > >> >>>> > Unpaid intern in BillsBasement at noware dot com > >> >>>> > >> >>>> > >> >>>> > >> >>>> -- > >> >>>> Unpaid intern in BillsBasement at noware dot com > >> >>> > >> >>> > >> >>> > >> >>> _____________________________________ > >> >>> Powered by www.kitware.com > >> >>> > >> >>> Visit other Kitware open-source projects at > >> >>> http://www.kitware.com/opensource/opensource.html > >> >>> > >> >>> Kitware offers ITK Training Courses, for more information visit: > >> >>> http://www.kitware.com/products/protraining.php > >> >>> > >> >>> Please keep messages on-topic and check the 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 > >> > > >> > >> > >> > >> -- > >> Unpaid intern in BillsBasement at noware dot com > > > > > > > > -- > Unpaid intern in BillsBasement at noware dot 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 arnaudgelas at gmail.com Wed Oct 29 12:19:35 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 17:19:35 +0100 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Bill, Not sure what you mean by link.txt? Do you mean my CMakeCache.txt? --- Note that if I had find_package( Qt5Widgets QUIET ) into example's cmakelists, then it works fine... I think it is really related to the cmake var ${vtk-module}_EXPORT_CODE_INSTALL in vtkModuleMacros.cmake On Wed, Oct 29, 2014 at 5:13 PM, Bill Lorensen wrote: > Built the arrow example against an installed ITK with Qt5 on fedora. > > Arnaud, > > Can you provide the link.txt file in the Arrow bin tree? > > Bill > > On Wed, Oct 29, 2014 at 11:50 AM, Bill Lorensen > wrote: > > Great. That means it is a VTK issue. I'm downloading qt5 on my fedora > > system. I'll see if I can reproduce there. > > > > > > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas > wrote: > >> Bill, > >> > >> Same link error with this example... > >> > >> > >> On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen > > >> wrote: > >>> > >>> Arnaud, > >>> > >>> Can you try to build one of the ITK wiki examples against your > >>> installed VTK? This might help narrow down the problem. Whether it is > >>> a VTK of ITK issue. > >>> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow > >>> > >>> Bill > >>> > >>> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas > >>> wrote: > >>> > Mike, > >>> > > >>> > It is difficult to refer to one single CMakeLists.txt, since it is > tied > >>> > up > >>> > to ITK's modularization. > >>> > > >>> > But here are the files to look at: > >>> > > >>> > > >>> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt > >>> > > >>> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake > >>> > > >>> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake > >>> > > >>> > Best > >>> > Arnaud > >>> > > >>> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander > > >>> > wrote: > >>> >> > >>> >> Can you share your CMakeLists.txt file? Are you using something like > >>> >> the > >>> >> following commands: > >>> >> > >>> >> ADD_EXECUTABLE(myexe ${MYSRCS}) > >>> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} > >>> >> ${VTK_LIBRARIES}) > >>> >> > >>> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas < > arnaudgelas at gmail.com> > >>> >> wrote: > >>> >>> > >>> >>> Bill, > >>> >>> > >>> >>> I can also confirm everything builds fine if VTK is not compiled > with > >>> >>> Qt5 > >>> >>> (which is part of my requirements...) > >>> >>> > >>> >>> > >>> >>> > >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen > >>> >>> > >>> >>> wrote: > >>> >>>> > >>> >>>> Arnaud, > >>> >>>> > >>> >>>> I just tried an ITK build against an installed VTK and it built > just > >>> >>>> fine. > >>> >>>> > >>> >>>> Bill > >>> >>>> > >>> >>>> > >>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen > >>> >>>> > >>> >>>> wrote: > >>> >>>> > I did not build against an installed VTK. > >>> >>>> > > >>> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas > >>> >>>> > > >>> >>>> > wrote: > >>> >>>> >> Bill, > >>> >>>> >> > >>> >>>> >> It seems builds fine as long as Qt5 is not involved in the > process > >>> >>>> >> (?) > >>> >>>> >> > >>> >>>> >> I just wonder if there is not something missing in vtk's cmake > >>> >>>> >> installed > >>> >>>> >> files to help finding Qt5::Widgets (?), or if we could only use > >>> >>>> >> required > >>> >>>> >> libraries from vtk which should not depend on Qt5 (?) > >>> >>>> >> > >>> >>>> >> Thanks, > >>> >>>> >> Arnaud > >>> >>>> >> > >>> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen > >>> >>>> >> > >>> >>>> >> wrote: > >>> >>>> >>> > >>> >>>> >>> Arnaud, > >>> >>>> >>> > >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build > against > >>> >>>> >>> the > >>> >>>> >>> nightly VTK. I'm not sure if that makes a difference. > >>> >>>> >>> > >>> >>>> >>> Bill > >>> >>>> >>> > >>> >>>> >>> > >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas > >>> >>>> >>> > >>> >>>> >>> wrote: > >>> >>>> >>> > Hi all, > >>> >>>> >>> > > >>> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk > >>> >>>> >>> > 6.1.0 > >>> >>>> >>> > (built > >>> >>>> >>> > with Qt5). Note I use cmake 2.8.12... > >>> >>>> >>> > > >>> >>>> >>> > I get link 1 error: > >>> >>>> >>> > ld library not found for -lQt5::Widgets > >>> >>>> >>> > > >>> >>>> >>> > Any idea how to fix it? > >>> >>>> >>> > > >>> >>>> >>> > Thanks, > >>> >>>> >>> > Arnaud > >>> >>>> >>> > _____________________________________ > >>> >>>> >>> > Powered by www.kitware.com > >>> >>>> >>> > > >>> >>>> >>> > Visit other Kitware open-source projects at > >>> >>>> >>> > http://www.kitware.com/opensource/opensource.html > >>> >>>> >>> > > >>> >>>> >>> > Kitware offers ITK Training Courses, for more information > >>> >>>> >>> > visit: > >>> >>>> >>> > http://www.kitware.com/products/protraining.php > >>> >>>> >>> > > >>> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: > >>> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ > >>> >>>> >>> > > >>> >>>> >>> > Follow this link to subscribe/unsubscribe: > >>> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users > >>> >>>> >>> > >>> >>>> >>> > >>> >>>> >>> > >>> >>>> >>> -- > >>> >>>> >>> Unpaid intern in BillsBasement at noware dot com > >>> >>>> >> > >>> >>>> >> > >>> >>>> > > >>> >>>> > > >>> >>>> > > >>> >>>> > -- > >>> >>>> > Unpaid intern in BillsBasement at noware dot com > >>> >>>> > >>> >>>> > >>> >>>> > >>> >>>> -- > >>> >>>> Unpaid intern in BillsBasement at noware dot com > >>> >>> > >>> >>> > >>> >>> > >>> >>> _____________________________________ > >>> >>> Powered by www.kitware.com > >>> >>> > >>> >>> Visit other Kitware open-source projects at > >>> >>> http://www.kitware.com/opensource/opensource.html > >>> >>> > >>> >>> Kitware offers ITK Training Courses, for more information visit: > >>> >>> http://www.kitware.com/products/protraining.php > >>> >>> > >>> >>> Please keep messages on-topic and check the 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 > >>> > > >>> > >>> > >>> > >>> -- > >>> Unpaid intern in BillsBasement at noware dot com > >> > >> > > > > > > > > -- > > Unpaid intern in BillsBasement at noware dot com > > > > -- > Unpaid intern in BillsBasement at noware dot 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 arnaudgelas at gmail.com Wed Oct 29 12:23:01 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Wed, 29 Oct 2014 17:23:01 +0100 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: David, Thanks for the input! I will give a try to the master branch of VTK. I have been trying: * VTK 6.1 (which is the last stable release, corresponding to the latest hash on the release branch) * cmake 2.8.12 Not that if that has been fixed onto master, it would be great to backport the corresponding patches onto the release branch??? Thank you very much!! I'll report tomorrow morning if it works with the master branch. I gotta go now... Best, Arnaud On Wed, Oct 29, 2014 at 5:19 PM, David Cole wrote: > Are you all using the same VTK here? I think older VTK trees have problems > with Qt5, but recent 'master' should work fine... Also, same version of > CMake? Or are you using older CMake? > > I think this is largely fixed already if you use the latest 'master' > versions of CMake, VTK and Qt5. > > (But I could be wrong.... I've not used Qt5 personally yet. Just recalling > things I've read on the lists recently....) > > HTH, > D > > > On Wed, Oct 29, 2014 at 12:13 PM, Bill Lorensen > wrote: > >> Built the arrow example against an installed ITK with Qt5 on fedora. >> >> Arnaud, >> >> Can you provide the link.txt file in the Arrow bin tree? >> >> Bill >> >> On Wed, Oct 29, 2014 at 11:50 AM, Bill Lorensen >> wrote: >> > Great. That means it is a VTK issue. I'm downloading qt5 on my fedora >> > system. I'll see if I can reproduce there. >> > >> > >> > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas >> wrote: >> >> Bill, >> >> >> >> Same link error with this example... >> >> >> >> >> >> On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen < >> bill.lorensen at gmail.com> >> >> wrote: >> >>> >> >>> Arnaud, >> >>> >> >>> Can you try to build one of the ITK wiki examples against your >> >>> installed VTK? This might help narrow down the problem. Whether it is >> >>> a VTK of ITK issue. >> >>> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow >> >>> >> >>> Bill >> >>> >> >>> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas > > >> >>> wrote: >> >>> > Mike, >> >>> > >> >>> > It is difficult to refer to one single CMakeLists.txt, since it is >> tied >> >>> > up >> >>> > to ITK's modularization. >> >>> > >> >>> > But here are the files to look at: >> >>> > >> >>> > >> >>> > >> https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt >> >>> > >> >>> > >> https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake >> >>> > >> >>> > >> https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake >> >>> > >> >>> > Best >> >>> > Arnaud >> >>> > >> >>> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander < >> chinander at gmail.com> >> >>> > wrote: >> >>> >> >> >>> >> Can you share your CMakeLists.txt file? Are you using something >> like >> >>> >> the >> >>> >> following commands: >> >>> >> >> >>> >> ADD_EXECUTABLE(myexe ${MYSRCS}) >> >>> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} >> >>> >> ${VTK_LIBRARIES}) >> >>> >> >> >>> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas < >> arnaudgelas at gmail.com> >> >>> >> wrote: >> >>> >>> >> >>> >>> Bill, >> >>> >>> >> >>> >>> I can also confirm everything builds fine if VTK is not compiled >> with >> >>> >>> Qt5 >> >>> >>> (which is part of my requirements...) >> >>> >>> >> >>> >>> >> >>> >>> >> >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen >> >>> >>> >> >>> >>> wrote: >> >>> >>>> >> >>> >>>> Arnaud, >> >>> >>>> >> >>> >>>> I just tried an ITK build against an installed VTK and it built >> just >> >>> >>>> fine. >> >>> >>>> >> >>> >>>> Bill >> >>> >>>> >> >>> >>>> >> >>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >> >>> >>>> >> >>> >>>> wrote: >> >>> >>>> > I did not build against an installed VTK. >> >>> >>>> > >> >>> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >> >>> >>>> > >> >>> >>>> > wrote: >> >>> >>>> >> Bill, >> >>> >>>> >> >> >>> >>>> >> It seems builds fine as long as Qt5 is not involved in the >> process >> >>> >>>> >> (?) >> >>> >>>> >> >> >>> >>>> >> I just wonder if there is not something missing in vtk's cmake >> >>> >>>> >> installed >> >>> >>>> >> files to help finding Qt5::Widgets (?), or if we could only >> use >> >>> >>>> >> required >> >>> >>>> >> libraries from vtk which should not depend on Qt5 (?) >> >>> >>>> >> >> >>> >>>> >> Thanks, >> >>> >>>> >> Arnaud >> >>> >>>> >> >> >>> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >> >>> >>>> >> >> >>> >>>> >> wrote: >> >>> >>>> >>> >> >>> >>>> >>> Arnaud, >> >>> >>>> >>> >> >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build >> against >> >>> >>>> >>> the >> >>> >>>> >>> nightly VTK. I'm not sure if that makes a difference. >> >>> >>>> >>> >> >>> >>>> >>> Bill >> >>> >>>> >>> >> >>> >>>> >>> >> >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >> >>> >>>> >>> >> >>> >>>> >>> wrote: >> >>> >>>> >>> > Hi all, >> >>> >>>> >>> > >> >>> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk >> >>> >>>> >>> > 6.1.0 >> >>> >>>> >>> > (built >> >>> >>>> >>> > with Qt5). Note I use cmake 2.8.12... >> >>> >>>> >>> > >> >>> >>>> >>> > I get link 1 error: >> >>> >>>> >>> > ld library not found for -lQt5::Widgets >> >>> >>>> >>> > >> >>> >>>> >>> > Any idea how to fix it? >> >>> >>>> >>> > >> >>> >>>> >>> > Thanks, >> >>> >>>> >>> > Arnaud >> >>> >>>> >>> > _____________________________________ >> >>> >>>> >>> > Powered by www.kitware.com >> >>> >>>> >>> > >> >>> >>>> >>> > Visit other Kitware open-source projects at >> >>> >>>> >>> > http://www.kitware.com/opensource/opensource.html >> >>> >>>> >>> > >> >>> >>>> >>> > Kitware offers ITK Training Courses, for more information >> >>> >>>> >>> > visit: >> >>> >>>> >>> > http://www.kitware.com/products/protraining.php >> >>> >>>> >>> > >> >>> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: >> >>> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ >> >>> >>>> >>> > >> >>> >>>> >>> > Follow this link to subscribe/unsubscribe: >> >>> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >> >>> >>>> >>> >> >>> >>>> >>> >> >>> >>>> >>> >> >>> >>>> >>> -- >> >>> >>>> >>> Unpaid intern in BillsBasement at noware dot com >> >>> >>>> >> >> >>> >>>> >> >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > >> >>> >>>> > -- >> >>> >>>> > Unpaid intern in BillsBasement at noware dot com >> >>> >>>> >> >>> >>>> >> >>> >>>> >> >>> >>>> -- >> >>> >>>> Unpaid intern in BillsBasement at noware dot com >> >>> >>> >> >>> >>> >> >>> >>> >> >>> >>> _____________________________________ >> >>> >>> Powered by www.kitware.com >> >>> >>> >> >>> >>> Visit other Kitware open-source projects at >> >>> >>> http://www.kitware.com/opensource/opensource.html >> >>> >>> >> >>> >>> Kitware offers ITK Training Courses, for more information visit: >> >>> >>> http://www.kitware.com/products/protraining.php >> >>> >>> >> >>> >>> Please keep messages on-topic and check the 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 >> >>> > >> >>> >> >>> >> >>> >> >>> -- >> >>> Unpaid intern in BillsBasement at noware dot com >> >> >> >> >> > >> > >> > >> > -- >> > Unpaid intern in BillsBasement at noware dot com >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 abdul.sw84 at gmail.com Wed Oct 29 13:21:39 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 18:21:39 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: I downloaded the latest version of ITK again, and when configuring, I couldn't find the ItkVtkGlue option. I attached what I have in CMake. On Wed, Oct 29, 2014 at 4:33 PM, John Drescher wrote: > On Wed, Oct 29, 2014 at 11:31 AM, Abdul Abdul > wrote: > > ITK is already being built. The picture is for the example. > > Then go back and build ITK. While you configure ITK4 make sure you > enable the itkvtkglue module. You do not get this by default or in a > binary download. This also requires that you have or build VTK. if > this is on windows I highly recommend that you build all of these from > source. > > John > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 85410 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From abdul.sw84 at gmail.com Wed Oct 29 13:24:14 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Wed, 29 Oct 2014 18:24:14 +0100 Subject: [ITK] [ITK-users] Where can I get ItKVtkGlue In-Reply-To: References: Message-ID: Hi Matt, Hi Matt, Thanks for your kind reply. I downloaded the latest version of ITK, and when I tried to make a "configuration", I couldn't find the ItkVtkGlue option. I hereby attach what I get in CMake. Thanks. On Wed, Oct 29, 2014 at 4:29 PM, Matt McCormick wrote: > Hi Abdul, > > ITKVtkGlue used to be a separate project, but it is now integrated > into ITK as the module ITKVtkGlue. You can enable in your ITK CMake > configuration by setting > > Module_ITKVtkGlue > > to ON. > > It requires a build of VTK. > > Hope this helps, > Matt > > On Wed, Oct 29, 2014 at 10:10 AM, Abdul Abdul > wrote: > > Hello, > > > > I'm trying to run this example: > > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > > > But, get the following when I "configure" in CMake: > > > > CMake Error at CMakeLists.txt:11 (find_package): > > By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project > > has asked CMake to find a package configuration file provided by > > "ItkVtkGlue", but CMake did not find one. > > > > Could not find a package configuration file provided by "ItkVtkGlue" with > > any of the following names: > > > > ItkVtkGlueConfig.cmake > > itkvtkglue-config.cmake > > > > Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set > > "ItkVtkGlue_DIR" to a directory containing one of the above files. If > > "ItkVtkGlue" provides a separate development package or SDK, be sure it > has > > been installed. > > > > It seems I need "ItkVtkGlue"? Where can I download it? And, what should > I do > > to combine it with the program? > > > > Thanks. > > > > > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the 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 -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 85410 bytes Desc: not available URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From drescherjm at gmail.com Wed Oct 29 13:30:00 2014 From: drescherjm at gmail.com (John Drescher) Date: Wed, 29 Oct 2014 13:30:00 -0400 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: On Wed, Oct 29, 2014 at 1:21 PM, Abdul Abdul wrote: > I downloaded the latest version of ITK again, and when configuring, I > couldn't find the ItkVtkGlue option. I attached what I have in CMake. You need to click the Advanced checkbox. I would also click the Grouped box as well. John _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 bill.lorensen at gmail.com Wed Oct 29 13:34:45 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 13:34:45 -0400 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: I just verified that I see the failure with VTK 6.1, but not VTK master. On Wed, Oct 29, 2014 at 12:23 PM, Arnaud Gelas wrote: > David, > > Thanks for the input! I will give a try to the master branch of VTK. > > I have been trying: > * VTK 6.1 (which is the last stable release, corresponding to the latest > hash on the release branch) > * cmake 2.8.12 > > Not that if that has been fixed onto master, it would be great to backport > the corresponding patches onto the release branch??? > > Thank you very much!! > > I'll report tomorrow morning if it works with the master branch. I gotta go > now... > > Best, > Arnaud > > On Wed, Oct 29, 2014 at 5:19 PM, David Cole wrote: >> >> Are you all using the same VTK here? I think older VTK trees have problems >> with Qt5, but recent 'master' should work fine... Also, same version of >> CMake? Or are you using older CMake? >> >> I think this is largely fixed already if you use the latest 'master' >> versions of CMake, VTK and Qt5. >> >> (But I could be wrong.... I've not used Qt5 personally yet. Just recalling >> things I've read on the lists recently....) >> >> HTH, >> D >> >> >> On Wed, Oct 29, 2014 at 12:13 PM, Bill Lorensen >> wrote: >>> >>> Built the arrow example against an installed ITK with Qt5 on fedora. >>> >>> Arnaud, >>> >>> Can you provide the link.txt file in the Arrow bin tree? >>> >>> Bill >>> >>> On Wed, Oct 29, 2014 at 11:50 AM, Bill Lorensen >>> wrote: >>> > Great. That means it is a VTK issue. I'm downloading qt5 on my fedora >>> > system. I'll see if I can reproduce there. >>> > >>> > >>> > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas >>> > wrote: >>> >> Bill, >>> >> >>> >> Same link error with this example... >>> >> >>> >> >>> >> On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen >>> >> >>> >> wrote: >>> >>> >>> >>> Arnaud, >>> >>> >>> >>> Can you try to build one of the ITK wiki examples against your >>> >>> installed VTK? This might help narrow down the problem. Whether it is >>> >>> a VTK of ITK issue. >>> >>> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow >>> >>> >>> >>> Bill >>> >>> >>> >>> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas >>> >>> >>> >>> wrote: >>> >>> > Mike, >>> >>> > >>> >>> > It is difficult to refer to one single CMakeLists.txt, since it is >>> >>> > tied >>> >>> > up >>> >>> > to ITK's modularization. >>> >>> > >>> >>> > But here are the files to look at: >>> >>> > >>> >>> > >>> >>> > >>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt >>> >>> > >>> >>> > >>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake >>> >>> > >>> >>> > >>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake >>> >>> > >>> >>> > Best >>> >>> > Arnaud >>> >>> > >>> >>> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander >>> >>> > >>> >>> > wrote: >>> >>> >> >>> >>> >> Can you share your CMakeLists.txt file? Are you using something >>> >>> >> like >>> >>> >> the >>> >>> >> following commands: >>> >>> >> >>> >>> >> ADD_EXECUTABLE(myexe ${MYSRCS}) >>> >>> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} >>> >>> >> ${VTK_LIBRARIES}) >>> >>> >> >>> >>> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas >>> >>> >> >>> >>> >> wrote: >>> >>> >>> >>> >>> >>> Bill, >>> >>> >>> >>> >>> >>> I can also confirm everything builds fine if VTK is not compiled >>> >>> >>> with >>> >>> >>> Qt5 >>> >>> >>> (which is part of my requirements...) >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen >>> >>> >>> >>> >>> >>> wrote: >>> >>> >>>> >>> >>> >>>> Arnaud, >>> >>> >>>> >>> >>> >>>> I just tried an ITK build against an installed VTK and it built >>> >>> >>>> just >>> >>> >>>> fine. >>> >>> >>>> >>> >>> >>>> Bill >>> >>> >>>> >>> >>> >>>> >>> >>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >>> >>> >>>> >>> >>> >>>> wrote: >>> >>> >>>> > I did not build against an installed VTK. >>> >>> >>>> > >>> >>> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >>> >>> >>>> > >>> >>> >>>> > wrote: >>> >>> >>>> >> Bill, >>> >>> >>>> >> >>> >>> >>>> >> It seems builds fine as long as Qt5 is not involved in the >>> >>> >>>> >> process >>> >>> >>>> >> (?) >>> >>> >>>> >> >>> >>> >>>> >> I just wonder if there is not something missing in vtk's >>> >>> >>>> >> cmake >>> >>> >>>> >> installed >>> >>> >>>> >> files to help finding Qt5::Widgets (?), or if we could only >>> >>> >>>> >> use >>> >>> >>>> >> required >>> >>> >>>> >> libraries from vtk which should not depend on Qt5 (?) >>> >>> >>>> >> >>> >>> >>>> >> Thanks, >>> >>> >>>> >> Arnaud >>> >>> >>>> >> >>> >>> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >>> >>> >>>> >> >>> >>> >>>> >> wrote: >>> >>> >>>> >>> >>> >>> >>>> >>> Arnaud, >>> >>> >>>> >>> >>> >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build >>> >>> >>>> >>> against >>> >>> >>>> >>> the >>> >>> >>>> >>> nightly VTK. I'm not sure if that makes a difference. >>> >>> >>>> >>> >>> >>> >>>> >>> Bill >>> >>> >>>> >>> >>> >>> >>>> >>> >>> >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >>> >>> >>>> >>> >>> >>> >>>> >>> wrote: >>> >>> >>>> >>> > Hi all, >>> >>> >>>> >>> > >>> >>> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk >>> >>> >>>> >>> > 6.1.0 >>> >>> >>>> >>> > (built >>> >>> >>>> >>> > with Qt5). Note I use cmake 2.8.12... >>> >>> >>>> >>> > >>> >>> >>>> >>> > I get link 1 error: >>> >>> >>>> >>> > ld library not found for -lQt5::Widgets >>> >>> >>>> >>> > >>> >>> >>>> >>> > Any idea how to fix it? >>> >>> >>>> >>> > >>> >>> >>>> >>> > Thanks, >>> >>> >>>> >>> > Arnaud >>> >>> >>>> >>> > _____________________________________ >>> >>> >>>> >>> > Powered by www.kitware.com >>> >>> >>>> >>> > >>> >>> >>>> >>> > Visit other Kitware open-source projects at >>> >>> >>>> >>> > http://www.kitware.com/opensource/opensource.html >>> >>> >>>> >>> > >>> >>> >>>> >>> > Kitware offers ITK Training Courses, for more information >>> >>> >>>> >>> > visit: >>> >>> >>>> >>> > http://www.kitware.com/products/protraining.php >>> >>> >>>> >>> > >>> >>> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: >>> >>> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ >>> >>> >>>> >>> > >>> >>> >>>> >>> > Follow this link to subscribe/unsubscribe: >>> >>> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >>>> >>> >>> >>> >>>> >>> >>> >>> >>>> >>> >>> >>> >>>> >>> -- >>> >>> >>>> >>> Unpaid intern in BillsBasement at noware dot com >>> >>> >>>> >> >>> >>> >>>> >> >>> >>> >>>> > >>> >>> >>>> > >>> >>> >>>> > >>> >>> >>>> > -- >>> >>> >>>> > Unpaid intern in BillsBasement at noware dot com >>> >>> >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> >>>> -- >>> >>> >>>> Unpaid intern in BillsBasement at noware dot com >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _____________________________________ >>> >>> >>> Powered by www.kitware.com >>> >>> >>> >>> >>> >>> Visit other Kitware open-source projects at >>> >>> >>> http://www.kitware.com/opensource/opensource.html >>> >>> >>> >>> >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> >>> >>> http://www.kitware.com/products/protraining.php >>> >>> >>> >>> >>> >>> Please keep messages on-topic and check the 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 >>> >>> > >>> >>> >>> >>> >>> >>> >>> >>> -- >>> >>> Unpaid intern in BillsBasement at noware dot com >>> >> >>> >> >>> > >>> > >>> > >>> > -- >>> > Unpaid intern in BillsBasement at noware dot com >>> >>> >>> >>> -- >>> Unpaid intern in BillsBasement at noware dot com >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.php >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/insight-users >> >> > -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 bill.lorensen at gmail.com Wed Oct 29 16:16:56 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 16:16:56 -0400 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Arnaud, This is the gerrit patch that fixed the issue: http://review.source.kitware.com/#/c/15423/ If you cherry pick onto your VTK source and verify that it fixes your link error, I'll try to get it applied to VTK6.1. Bill On Wed, Oct 29, 2014 at 1:34 PM, Bill Lorensen wrote: > I just verified that I see the failure with VTK 6.1, but not VTK master. > > > On Wed, Oct 29, 2014 at 12:23 PM, Arnaud Gelas wrote: >> David, >> >> Thanks for the input! I will give a try to the master branch of VTK. >> >> I have been trying: >> * VTK 6.1 (which is the last stable release, corresponding to the latest >> hash on the release branch) >> * cmake 2.8.12 >> >> Not that if that has been fixed onto master, it would be great to backport >> the corresponding patches onto the release branch??? >> >> Thank you very much!! >> >> I'll report tomorrow morning if it works with the master branch. I gotta go >> now... >> >> Best, >> Arnaud >> >> On Wed, Oct 29, 2014 at 5:19 PM, David Cole wrote: >>> >>> Are you all using the same VTK here? I think older VTK trees have problems >>> with Qt5, but recent 'master' should work fine... Also, same version of >>> CMake? Or are you using older CMake? >>> >>> I think this is largely fixed already if you use the latest 'master' >>> versions of CMake, VTK and Qt5. >>> >>> (But I could be wrong.... I've not used Qt5 personally yet. Just recalling >>> things I've read on the lists recently....) >>> >>> HTH, >>> D >>> >>> >>> On Wed, Oct 29, 2014 at 12:13 PM, Bill Lorensen >>> wrote: >>>> >>>> Built the arrow example against an installed ITK with Qt5 on fedora. >>>> >>>> Arnaud, >>>> >>>> Can you provide the link.txt file in the Arrow bin tree? >>>> >>>> Bill >>>> >>>> On Wed, Oct 29, 2014 at 11:50 AM, Bill Lorensen >>>> wrote: >>>> > Great. That means it is a VTK issue. I'm downloading qt5 on my fedora >>>> > system. I'll see if I can reproduce there. >>>> > >>>> > >>>> > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas >>>> > wrote: >>>> >> Bill, >>>> >> >>>> >> Same link error with this example... >>>> >> >>>> >> >>>> >> On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen >>>> >> >>>> >> wrote: >>>> >>> >>>> >>> Arnaud, >>>> >>> >>>> >>> Can you try to build one of the ITK wiki examples against your >>>> >>> installed VTK? This might help narrow down the problem. Whether it is >>>> >>> a VTK of ITK issue. >>>> >>> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow >>>> >>> >>>> >>> Bill >>>> >>> >>>> >>> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas >>>> >>> >>>> >>> wrote: >>>> >>> > Mike, >>>> >>> > >>>> >>> > It is difficult to refer to one single CMakeLists.txt, since it is >>>> >>> > tied >>>> >>> > up >>>> >>> > to ITK's modularization. >>>> >>> > >>>> >>> > But here are the files to look at: >>>> >>> > >>>> >>> > >>>> >>> > >>>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt >>>> >>> > >>>> >>> > >>>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake >>>> >>> > >>>> >>> > >>>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake >>>> >>> > >>>> >>> > Best >>>> >>> > Arnaud >>>> >>> > >>>> >>> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander >>>> >>> > >>>> >>> > wrote: >>>> >>> >> >>>> >>> >> Can you share your CMakeLists.txt file? Are you using something >>>> >>> >> like >>>> >>> >> the >>>> >>> >> following commands: >>>> >>> >> >>>> >>> >> ADD_EXECUTABLE(myexe ${MYSRCS}) >>>> >>> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} >>>> >>> >> ${VTK_LIBRARIES}) >>>> >>> >> >>>> >>> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas >>>> >>> >> >>>> >>> >> wrote: >>>> >>> >>> >>>> >>> >>> Bill, >>>> >>> >>> >>>> >>> >>> I can also confirm everything builds fine if VTK is not compiled >>>> >>> >>> with >>>> >>> >>> Qt5 >>>> >>> >>> (which is part of my requirements...) >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen >>>> >>> >>> >>>> >>> >>> wrote: >>>> >>> >>>> >>>> >>> >>>> Arnaud, >>>> >>> >>>> >>>> >>> >>>> I just tried an ITK build against an installed VTK and it built >>>> >>> >>>> just >>>> >>> >>>> fine. >>>> >>> >>>> >>>> >>> >>>> Bill >>>> >>> >>>> >>>> >>> >>>> >>>> >>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >>>> >>> >>>> >>>> >>> >>>> wrote: >>>> >>> >>>> > I did not build against an installed VTK. >>>> >>> >>>> > >>>> >>> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >>>> >>> >>>> > >>>> >>> >>>> > wrote: >>>> >>> >>>> >> Bill, >>>> >>> >>>> >> >>>> >>> >>>> >> It seems builds fine as long as Qt5 is not involved in the >>>> >>> >>>> >> process >>>> >>> >>>> >> (?) >>>> >>> >>>> >> >>>> >>> >>>> >> I just wonder if there is not something missing in vtk's >>>> >>> >>>> >> cmake >>>> >>> >>>> >> installed >>>> >>> >>>> >> files to help finding Qt5::Widgets (?), or if we could only >>>> >>> >>>> >> use >>>> >>> >>>> >> required >>>> >>> >>>> >> libraries from vtk which should not depend on Qt5 (?) >>>> >>> >>>> >> >>>> >>> >>>> >> Thanks, >>>> >>> >>>> >> Arnaud >>>> >>> >>>> >> >>>> >>> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >>>> >>> >>>> >> >>>> >>> >>>> >> wrote: >>>> >>> >>>> >>> >>>> >>> >>>> >>> Arnaud, >>>> >>> >>>> >>> >>>> >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build >>>> >>> >>>> >>> against >>>> >>> >>>> >>> the >>>> >>> >>>> >>> nightly VTK. I'm not sure if that makes a difference. >>>> >>> >>>> >>> >>>> >>> >>>> >>> Bill >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >>>> >>> >>>> >>> >>>> >>> >>>> >>> wrote: >>>> >>> >>>> >>> > Hi all, >>>> >>> >>>> >>> > >>>> >>> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk >>>> >>> >>>> >>> > 6.1.0 >>>> >>> >>>> >>> > (built >>>> >>> >>>> >>> > with Qt5). Note I use cmake 2.8.12... >>>> >>> >>>> >>> > >>>> >>> >>>> >>> > I get link 1 error: >>>> >>> >>>> >>> > ld library not found for -lQt5::Widgets >>>> >>> >>>> >>> > >>>> >>> >>>> >>> > Any idea how to fix it? >>>> >>> >>>> >>> > >>>> >>> >>>> >>> > Thanks, >>>> >>> >>>> >>> > Arnaud >>>> >>> >>>> >>> > _____________________________________ >>>> >>> >>>> >>> > Powered by www.kitware.com >>>> >>> >>>> >>> > >>>> >>> >>>> >>> > Visit other Kitware open-source projects at >>>> >>> >>>> >>> > http://www.kitware.com/opensource/opensource.html >>>> >>> >>>> >>> > >>>> >>> >>>> >>> > Kitware offers ITK Training Courses, for more information >>>> >>> >>>> >>> > visit: >>>> >>> >>>> >>> > http://www.kitware.com/products/protraining.php >>>> >>> >>>> >>> > >>>> >>> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: >>>> >>> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ >>>> >>> >>>> >>> > >>>> >>> >>>> >>> > Follow this link to subscribe/unsubscribe: >>>> >>> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> >>>> >>> Unpaid intern in BillsBasement at noware dot com >>>> >>> >>>> >> >>>> >>> >>>> >> >>>> >>> >>>> > >>>> >>> >>>> > >>>> >>> >>>> > >>>> >>> >>>> > -- >>>> >>> >>>> > Unpaid intern in BillsBasement at noware dot com >>>> >>> >>>> >>>> >>> >>>> >>>> >>> >>>> >>>> >>> >>>> -- >>>> >>> >>>> Unpaid intern in BillsBasement at noware dot com >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> >>>> >>> >>> _____________________________________ >>>> >>> >>> Powered by www.kitware.com >>>> >>> >>> >>>> >>> >>> Visit other Kitware open-source projects at >>>> >>> >>> http://www.kitware.com/opensource/opensource.html >>>> >>> >>> >>>> >>> >>> Kitware offers ITK Training Courses, for more information visit: >>>> >>> >>> http://www.kitware.com/products/protraining.php >>>> >>> >>> >>>> >>> >>> Please keep messages on-topic and check the 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 >>>> >>> > >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> Unpaid intern in BillsBasement at noware dot com >>>> >> >>>> >> >>>> > >>>> > >>>> > >>>> > -- >>>> > Unpaid intern in BillsBasement at noware dot com >>>> >>>> >>>> >>>> -- >>>> Unpaid intern in BillsBasement at noware dot com >>>> _____________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at >>>> http://www.kitware.com/opensource/opensource.html >>>> >>>> Kitware offers ITK Training Courses, for more information visit: >>>> http://www.kitware.com/products/protraining.php >>>> >>>> Please keep messages on-topic and check the ITK FAQ at: >>>> http://www.itk.org/Wiki/ITK_FAQ >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> > > > > -- > Unpaid intern in BillsBasement at noware dot com -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 bill.lorensen at gmail.com Wed Oct 29 16:22:31 2014 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Wed, 29 Oct 2014 16:22:31 -0400 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Actually, I get a conflict when I cherry pick. A git expert will need to comment on how to update vtk6.1 On Wed, Oct 29, 2014 at 4:16 PM, Bill Lorensen wrote: > Arnaud, > > This is the gerrit patch that fixed the issue: > http://review.source.kitware.com/#/c/15423/ > > If you cherry pick onto your VTK source and verify that it fixes your > link error, I'll try to get it applied to VTK6.1. > > Bill > > > On Wed, Oct 29, 2014 at 1:34 PM, Bill Lorensen wrote: >> I just verified that I see the failure with VTK 6.1, but not VTK master. >> >> >> On Wed, Oct 29, 2014 at 12:23 PM, Arnaud Gelas wrote: >>> David, >>> >>> Thanks for the input! I will give a try to the master branch of VTK. >>> >>> I have been trying: >>> * VTK 6.1 (which is the last stable release, corresponding to the latest >>> hash on the release branch) >>> * cmake 2.8.12 >>> >>> Not that if that has been fixed onto master, it would be great to backport >>> the corresponding patches onto the release branch??? >>> >>> Thank you very much!! >>> >>> I'll report tomorrow morning if it works with the master branch. I gotta go >>> now... >>> >>> Best, >>> Arnaud >>> >>> On Wed, Oct 29, 2014 at 5:19 PM, David Cole wrote: >>>> >>>> Are you all using the same VTK here? I think older VTK trees have problems >>>> with Qt5, but recent 'master' should work fine... Also, same version of >>>> CMake? Or are you using older CMake? >>>> >>>> I think this is largely fixed already if you use the latest 'master' >>>> versions of CMake, VTK and Qt5. >>>> >>>> (But I could be wrong.... I've not used Qt5 personally yet. Just recalling >>>> things I've read on the lists recently....) >>>> >>>> HTH, >>>> D >>>> >>>> >>>> On Wed, Oct 29, 2014 at 12:13 PM, Bill Lorensen >>>> wrote: >>>>> >>>>> Built the arrow example against an installed ITK with Qt5 on fedora. >>>>> >>>>> Arnaud, >>>>> >>>>> Can you provide the link.txt file in the Arrow bin tree? >>>>> >>>>> Bill >>>>> >>>>> On Wed, Oct 29, 2014 at 11:50 AM, Bill Lorensen >>>>> wrote: >>>>> > Great. That means it is a VTK issue. I'm downloading qt5 on my fedora >>>>> > system. I'll see if I can reproduce there. >>>>> > >>>>> > >>>>> > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas >>>>> > wrote: >>>>> >> Bill, >>>>> >> >>>>> >> Same link error with this example... >>>>> >> >>>>> >> >>>>> >> On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen >>>>> >> >>>>> >> wrote: >>>>> >>> >>>>> >>> Arnaud, >>>>> >>> >>>>> >>> Can you try to build one of the ITK wiki examples against your >>>>> >>> installed VTK? This might help narrow down the problem. Whether it is >>>>> >>> a VTK of ITK issue. >>>>> >>> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow >>>>> >>> >>>>> >>> Bill >>>>> >>> >>>>> >>> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas >>>>> >>> >>>>> >>> wrote: >>>>> >>> > Mike, >>>>> >>> > >>>>> >>> > It is difficult to refer to one single CMakeLists.txt, since it is >>>>> >>> > tied >>>>> >>> > up >>>>> >>> > to ITK's modularization. >>>>> >>> > >>>>> >>> > But here are the files to look at: >>>>> >>> > >>>>> >>> > >>>>> >>> > >>>>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt >>>>> >>> > >>>>> >>> > >>>>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake >>>>> >>> > >>>>> >>> > >>>>> >>> > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake >>>>> >>> > >>>>> >>> > Best >>>>> >>> > Arnaud >>>>> >>> > >>>>> >>> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander >>>>> >>> > >>>>> >>> > wrote: >>>>> >>> >> >>>>> >>> >> Can you share your CMakeLists.txt file? Are you using something >>>>> >>> >> like >>>>> >>> >> the >>>>> >>> >> following commands: >>>>> >>> >> >>>>> >>> >> ADD_EXECUTABLE(myexe ${MYSRCS}) >>>>> >>> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} >>>>> >>> >> ${VTK_LIBRARIES}) >>>>> >>> >> >>>>> >>> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas >>>>> >>> >> >>>>> >>> >> wrote: >>>>> >>> >>> >>>>> >>> >>> Bill, >>>>> >>> >>> >>>>> >>> >>> I can also confirm everything builds fine if VTK is not compiled >>>>> >>> >>> with >>>>> >>> >>> Qt5 >>>>> >>> >>> (which is part of my requirements...) >>>>> >>> >>> >>>>> >>> >>> >>>>> >>> >>> >>>>> >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen >>>>> >>> >>> >>>>> >>> >>> wrote: >>>>> >>> >>>> >>>>> >>> >>>> Arnaud, >>>>> >>> >>>> >>>>> >>> >>>> I just tried an ITK build against an installed VTK and it built >>>>> >>> >>>> just >>>>> >>> >>>> fine. >>>>> >>> >>>> >>>>> >>> >>>> Bill >>>>> >>> >>>> >>>>> >>> >>>> >>>>> >>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen >>>>> >>> >>>> >>>>> >>> >>>> wrote: >>>>> >>> >>>> > I did not build against an installed VTK. >>>>> >>> >>>> > >>>>> >>> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas >>>>> >>> >>>> > >>>>> >>> >>>> > wrote: >>>>> >>> >>>> >> Bill, >>>>> >>> >>>> >> >>>>> >>> >>>> >> It seems builds fine as long as Qt5 is not involved in the >>>>> >>> >>>> >> process >>>>> >>> >>>> >> (?) >>>>> >>> >>>> >> >>>>> >>> >>>> >> I just wonder if there is not something missing in vtk's >>>>> >>> >>>> >> cmake >>>>> >>> >>>> >> installed >>>>> >>> >>>> >> files to help finding Qt5::Widgets (?), or if we could only >>>>> >>> >>>> >> use >>>>> >>> >>>> >> required >>>>> >>> >>>> >> libraries from vtk which should not depend on Qt5 (?) >>>>> >>> >>>> >> >>>>> >>> >>>> >> Thanks, >>>>> >>> >>>> >> Arnaud >>>>> >>> >>>> >> >>>>> >>> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen >>>>> >>> >>>> >> >>>>> >>> >>>> >> wrote: >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> Arnaud, >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build >>>>> >>> >>>> >>> against >>>>> >>> >>>> >>> the >>>>> >>> >>>> >>> nightly VTK. I'm not sure if that makes a difference. >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> Bill >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> wrote: >>>>> >>> >>>> >>> > Hi all, >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue with vtk >>>>> >>> >>>> >>> > 6.1.0 >>>>> >>> >>>> >>> > (built >>>>> >>> >>>> >>> > with Qt5). Note I use cmake 2.8.12... >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > I get link 1 error: >>>>> >>> >>>> >>> > ld library not found for -lQt5::Widgets >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > Any idea how to fix it? >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > Thanks, >>>>> >>> >>>> >>> > Arnaud >>>>> >>> >>>> >>> > _____________________________________ >>>>> >>> >>>> >>> > Powered by www.kitware.com >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > Visit other Kitware open-source projects at >>>>> >>> >>>> >>> > http://www.kitware.com/opensource/opensource.html >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > Kitware offers ITK Training Courses, for more information >>>>> >>> >>>> >>> > visit: >>>>> >>> >>>> >>> > http://www.kitware.com/products/protraining.php >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > Please keep messages on-topic and check the ITK FAQ at: >>>>> >>> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > Follow this link to subscribe/unsubscribe: >>>>> >>> >>>> >>> > http://public.kitware.com/mailman/listinfo/insight-users >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> >>>>> >>> >>>> >>> -- >>>>> >>> >>>> >>> Unpaid intern in BillsBasement at noware dot com >>>>> >>> >>>> >> >>>>> >>> >>>> >> >>>>> >>> >>>> > >>>>> >>> >>>> > >>>>> >>> >>>> > >>>>> >>> >>>> > -- >>>>> >>> >>>> > Unpaid intern in BillsBasement at noware dot com >>>>> >>> >>>> >>>>> >>> >>>> >>>>> >>> >>>> >>>>> >>> >>>> -- >>>>> >>> >>>> Unpaid intern in BillsBasement at noware dot com >>>>> >>> >>> >>>>> >>> >>> >>>>> >>> >>> >>>>> >>> >>> _____________________________________ >>>>> >>> >>> Powered by www.kitware.com >>>>> >>> >>> >>>>> >>> >>> Visit other Kitware open-source projects at >>>>> >>> >>> http://www.kitware.com/opensource/opensource.html >>>>> >>> >>> >>>>> >>> >>> Kitware offers ITK Training Courses, for more information visit: >>>>> >>> >>> http://www.kitware.com/products/protraining.php >>>>> >>> >>> >>>>> >>> >>> Please keep messages on-topic and check the 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 >>>>> >>> > >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> -- >>>>> >>> Unpaid intern in BillsBasement at noware dot com >>>>> >> >>>>> >> >>>>> > >>>>> > >>>>> > >>>>> > -- >>>>> > Unpaid intern in BillsBasement at noware dot com >>>>> >>>>> >>>>> >>>>> -- >>>>> Unpaid intern in BillsBasement at noware dot com >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.php >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> >>> >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com > > > > -- > Unpaid intern in BillsBasement at noware dot com -- Unpaid intern in BillsBasement at noware dot com _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 bschaffer at superstem.org Wed Oct 29 17:03:54 2014 From: bschaffer at superstem.org (Dr Bernhard Schaffer) Date: Wed, 29 Oct 2014 22:03:54 +0100 Subject: [ITK] templating typdef question Message-ID: <000601cff3bb$da4da7f0$8ee8f7d0$@superstem.org> Hi, This is my second email to this list. I'm still not so familiar with typedefs in coding, and I've the current problem: I have my own "image" objects which can be 2D or 3D and of different number type. If I assume they are only 2D and float I can do something like this: (The cyan lines show methods of 'my' object.) const unsigned int DIMENSION = 2; typedef itk::ImportImageFilter ImportFilterType; ImportFilterType::Pointer importFilter = ImportFilterType::New(); ImportFilterType::SizeType size; size[0] = MYIMAGE.GetXSIZE(); size[1] = MYIMAGE.GetYSIZE(); ImportFilterType::IndexType start; start.Fill( 0 ); ImportFilterType::RegionType region; region.SetIndex( start ); region.SetSize( size ); importFilter->SetRegion( region ); const itk::SpacePrecisionType origin[ DIMENSION ] = { 0.0, 0.0 }; importFilter->SetOrigin( origin ); const itk::SpacePrecisionType spacing[ DIMENSION ] = { 1.0, 1.0 }; importFilter->SetSpacing( spacing ); const bool importImageFilterWillOwnTheBuffer = false; float *localBuffer = MYIMAGE.GETPOINTER(); importFilter->SetImportPointer( localBuffer, size[0]*size[1], importImageFilterWillOwnTheBuffer ); typedef itk::Image< float,DIMENSION > InputImageType; typedef itk::Image< float,DIMENSION > OutputImageType; typedef itk::CurvatureFlowImageFilter< InputImageType, OutputImageType > FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput( importFilter->GetOutput() ); filter->SetTimeStep( timeStep ); filter->SetNumberOfIterations( iterations ); filter->Update(); typedef itk::ImageRegionIterator< OutputImageType > IteratorType; OutputImageType::Pointer filtered = filter->GetOutput(); [.] If my image is 3D I can do accordingly: (Yellow is the difference to above) const unsigned int DIMENSION = 3; typedef itk::ImportImageFilter ImportFilterType; ImportFilterType::Pointer importFilter = ImportFilterType::New(); ImportFilterType::SizeType size; size[0] = MYIMAGE.GetXSIZE(); size[1] = MYIMAGE.GetYSIZE(); size[2] = MYIMAGE.GetZSIZE(); ImportFilterType::IndexType start; start.Fill( 0 ); ImportFilterType::RegionType region; region.SetIndex( start ); region.SetSize( size ); importFilter->SetRegion( region ); const itk::SpacePrecisionType origin[ DIMENSION ] = { 0.0, 0.0, 0.0 }; importFilter->SetOrigin( origin ); const itk::SpacePrecisionType spacing[ DIMENSION ] = { 1.0, 1.0, 1.0 }; importFilter->SetSpacing( spacing ); const bool importImageFilterWillOwnTheBuffer = false; float *localBuffer = MYIMAGE.GETPOINTER(); importFilter->SetImportPointer( localBuffer, size[0]*size[1]*size[2], importImageFilterWillOwnTheBuffer ); typedef itk::Image< float,DIMENSION > InputImageType; typedef itk::Image< float,DIMENSION > OutputImageType; typedef itk::CurvatureFlowImageFilter< InputImageType, OutputImageType > FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput( importFilter->GetOutput() ); filter->SetTimeStep( timeStep ); filter->SetNumberOfIterations( iterations ); filter->Update(); typedef itk::ImageRegionIterator< OutputImageType > IteratorType; OutputImageType::Pointer filtered = filter->GetOutput(); [.] The problem I have is the following. I can query my object about its dimensionality, but I can't do the following: const unsigned int DIMENSION = MYIMAGE.GETDIMENSIONALITY(); because the typedefs are evaluated on compilation not on runtime. So my way around this is, to actually duplicate all the code and have both my examples in a switch-case: switch(MYIMAGE.GETDIMENSIONALITY()) { case(2): { . EXAMPLE 2D as above } break; case(3): { . EXAMPLE 3D as above } break; } Which is rather obvious code duplication. Is there a better way to do this? (there has to!) The problem branches out, if I also allow the type float to be specified by my object as in switch(MYIMAGE.GETDATATYPE()) { case(1):.float.; case(2):.double.; case(3):. . } I would very much appreciate a few lines of (pseudo-) code showing me how I can do this better. Thank you very much, Best regards, Bernhard -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Wed Oct 29 17:16:24 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 29 Oct 2014 17:16:24 -0400 Subject: [ITK] [ITK-users] Where can I get ItKVtkGlue In-Reply-To: References: Message-ID: Hi Abdul, You must click the "Advanced" checkbox to see this variable. HTH, Matt On Wed, Oct 29, 2014 at 1:24 PM, Abdul Abdul wrote: > Hi Matt, > > Hi Matt, > > Thanks for your kind reply. I downloaded the latest version of ITK, and when > I tried to make a "configuration", I couldn't find the ItkVtkGlue option. > > I hereby attach what I get in CMake. > > Thanks. > > On Wed, Oct 29, 2014 at 4:29 PM, Matt McCormick > wrote: >> >> Hi Abdul, >> >> ITKVtkGlue used to be a separate project, but it is now integrated >> into ITK as the module ITKVtkGlue. You can enable in your ITK CMake >> configuration by setting >> >> Module_ITKVtkGlue >> >> to ON. >> >> It requires a build of VTK. >> >> Hope this helps, >> Matt >> >> On Wed, Oct 29, 2014 at 10:10 AM, Abdul Abdul >> wrote: >> > Hello, >> > >> > I'm trying to run this example: >> > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >> > >> > But, get the following when I "configure" in CMake: >> > >> > CMake Error at CMakeLists.txt:11 (find_package): >> > By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this >> > project >> > has asked CMake to find a package configuration file provided by >> > "ItkVtkGlue", but CMake did not find one. >> > >> > Could not find a package configuration file provided by "ItkVtkGlue" >> > with >> > any of the following names: >> > >> > ItkVtkGlueConfig.cmake >> > itkvtkglue-config.cmake >> > >> > Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set >> > "ItkVtkGlue_DIR" to a directory containing one of the above files. If >> > "ItkVtkGlue" provides a separate development package or SDK, be sure it >> > has >> > been installed. >> > >> > It seems I need "ItkVtkGlue"? Where can I download it? And, what should >> > I do >> > to combine it with the program? >> > >> > Thanks. >> > >> > >> > >> > _____________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Kitware offers ITK Training Courses, for more information visit: >> > http://www.kitware.com/products/protraining.php >> > >> > Please keep messages on-topic and check the 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 Oct 29 17:28:19 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 29 Oct 2014 17:28:19 -0400 Subject: [ITK] templating typdef question In-Reply-To: <000601cff3bb$da4da7f0$8ee8f7d0$@superstem.org> References: <000601cff3bb$da4da7f0$8ee8f7d0$@superstem.org> Message-ID: Hi Bernhard, Welcome to ITK! The basic strategy is to put all the templated code in a template function or class. This prevents duplicated code (the root of almost all evil). Then, use a switch statement and call the appropriate templates. An example is here [1], which is long because it switches over both a number of pixel types and dimensions, but it demonstrates the idea. Inside the templated code, use for loops instead explicit assignment to set each dimension value. Also, use code like Image::SpacingType spacing; spacing.Fill( 1.0 ); instead of itk::SpacePrecisionType spacing[2]; spacing[0] = 1.0; spacing[1] = 1.0; Hope this helps, Matt [1] http://itk.org/ITKExamples/src/IO/ImageBase/ReadUnknownImageType/Documentation.html On Wed, Oct 29, 2014 at 5:03 PM, Dr Bernhard Schaffer wrote: > Hi, > > This is my second email to this list. I?m still not so familiar with > typedefs in coding, and I?ve the current problem: > > > > I have my own ?image? objects which can be 2D or 3D and of different number > type. If I assume they are only 2D and float I can do something like this: > > (The cyan lines show methods of ?my? object.) > > > > > > const unsigned int DIMENSION = 2; > > > > typedef itk::ImportImageFilter > ImportFilterType; > > ImportFilterType::Pointer importFilter = ImportFilterType::New(); > > > > ImportFilterType::SizeType size; > > size[0] = MYIMAGE.GetXSIZE(); > > size[1] = MYIMAGE.GetYSIZE(); > > > > ImportFilterType::IndexType start; > > start.Fill( 0 ); > > > > ImportFilterType::RegionType region; > > region.SetIndex( start ); > > region.SetSize( size ); > > importFilter->SetRegion( region ); > > > > const itk::SpacePrecisionType origin[ DIMENSION ] = { 0.0, 0.0 }; > > importFilter->SetOrigin( origin ); > > > > const itk::SpacePrecisionType spacing[ DIMENSION ] = { 1.0, 1.0 > }; > > importFilter->SetSpacing( spacing ); > > > > const bool importImageFilterWillOwnTheBuffer = false; > > > > float *localBuffer = MYIMAGE.GETPOINTER(); > > importFilter->SetImportPointer( localBuffer, size[0]*size[1], > importImageFilterWillOwnTheBuffer ); > > > > typedef itk::Image< float,DIMENSION > InputImageType; > > typedef itk::Image< float,DIMENSION > OutputImageType; > > > > typedef itk::CurvatureFlowImageFilter< InputImageType, > OutputImageType > FilterType; > > FilterType::Pointer filter = FilterType::New(); > > > > filter->SetInput( importFilter->GetOutput() ); > > filter->SetTimeStep( timeStep ); > > filter->SetNumberOfIterations( iterations ); > > filter->Update(); > > typedef itk::ImageRegionIterator< OutputImageType > > IteratorType; > > OutputImageType::Pointer filtered = filter->GetOutput(); > > [?] > > > > If my image is 3D I can do accordingly: (Yellow is the difference to above) > > > > const unsigned int DIMENSION = 3; > > > > typedef itk::ImportImageFilter > ImportFilterType; > > ImportFilterType::Pointer importFilter = ImportFilterType::New(); > > > > ImportFilterType::SizeType size; > > size[0] = MYIMAGE.GetXSIZE(); > > size[1] = MYIMAGE.GetYSIZE(); > > size[2] = MYIMAGE.GetZSIZE(); > > > > > > ImportFilterType::IndexType start; > > start.Fill( 0 ); > > > > ImportFilterType::RegionType region; > > region.SetIndex( start ); > > region.SetSize( size ); > > importFilter->SetRegion( region ); > > > > const itk::SpacePrecisionType origin[ DIMENSION ] = { 0.0, 0.0, 0.0 }; > > importFilter->SetOrigin( origin ); > > > > const itk::SpacePrecisionType spacing[ DIMENSION ] = { 1.0, 1.0, > 1.0 }; > > importFilter->SetSpacing( spacing ); > > > > const bool importImageFilterWillOwnTheBuffer = false; > > float *localBuffer = MYIMAGE.GETPOINTER(); > > importFilter->SetImportPointer( localBuffer, > size[0]*size[1]*size[2], importImageFilterWillOwnTheBuffer ); > > > > typedef itk::Image< float,DIMENSION > InputImageType; > > typedef itk::Image< float,DIMENSION > OutputImageType; > > > > typedef itk::CurvatureFlowImageFilter< InputImageType, > OutputImageType > FilterType; > > FilterType::Pointer filter = FilterType::New(); > > > > filter->SetInput( importFilter->GetOutput() ); > > filter->SetTimeStep( timeStep ); > > filter->SetNumberOfIterations( iterations ); > > filter->Update(); > > typedef itk::ImageRegionIterator< OutputImageType > > IteratorType; > > OutputImageType::Pointer filtered = filter->GetOutput(); > > [?] > > > > The problem I have is the following. I can query my object about its > dimensionality, but I can?t do the following: > > > > const unsigned int DIMENSION = MYIMAGE.GETDIMENSIONALITY(); > > > > because the typedefs are evaluated on compilation not on runtime. So my > way around this is, to actually duplicate all the code and have both my > examples in a switch-case: > > > > switch(MYIMAGE.GETDIMENSIONALITY()) > > { > > case(2): > > { > > ? EXAMPLE 2D as above > > } > > break; > > case(3): > > { > > ? EXAMPLE 3D as above > > } > > break; > > } > > > > Which is rather obvious code duplication. Is there a better way to do this? > (there has to!) The problem branches out, if I also allow the type float to > be specified by my object as in > > switch(MYIMAGE.GETDATATYPE()) > > { > > case(1):?float?; > > case(2):?double?; > > case(3):? > > ? > > } > > > > > > I would very much appreciate a few lines of (pseudo-) code showing me how I > can do this better. > > > > Thank you very much, > > Best regards, > > Bernhard > > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From llliu at umich.edu Wed Oct 29 21:14:07 2014 From: llliu at umich.edu (Lianli Liu) Date: Wed, 29 Oct 2014 21:14:07 -0400 Subject: [ITK] [ITK-users] difference between warpimagefilter and displacmentfield transform Message-ID: Hi all, Can anyone kindly explain the difference between the two? It seems to me that the both apply a displacment to each pixel in the image. Thanks! Best, Lianli -------------- 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 Oct 29 22:39:46 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Wed, 29 Oct 2014 22:39:46 -0400 Subject: [ITK] [ITK-users] difference between warpimagefilter and displacmentfield transform In-Reply-To: References: Message-ID: Hi Lianli, Yes, either one can be used. Thanks, Matt On Wed, Oct 29, 2014 at 9:14 PM, Lianli Liu wrote: > Hi all, > > Can anyone kindly explain the difference between the two? It seems to me > that the both apply a displacment to each pixel in the image. Thanks! > > Best, > Lianli > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 arnaudgelas at gmail.com Thu Oct 30 03:39:10 2014 From: arnaudgelas at gmail.com (Arnaud Gelas) Date: Thu, 30 Oct 2014 08:39:10 +0100 Subject: [ITK] [ITK-users] linking error ITK, VTK, Qt5 In-Reply-To: References: <53986491-181D-4214-9C9B-EF08DAB02F22@gmail.com> Message-ID: Hi Bill, Thanks for link to the corresponding patch on gerrit! >From the release branch, if you cherry-pick this commit, then it fixes the issue. $ git checkout release $ git cherry-pick 23fbbebc3cfc63ebf13b7321e9c198a5ad000e5c It would be really great if this patch could be applied onto the release branch!!! Thank you very much!!! Cheers, Arnaud On Wed, Oct 29, 2014 at 9:22 PM, Bill Lorensen wrote: > Actually, I get a conflict when I cherry pick. A git expert will need > to comment on how to update vtk6.1 > > > On Wed, Oct 29, 2014 at 4:16 PM, Bill Lorensen > wrote: > > Arnaud, > > > > This is the gerrit patch that fixed the issue: > > http://review.source.kitware.com/#/c/15423/ > > > > If you cherry pick onto your VTK source and verify that it fixes your > > link error, I'll try to get it applied to VTK6.1. > > > > Bill > > > > > > On Wed, Oct 29, 2014 at 1:34 PM, Bill Lorensen > wrote: > >> I just verified that I see the failure with VTK 6.1, but not VTK master. > >> > >> > >> On Wed, Oct 29, 2014 at 12:23 PM, Arnaud Gelas > wrote: > >>> David, > >>> > >>> Thanks for the input! I will give a try to the master branch of VTK. > >>> > >>> I have been trying: > >>> * VTK 6.1 (which is the last stable release, corresponding to the > latest > >>> hash on the release branch) > >>> * cmake 2.8.12 > >>> > >>> Not that if that has been fixed onto master, it would be great to > backport > >>> the corresponding patches onto the release branch??? > >>> > >>> Thank you very much!! > >>> > >>> I'll report tomorrow morning if it works with the master branch. I > gotta go > >>> now... > >>> > >>> Best, > >>> Arnaud > >>> > >>> On Wed, Oct 29, 2014 at 5:19 PM, David Cole wrote: > >>>> > >>>> Are you all using the same VTK here? I think older VTK trees have > problems > >>>> with Qt5, but recent 'master' should work fine... Also, same version > of > >>>> CMake? Or are you using older CMake? > >>>> > >>>> I think this is largely fixed already if you use the latest 'master' > >>>> versions of CMake, VTK and Qt5. > >>>> > >>>> (But I could be wrong.... I've not used Qt5 personally yet. Just > recalling > >>>> things I've read on the lists recently....) > >>>> > >>>> HTH, > >>>> D > >>>> > >>>> > >>>> On Wed, Oct 29, 2014 at 12:13 PM, Bill Lorensen < > bill.lorensen at gmail.com> > >>>> wrote: > >>>>> > >>>>> Built the arrow example against an installed ITK with Qt5 on fedora. > >>>>> > >>>>> Arnaud, > >>>>> > >>>>> Can you provide the link.txt file in the Arrow bin tree? > >>>>> > >>>>> Bill > >>>>> > >>>>> On Wed, Oct 29, 2014 at 11:50 AM, Bill Lorensen < > bill.lorensen at gmail.com> > >>>>> wrote: > >>>>> > Great. That means it is a VTK issue. I'm downloading qt5 on my > fedora > >>>>> > system. I'll see if I can reproduce there. > >>>>> > > >>>>> > > >>>>> > On Wed, Oct 29, 2014 at 11:46 AM, Arnaud Gelas < > arnaudgelas at gmail.com> > >>>>> > wrote: > >>>>> >> Bill, > >>>>> >> > >>>>> >> Same link error with this example... > >>>>> >> > >>>>> >> > >>>>> >> On Wed, Oct 29, 2014 at 4:31 PM, Bill Lorensen > >>>>> >> > >>>>> >> wrote: > >>>>> >>> > >>>>> >>> Arnaud, > >>>>> >>> > >>>>> >>> Can you try to build one of the ITK wiki examples against your > >>>>> >>> installed VTK? This might help narrow down the problem. Whether > it is > >>>>> >>> a VTK of ITK issue. > >>>>> >>> http://www.vtk.org/Wiki/VTK/Examples/Cxx/GeometricObjects/Arrow > >>>>> >>> > >>>>> >>> Bill > >>>>> >>> > >>>>> >>> On Wed, Oct 29, 2014 at 11:11 AM, Arnaud Gelas > >>>>> >>> > >>>>> >>> wrote: > >>>>> >>> > Mike, > >>>>> >>> > > >>>>> >>> > It is difficult to refer to one single CMakeLists.txt, since > it is > >>>>> >>> > tied > >>>>> >>> > up > >>>>> >>> > to ITK's modularization. > >>>>> >>> > > >>>>> >>> > But here are the files to look at: > >>>>> >>> > > >>>>> >>> > > >>>>> >>> > > >>>>> >>> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/CMakeLists.txt > >>>>> >>> > > >>>>> >>> > > >>>>> >>> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module-init.cmake > >>>>> >>> > > >>>>> >>> > > >>>>> >>> > > https://github.com/Kitware/ITK/blob/master/Modules/Bridge/VtkGlue/itk-module.cmake > >>>>> >>> > > >>>>> >>> > Best > >>>>> >>> > Arnaud > >>>>> >>> > > >>>>> >>> > On Wed, Oct 29, 2014 at 4:03 PM, Mike Chinander > >>>>> >>> > > >>>>> >>> > wrote: > >>>>> >>> >> > >>>>> >>> >> Can you share your CMakeLists.txt file? Are you using > something > >>>>> >>> >> like > >>>>> >>> >> the > >>>>> >>> >> following commands: > >>>>> >>> >> > >>>>> >>> >> ADD_EXECUTABLE(myexe ${MYSRCS}) > >>>>> >>> >> TARGET_LINK_LIBRARIES(myexe Qt5::Widgets ${ITK_LIBRARIES} > >>>>> >>> >> ${VTK_LIBRARIES}) > >>>>> >>> >> > >>>>> >>> >> On Wed, Oct 29, 2014 at 9:48 AM, Arnaud Gelas > >>>>> >>> >> > >>>>> >>> >> wrote: > >>>>> >>> >>> > >>>>> >>> >>> Bill, > >>>>> >>> >>> > >>>>> >>> >>> I can also confirm everything builds fine if VTK is not > compiled > >>>>> >>> >>> with > >>>>> >>> >>> Qt5 > >>>>> >>> >>> (which is part of my requirements...) > >>>>> >>> >>> > >>>>> >>> >>> > >>>>> >>> >>> > >>>>> >>> >>> On Wed, Oct 29, 2014 at 3:37 PM, Bill Lorensen > >>>>> >>> >>> > >>>>> >>> >>> wrote: > >>>>> >>> >>>> > >>>>> >>> >>>> Arnaud, > >>>>> >>> >>>> > >>>>> >>> >>>> I just tried an ITK build against an installed VTK and it > built > >>>>> >>> >>>> just > >>>>> >>> >>>> fine. > >>>>> >>> >>>> > >>>>> >>> >>>> Bill > >>>>> >>> >>>> > >>>>> >>> >>>> > >>>>> >>> >>>> On Wed, Oct 29, 2014 at 8:32 AM, Bill Lorensen > >>>>> >>> >>>> > >>>>> >>> >>>> wrote: > >>>>> >>> >>>> > I did not build against an installed VTK. > >>>>> >>> >>>> > > >>>>> >>> >>>> > On Wed, Oct 29, 2014 at 8:23 AM, Arnaud Gelas > >>>>> >>> >>>> > > >>>>> >>> >>>> > wrote: > >>>>> >>> >>>> >> Bill, > >>>>> >>> >>>> >> > >>>>> >>> >>>> >> It seems builds fine as long as Qt5 is not involved in > the > >>>>> >>> >>>> >> process > >>>>> >>> >>>> >> (?) > >>>>> >>> >>>> >> > >>>>> >>> >>>> >> I just wonder if there is not something missing in vtk's > >>>>> >>> >>>> >> cmake > >>>>> >>> >>>> >> installed > >>>>> >>> >>>> >> files to help finding Qt5::Widgets (?), or if we could > only > >>>>> >>> >>>> >> use > >>>>> >>> >>>> >> required > >>>>> >>> >>>> >> libraries from vtk which should not depend on Qt5 (?) > >>>>> >>> >>>> >> > >>>>> >>> >>>> >> Thanks, > >>>>> >>> >>>> >> Arnaud > >>>>> >>> >>>> >> > >>>>> >>> >>>> >> On Wed, Oct 29, 2014 at 1:15 PM, Bill Lorensen > >>>>> >>> >>>> >> > >>>>> >>> >>>> >> wrote: > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> Arnaud, > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> I build ITK with itkVtkGlue fine on my Mac, but I build > >>>>> >>> >>>> >>> against > >>>>> >>> >>>> >>> the > >>>>> >>> >>>> >>> nightly VTK. I'm not sure if that makes a difference. > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> Bill > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> On Wed, Oct 29, 2014 at 6:26 AM, Arnaud Gelas > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> wrote: > >>>>> >>> >>>> >>> > Hi all, > >>>>> >>> >>>> >>> > > >>>>> >>> >>>> >>> > I am trying to compile on mac (10.8.5) ITKVtkGlue > with vtk > >>>>> >>> >>>> >>> > 6.1.0 > >>>>> >>> >>>> >>> > (built > >>>>> >>> >>>> >>> > with Qt5). Note I use cmake 2.8.12... > >>>>> >>> >>>> >>> > > >>>>> >>> >>>> >>> > I get link 1 error: > >>>>> >>> >>>> >>> > ld library not found for -lQt5::Widgets > >>>>> >>> >>>> >>> > > >>>>> >>> >>>> >>> > Any idea how to fix it? > >>>>> >>> >>>> >>> > > >>>>> >>> >>>> >>> > Thanks, > >>>>> >>> >>>> >>> > Arnaud > >>>>> >>> >>>> >>> > _____________________________________ > >>>>> >>> >>>> >>> > Powered by www.kitware.com > >>>>> >>> >>>> >>> > > >>>>> >>> >>>> >>> > Visit other Kitware open-source projects at > >>>>> >>> >>>> >>> > http://www.kitware.com/opensource/opensource.html > >>>>> >>> >>>> >>> > > >>>>> >>> >>>> >>> > Kitware offers ITK Training Courses, for more > information > >>>>> >>> >>>> >>> > visit: > >>>>> >>> >>>> >>> > http://www.kitware.com/products/protraining.php > >>>>> >>> >>>> >>> > > >>>>> >>> >>>> >>> > Please keep messages on-topic and check the ITK FAQ > at: > >>>>> >>> >>>> >>> > http://www.itk.org/Wiki/ITK_FAQ > >>>>> >>> >>>> >>> > > >>>>> >>> >>>> >>> > Follow this link to subscribe/unsubscribe: > >>>>> >>> >>>> >>> > > http://public.kitware.com/mailman/listinfo/insight-users > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> > >>>>> >>> >>>> >>> -- > >>>>> >>> >>>> >>> Unpaid intern in BillsBasement at noware dot com > >>>>> >>> >>>> >> > >>>>> >>> >>>> >> > >>>>> >>> >>>> > > >>>>> >>> >>>> > > >>>>> >>> >>>> > > >>>>> >>> >>>> > -- > >>>>> >>> >>>> > Unpaid intern in BillsBasement at noware dot com > >>>>> >>> >>>> > >>>>> >>> >>>> > >>>>> >>> >>>> > >>>>> >>> >>>> -- > >>>>> >>> >>>> Unpaid intern in BillsBasement at noware dot com > >>>>> >>> >>> > >>>>> >>> >>> > >>>>> >>> >>> > >>>>> >>> >>> _____________________________________ > >>>>> >>> >>> Powered by www.kitware.com > >>>>> >>> >>> > >>>>> >>> >>> Visit other Kitware open-source projects at > >>>>> >>> >>> http://www.kitware.com/opensource/opensource.html > >>>>> >>> >>> > >>>>> >>> >>> Kitware offers ITK Training Courses, for more information > visit: > >>>>> >>> >>> http://www.kitware.com/products/protraining.php > >>>>> >>> >>> > >>>>> >>> >>> Please keep messages on-topic and check the 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 > >>>>> >>> > > >>>>> >>> > >>>>> >>> > >>>>> >>> > >>>>> >>> -- > >>>>> >>> Unpaid intern in BillsBasement at noware dot com > >>>>> >> > >>>>> >> > >>>>> > > >>>>> > > >>>>> > > >>>>> > -- > >>>>> > Unpaid intern in BillsBasement at noware dot com > >>>>> > >>>>> > >>>>> > >>>>> -- > >>>>> Unpaid intern in BillsBasement at noware dot com > >>>>> _____________________________________ > >>>>> Powered by www.kitware.com > >>>>> > >>>>> Visit other Kitware open-source projects at > >>>>> http://www.kitware.com/opensource/opensource.html > >>>>> > >>>>> Kitware offers ITK Training Courses, for more information visit: > >>>>> http://www.kitware.com/products/protraining.php > >>>>> > >>>>> Please keep messages on-topic and check the ITK FAQ at: > >>>>> http://www.itk.org/Wiki/ITK_FAQ > >>>>> > >>>>> Follow this link to subscribe/unsubscribe: > >>>>> http://public.kitware.com/mailman/listinfo/insight-users > >>>> > >>>> > >>> > >> > >> > >> > >> -- > >> Unpaid intern in BillsBasement at noware dot com > > > > > > > > -- > > Unpaid intern in BillsBasement at noware dot com > > > > -- > Unpaid intern in BillsBasement at noware dot 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 bschaffer at superstem.org Thu Oct 30 03:43:51 2014 From: bschaffer at superstem.org (Dr Bernhard Schaffer) Date: Thu, 30 Oct 2014 08:43:51 +0100 Subject: [ITK] templating typdef question In-Reply-To: References: <000601cff3bb$da4da7f0$8ee8f7d0$@superstem.org> Message-ID: <003f01cff415$40b55570$c2200050$@superstem.org> Thanks for the fast reply. I'll give it a try and let you know if I hit any obstacles. (The next time I can spend some time on ITK coding - it comes in waves as it's a spare time project). A general question for this community though: I've emailed to "community at itk.org" a couple of weeks ago and didn't receive any answer (I don't mind too much, I just don't want to do it incorrectly). This time I've written to community at itk.org and to insight-users at itk.org separately. Which one is the preferred group to ask these questions? Further, do you generally prefer getting coding questions on this mailing list, or on more general sites like Stackoverflow.com? And finally (after listening in to this group for 3 weeks or so): Thank you Matt for being so responsive! I know from experience that keeping responsive in such a site is a lot of effort. Very much appreciated. Regards, Bernhard -----Original Message----- From: Matt McCormick [mailto:matt.mccormick at kitware.com] Sent: 29 October 2014 22:28 To: Dr Bernhard Schaffer Cc: community at itk.org Subject: Re: [ITK] templating typdef question Hi Bernhard, Welcome to ITK! The basic strategy is to put all the templated code in a template function or class. This prevents duplicated code (the root of almost all evil). Then, use a switch statement and call the appropriate templates. An example is here [1], which is long because it switches over both a number of pixel types and dimensions, but it demonstrates the idea. Inside the templated code, use for loops instead explicit assignment to set each dimension value. Also, use code like Image::SpacingType spacing; spacing.Fill( 1.0 ); instead of itk::SpacePrecisionType spacing[2]; spacing[0] = 1.0; spacing[1] = 1.0; Hope this helps, Matt [1] http://itk.org/ITKExamples/src/IO/ImageBase/ReadUnknownImageType/Documentation.html On Wed, Oct 29, 2014 at 5:03 PM, Dr Bernhard Schaffer wrote: > Hi, > > This is my second email to this list. I?m still not so familiar with > typedefs in coding, and I?ve the current problem: > > > > I have my own ?image? objects which can be 2D or 3D and of different > number type. If I assume they are only 2D and float I can do something like this: > > (The cyan lines show methods of ?my? object.) > > > > > > const unsigned int DIMENSION = 2; > > > > typedef itk::ImportImageFilter > ImportFilterType; > > ImportFilterType::Pointer importFilter = ImportFilterType::New(); > > > > ImportFilterType::SizeType size; > > size[0] = MYIMAGE.GetXSIZE(); > > size[1] = MYIMAGE.GetYSIZE(); > > > > ImportFilterType::IndexType start; > > start.Fill( 0 ); > > > > ImportFilterType::RegionType region; > > region.SetIndex( start ); > > region.SetSize( size ); > > importFilter->SetRegion( region ); > > > > const itk::SpacePrecisionType origin[ DIMENSION ] = { 0.0, 0.0 }; > > importFilter->SetOrigin( origin ); > > > > const itk::SpacePrecisionType spacing[ DIMENSION ] = { > 1.0, 1.0 }; > > importFilter->SetSpacing( spacing ); > > > > const bool importImageFilterWillOwnTheBuffer = false; > > > > float *localBuffer = MYIMAGE.GETPOINTER(); > > importFilter->SetImportPointer( localBuffer, > size[0]*size[1], importImageFilterWillOwnTheBuffer ); > > > > typedef itk::Image< float,DIMENSION > InputImageType; > > typedef itk::Image< float,DIMENSION > OutputImageType; > > > > typedef itk::CurvatureFlowImageFilter< InputImageType, > OutputImageType > FilterType; > > FilterType::Pointer filter = FilterType::New(); > > > > filter->SetInput( importFilter->GetOutput() ); > > filter->SetTimeStep( timeStep ); > > filter->SetNumberOfIterations( iterations ); > > filter->Update(); > > typedef itk::ImageRegionIterator< OutputImageType > > IteratorType; > > OutputImageType::Pointer filtered = filter->GetOutput(); > > [?] > > > > If my image is 3D I can do accordingly: (Yellow is the difference to > above) > > > > const unsigned int DIMENSION = 3; > > > > typedef itk::ImportImageFilter > ImportFilterType; > > ImportFilterType::Pointer importFilter = ImportFilterType::New(); > > > > ImportFilterType::SizeType size; > > size[0] = MYIMAGE.GetXSIZE(); > > size[1] = MYIMAGE.GetYSIZE(); > > size[2] = MYIMAGE.GetZSIZE(); > > > > > > ImportFilterType::IndexType start; > > start.Fill( 0 ); > > > > ImportFilterType::RegionType region; > > region.SetIndex( start ); > > region.SetSize( size ); > > importFilter->SetRegion( region ); > > > > const itk::SpacePrecisionType origin[ DIMENSION ] = { 0.0, 0.0, 0.0 }; > > importFilter->SetOrigin( origin ); > > > > const itk::SpacePrecisionType spacing[ DIMENSION ] = { > 1.0, 1.0, > 1.0 }; > > importFilter->SetSpacing( spacing ); > > > > const bool importImageFilterWillOwnTheBuffer = false; > > float *localBuffer = MYIMAGE.GETPOINTER(); > > importFilter->SetImportPointer( localBuffer, > size[0]*size[1]*size[2], importImageFilterWillOwnTheBuffer ); > > > > typedef itk::Image< float,DIMENSION > InputImageType; > > typedef itk::Image< float,DIMENSION > OutputImageType; > > > > typedef itk::CurvatureFlowImageFilter< InputImageType, > OutputImageType > FilterType; > > FilterType::Pointer filter = FilterType::New(); > > > > filter->SetInput( importFilter->GetOutput() ); > > filter->SetTimeStep( timeStep ); > > filter->SetNumberOfIterations( iterations ); > > filter->Update(); > > typedef itk::ImageRegionIterator< OutputImageType > > IteratorType; > > OutputImageType::Pointer filtered = filter->GetOutput(); > > [?] > > > > The problem I have is the following. I can query my object about its > dimensionality, but I can?t do the following: > > > > const unsigned int DIMENSION = MYIMAGE.GETDIMENSIONALITY(); > > > > because the typedefs are evaluated on compilation not on runtime. So my > way around this is, to actually duplicate all the code and have both > my examples in a switch-case: > > > > switch(MYIMAGE.GETDIMENSIONALITY()) > > { > > case(2): > > { > > ? EXAMPLE 2D as above > > } > > break; > > case(3): > > { > > ? EXAMPLE 3D as above > > } > > break; > > } > > > > Which is rather obvious code duplication. Is there a better way to do this? > (there has to!) The problem branches out, if I also allow the type > float to be specified by my object as in > > switch(MYIMAGE.GETDATATYPE()) > > { > > case(1):?float?; > > case(2):?double?; > > case(3):? > > ? > > } > > > > > > I would very much appreciate a few lines of (pseudo-) code showing me > how I can do this better. > > > > Thank you very much, > > Best regards, > > Bernhard > > > > > _______________________________________________ > Community mailing list > Community at itk.org > http://public.kitware.com/mailman/listinfo/community > From rabysam28 at gmail.com Thu Oct 30 11:37:23 2014 From: rabysam28 at gmail.com (Sam Raby) Date: Thu, 30 Oct 2014 10:37:23 -0500 Subject: [ITK] Error in compilation of ITK In-Reply-To: References: <0190D7D4-481B-48CB-8996-764A0BC141CF@gmail.com> <172DD98E-0E86-4AFF-BA76-C3DAE7FDF64E@gmail.com> Message-ID: I thought to close this thread that I had started, using the following link: http://itk-users.7.n7.nabble.com/ITK-users-linking-error-ITK-VTK-Qt5-tt34780.html#none Thanks for fixing this. -S On Sat, Mar 29, 2014 at 4:28 PM, Matt McCormick wrote: > Hi Sam, > > There may be more answers for this question on the CMake list. > > HTH, > Matt > > On Fri, Mar 28, 2014 at 6:06 PM, Sam Raby wrote: > > Thanks. > > fyi, I just complied ITK-4.5.0, and I got the same compilation error. > > > > -S > > > > > > On Fri, Mar 28, 2014 at 5:00 PM, Michka Popoff > > wrote: > >> > >> Yes, seems to be the same error. > >> > >> In fact, Qt5 is only supported by VTK since 6.1. > >> The ITK community has not set up tests for this and I think not a lot of > >> people tried VTK+ITK+Qt5, so there is no guarantee it will work out of > the > >> box. > >> I think the errors comes because ITK includes VTK, and VTK includes Qt5. > >> But I don't exactly know were the error is coming from. > >> > >> Maybe somebody else on the list has an an idea ? This goes beyond my > >> capabilities. But we need a fix for this :) > >> > >> On 28 mars 2014, at 22:52, Sam Raby wrote: > >> > >> Michka, I came acroos the following link. I have not tried it though, > as I > >> was not sure about it: > >> > >> http://markmail.org/message/fjyiphxyv5wnoplp > >> > >> > >> > >> > >> On Fri, Mar 28, 2014 at 4:42 PM, Sam Raby wrote: > >>> > >>> I have checked out the latest version of ITK and VTK. > >>> > >>> My VTK is Qt-enabled. The QT version is 5.0-2. Is there any variable > that > >>> I should set in ITK ccmake, so that it can see my Qt? I did not know > ITK is > >>> sort of linked with Qt during its compilation? > >>> thanks, > >>> > >>> > >>> On Fri, Mar 28, 2014 at 4:32 PM, Michka Popoff > > >>> wrote: > >>>> > >>>> Hi > >>>> > >>>> which version of ITK and VTK are you trying to compile ? > >>>> > >>>> The error message is telling you that it can not find Qt5. Have you > Qt5 > >>>> installed ? > >>>> > >>>> Michka > >>>> > >>>> Le 28 mars 2014 ? 22:28, Sam Raby a ?crit : > >>>> > >>>> Hello, > >>>> > >>>> I am compliining ITK wiith ItkVtkGlue ON. ITK and VTK both are the > >>>> latest versuib that I got from github. > >>>> I am getting the following error and was wondering whether you know > why > >>>> the complication encounters the following error, as I could not > figure this > >>>> out? > >>>> > >>>> [ 69%] Building CXX object > >>>> > Modules/Core/Common/test/CMakeFiles/ITKCommon1TestDriver.dir/itkImageRandomIteratorTest.cxx.o > >>>> [ 70%] Building CXX object > >>>> > Modules/Core/Common/test/CMakeFiles/ITKCommon2TestDriver.dir/itkTreeContainerTest.cxx.o > >>>> [ 70%] Building CXX object > >>>> > Modules/Core/Common/test/CMakeFiles/ITKCommon2TestDriver.dir/itkVariableLengthVectorTest.cxx.o > >>>> [ 70%] Building CXX object > >>>> > Modules/Core/Common/test/CMakeFiles/ITKCommon2TestDriver.dir/itkSpatialFunctionTest.cxx.o > >>>> /usr/bin/ld: cannot find -lQt5::Widgets > >>>> collect2: ld returned 1 exit status > >>>> make[2]: *** [bin/ITKVtkGlueTestDriver] Error 1 > >>>> make[1]: *** > >>>> [Modules/Bridge/VtkGlue/test/CMakeFiles/ITKVtkGlueTestDriver.dir/all] > Error > >>>> 2 > >>>> make[1]: *** Waiting for unfinished jobs.... > >>>> > >>>> > >>>> Thanks > >>>> > >>>> _______________________________________________ > >>>> Community mailing list > >>>> Community at itk.org > >>>> http://public.kitware.com/cgi-bin/mailman/listinfo/community > >>>> > >>>> > >>> > >> > >> > > > > > > _______________________________________________ > > Community mailing list > > Community at itk.org > > http://public.kitware.com/cgi-bin/mailman/listinfo/community > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mccormick at kitware.com Thu Oct 30 15:55:46 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 30 Oct 2014 15:55:46 -0400 Subject: [ITK] Error in compilation of ITK In-Reply-To: References: <0190D7D4-481B-48CB-8996-764A0BC141CF@gmail.com> <172DD98E-0E86-4AFF-BA76-C3DAE7FDF64E@gmail.com> Message-ID: Thanks for following up on the thread, Sam. On Thu, Oct 30, 2014 at 11:37 AM, Sam Raby wrote: > I thought to close this thread that I had started, using the following link: > > http://itk-users.7.n7.nabble.com/ITK-users-linking-error-ITK-VTK-Qt5-tt34780.html#none > > Thanks for fixing this. > > -S > > > > On Sat, Mar 29, 2014 at 4:28 PM, Matt McCormick > wrote: >> >> Hi Sam, >> >> There may be more answers for this question on the CMake list. >> >> HTH, >> Matt >> >> On Fri, Mar 28, 2014 at 6:06 PM, Sam Raby wrote: >> > Thanks. >> > fyi, I just complied ITK-4.5.0, and I got the same compilation error. >> > >> > -S >> > >> > >> > On Fri, Mar 28, 2014 at 5:00 PM, Michka Popoff >> > wrote: >> >> >> >> Yes, seems to be the same error. >> >> >> >> In fact, Qt5 is only supported by VTK since 6.1. >> >> The ITK community has not set up tests for this and I think not a lot >> >> of >> >> people tried VTK+ITK+Qt5, so there is no guarantee it will work out of >> >> the >> >> box. >> >> I think the errors comes because ITK includes VTK, and VTK includes >> >> Qt5. >> >> But I don't exactly know were the error is coming from. >> >> >> >> Maybe somebody else on the list has an an idea ? This goes beyond my >> >> capabilities. But we need a fix for this :) >> >> >> >> On 28 mars 2014, at 22:52, Sam Raby wrote: >> >> >> >> Michka, I came acroos the following link. I have not tried it though, >> >> as I >> >> was not sure about it: >> >> >> >> http://markmail.org/message/fjyiphxyv5wnoplp >> >> >> >> >> >> >> >> >> >> On Fri, Mar 28, 2014 at 4:42 PM, Sam Raby wrote: >> >>> >> >>> I have checked out the latest version of ITK and VTK. >> >>> >> >>> My VTK is Qt-enabled. The QT version is 5.0-2. Is there any variable >> >>> that >> >>> I should set in ITK ccmake, so that it can see my Qt? I did not know >> >>> ITK is >> >>> sort of linked with Qt during its compilation? >> >>> thanks, >> >>> >> >>> >> >>> On Fri, Mar 28, 2014 at 4:32 PM, Michka Popoff >> >>> >> >>> wrote: >> >>>> >> >>>> Hi >> >>>> >> >>>> which version of ITK and VTK are you trying to compile ? >> >>>> >> >>>> The error message is telling you that it can not find Qt5. Have you >> >>>> Qt5 >> >>>> installed ? >> >>>> >> >>>> Michka >> >>>> >> >>>> Le 28 mars 2014 ? 22:28, Sam Raby a ?crit : >> >>>> >> >>>> Hello, >> >>>> >> >>>> I am compliining ITK wiith ItkVtkGlue ON. ITK and VTK both are the >> >>>> latest versuib that I got from github. >> >>>> I am getting the following error and was wondering whether you know >> >>>> why >> >>>> the complication encounters the following error, as I could not >> >>>> figure this >> >>>> out? >> >>>> >> >>>> [ 69%] Building CXX object >> >>>> >> >>>> Modules/Core/Common/test/CMakeFiles/ITKCommon1TestDriver.dir/itkImageRandomIteratorTest.cxx.o >> >>>> [ 70%] Building CXX object >> >>>> >> >>>> Modules/Core/Common/test/CMakeFiles/ITKCommon2TestDriver.dir/itkTreeContainerTest.cxx.o >> >>>> [ 70%] Building CXX object >> >>>> >> >>>> Modules/Core/Common/test/CMakeFiles/ITKCommon2TestDriver.dir/itkVariableLengthVectorTest.cxx.o >> >>>> [ 70%] Building CXX object >> >>>> >> >>>> Modules/Core/Common/test/CMakeFiles/ITKCommon2TestDriver.dir/itkSpatialFunctionTest.cxx.o >> >>>> /usr/bin/ld: cannot find -lQt5::Widgets >> >>>> collect2: ld returned 1 exit status >> >>>> make[2]: *** [bin/ITKVtkGlueTestDriver] Error 1 >> >>>> make[1]: *** >> >>>> [Modules/Bridge/VtkGlue/test/CMakeFiles/ITKVtkGlueTestDriver.dir/all] >> >>>> Error >> >>>> 2 >> >>>> make[1]: *** Waiting for unfinished jobs.... >> >>>> >> >>>> >> >>>> Thanks >> >>>> >> >>>> _______________________________________________ >> >>>> Community mailing list >> >>>> Community at itk.org >> >>>> http://public.kitware.com/cgi-bin/mailman/listinfo/community >> >>>> >> >>>> >> >>> >> >> >> >> >> > >> > >> > _______________________________________________ >> > Community mailing list >> > Community at itk.org >> > http://public.kitware.com/cgi-bin/mailman/listinfo/community >> > > > From matt.mccormick at kitware.com Thu Oct 30 16:00:55 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 30 Oct 2014 16:00:55 -0400 Subject: [ITK] Segfault while running Examples/IO/ImageFileReader In-Reply-To: <5451DBBD.7020806@gmail.com> References: <5450FDFA.1000500@gmail.com> <5451DBBD.7020806@gmail.com> Message-ID: Hi Jan, The CMake configuration of HDF5 could use some improvements. Until that happens, the best approach is to create a separate version of HDF5 to distribute, then build VTK and ITK against this version. Otherwise, the internal HDF5 to ITK and VTK can conflict. HTH, Matt On Thu, Oct 30, 2014 at 2:33 AM, Jan Dorazil wrote: > Thank you, > it did help, so it is unavoidable to use system hdf5? Is the vtk version of > hdf5 somehow incompatible with my os? I would like to create package of itk > for my distribution and assign only dependencies that really are > dependencies - hdf5 isnt distributed with my os installation. > > > On 10/29/2014 04:31 PM, Matt McCormick wrote: >> >> Hi Jan, >> >> Does it help to configure both your ITK and your VTK to use the system >> HDF5? >> >> Thanks, >> Matt >> >> On Wed, Oct 29, 2014 at 10:47 AM, Jan Dorazil wrote: >>> >>> Hello, >>> after successfully building the example ImageFileReader I have >>> encountered >>> segmentation fault error while running the built binary. >>> back trace: >>> #0 0xb0c88175 in __GI__IO_default_xsputn () from /lib/libc.so.6 >>> #1 0xb0c58e73 in vfprintf () from /lib/libc.so.6 >>> #2 0xb0c82dc1 in vasprintf () from /lib/libc.so.6 >>> #3 0xb6614704 in vtk__H5E_printf_stack () from >>> /usr/lib/libvtkhdf5-6.1.so.1 >>> #4 0xb67c7711 in vtk__H5I_inc_ref () from /usr/lib/libvtkhdf5-6.1.so.1 >>> #5 0xb66145ac in vtk__H5E_push_stack () from >>> /usr/lib/libvtkhdf5-6.1.so.1 >>> #6 0xb661474c in vtk__H5E_printf_stack () from >>> /usr/lib/libvtkhdf5-6.1.so.1 >>> #7 0xb67c7711 in vtk__H5I_inc_ref () from /usr/lib/libvtkhdf5-6.1.so.1 >>> #8 0xb66145ac in vtk__H5E_push_stack () from >>> /usr/lib/libvtkhdf5-6.1.so.1 >>> #9 0xb661474c in vtk__H5E_printf_stack () from >>> /usr/lib/libvtkhdf5-6.1.so.1 >>> #10 0xb67c7711 in vtk__H5I_inc_ref () from /usr/lib/libvtkhdf5-6.1.so.1 >>> #11 0xb66145ac in vtk__H5E_push_stack () from >>> /usr/lib/libvtkhdf5-6.1.so.1 >>> #12 0xb661474c in vtk__H5E_printf_stack () from >>> /usr/lib/libvtkhdf5-6.1.so.1 >>> #13 0xb67c7711 in vtk__H5I_inc_ref () from /usr/lib/libvtkhdf5-6.1.so.1 >>> #14 0xb66145ac in vtk__H5E_push_stack () from >>> /usr/lib/libvtkhdf5-6.1.so.1 >>> #15 0xb661474c in vtk__H5E_printf_stack () from >>> /usr/lib/libvtkhdf5-6.1.so.1 >>> .... >>> ITK version 4.6.1 >>> built with: >>> -DBUILD_SHARED_LIBS=ON \ >>> -DBUILD_DOCUMENTATION=ON \ >>> -DITK_DOXYGEN_HTML=ON \ >>> -DITK_DOXYGEN_ECLIPSEHELP=OFF \ >>> -DModule_ITKVtkGlue=ON \ >>> -DModule_ITKVideoBridgeOpenCV=ON \ >>> -DITK_USE_SYSTEM_ZLIB=ON \ >>> -DITK_USE_SYSTEM_JPEG=ON \ >>> -DITK_USE_SYSTEM_TIFF=ON \ >>> -DITK_USE_SYSTEM_PNG=ON \ >>> -DITK_USE_SYSTEM_FFTW=ON \ >>> -DCMAKE_INSTALL_PREFIX=/usr \ >>> -DCMAKE_BUILD_TYPE=Release .. >>> >>> >>> VTK version: 6.1.0 >>> built with: >>> -DCMAKE_INSTALL_PREFIX=/usr \ >>> -DCMAKE_BUILD_TYPE=Release \ >>> -DVTK_Group_Qt=ON \ >>> -DBUILD_SHARED_LIBS=ON .. >>> >>> Could anybody help me please? >>> >>> >>> >>> _______________________________________________ >>> Community mailing list >>> Community at itk.org >>> http://public.kitware.com/mailman/listinfo/community > > From matt.mccormick at kitware.com Thu Oct 30 16:47:52 2014 From: matt.mccormick at kitware.com (Matt McCormick) Date: Thu, 30 Oct 2014 16:47:52 -0400 Subject: [ITK] templating typdef question In-Reply-To: <003f01cff415$40b55570$c2200050$@superstem.org> References: <000601cff3bb$da4da7f0$8ee8f7d0$@superstem.org> <003f01cff415$40b55570$c2200050$@superstem.org> Message-ID: Hi Bernhard, On Thu, Oct 30, 2014 at 3:43 AM, Dr Bernhard Schaffer wrote: > Thanks for the fast reply. I'll give it a try and let you know if I hit any obstacles. > (The next time I can spend some time on ITK coding - it comes in waves as it's a spare time project). Thanks for the feedback! > A general question for this community though: > > I've emailed to "community at itk.org" a couple of weeks ago and didn't receive any answer (I don't mind too much, I just don't want to do it incorrectly). > This time I've written to community at itk.org and to insight-users at itk.org separately. Which one is the preferred group to ask these questions? > > Further, do you generally prefer getting coding questions on this mailing list, or on more general sites like Stackoverflow.com? I saw your previous post, which was a good one. Unfortunately, the Voronoi segmentation is an area of the toolkit that could use more gardening. I have some work in progress on the Vororoi code [1] and an example [2]. Current activity in the ITK community primarily occurs around the mailing lists. The community at itk.org list was an effort to consolidate lists, and it is the best default choice in my opinion. However, netizens will go where netizens will go, and communication via mailing lists, at least at a directly, is not as popular. I believe a lot of activity to the lists is through the Nabble forum [3]. StackOverflow.com is a wonderful site, but it is currently not monitored as well, and there is less activity there. > And finally (after listening in to this group for 3 weeks or so): Thank you Matt for being so responsive! I know from experience that keeping responsive in such a site is a lot of effort. Very much appreciated. Thank you for the kind words -- they are very much appreciated! Credit should also be given to the NIH National Library of Medicine, which helps support the ITK community. Matt [1] http://review.source.kitware.com/#/c/17794/ [2] http://review.source.kitware.com/#/c/17631/ [3] http://itk-users.7.n7.nabble.com/ From abdul.sw84 at gmail.com Thu Oct 30 17:37:35 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Thu, 30 Oct 2014 22:37:35 +0100 Subject: [ITK] [ITK-users] Where can I get ItKVtkGlue In-Reply-To: References: Message-ID: Hi Matt, You are right. Got it. Thanks a lot. On Wed, Oct 29, 2014 at 4:29 PM, Matt McCormick wrote: > Hi Abdul, > > ITKVtkGlue used to be a separate project, but it is now integrated > into ITK as the module ITKVtkGlue. You can enable in your ITK CMake > configuration by setting > > Module_ITKVtkGlue > > to ON. > > It requires a build of VTK. > > Hope this helps, > Matt > > On Wed, Oct 29, 2014 at 10:10 AM, Abdul Abdul > wrote: > > Hello, > > > > I'm trying to run this example: > > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > > > But, get the following when I "configure" in CMake: > > > > CMake Error at CMakeLists.txt:11 (find_package): > > By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project > > has asked CMake to find a package configuration file provided by > > "ItkVtkGlue", but CMake did not find one. > > > > Could not find a package configuration file provided by "ItkVtkGlue" with > > any of the following names: > > > > ItkVtkGlueConfig.cmake > > itkvtkglue-config.cmake > > > > Add the installation prefix of "ItkVtkGlue" to CMAKE_PREFIX_PATH or set > > "ItkVtkGlue_DIR" to a directory containing one of the above files. If > > "ItkVtkGlue" provides a separate development package or SDK, be sure it > has > > been installed. > > > > It seems I need "ItkVtkGlue"? Where can I download it? And, what should > I do > > to combine it with the program? > > > > Thanks. > > > > > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the 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 abdul.sw84 at gmail.com Thu Oct 30 17:38:04 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Thu, 30 Oct 2014 22:38:04 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: Yes, you are right John. Thanks a lot. On Wed, Oct 29, 2014 at 6:30 PM, John Drescher wrote: > On Wed, Oct 29, 2014 at 1:21 PM, Abdul Abdul wrote: > > I downloaded the latest version of ITK again, and when configuring, I > > couldn't find the ItkVtkGlue option. I attached what I have in CMake. > > You need to click the Advanced checkbox. I would also click the > Grouped box as well. > > John > -------------- 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 abdul.sw84 at gmail.com Thu Oct 30 17:47:20 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Thu, 30 Oct 2014 22:47:20 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: I was able to do the configuration and generation successfully. I'm using Visual Studio to run the program. I got the following when trying to do so: LINK : fatal error LNK1181: cannot open input file 'C:\VTKBin\lib\Release\vtkalglib-6.1.lib' 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Release Win32 ---- Do you know why is that? I know that I can run that from the command line and pass an image, but, I don't have the release of the program. Thanks. On Thu, Oct 30, 2014 at 10:38 PM, Abdul Abdul wrote: > Yes, you are right John. Thanks a lot. > > On Wed, Oct 29, 2014 at 6:30 PM, John Drescher > wrote: > >> On Wed, Oct 29, 2014 at 1:21 PM, Abdul Abdul >> wrote: >> > I downloaded the latest version of ITK again, and when configuring, I >> > couldn't find the ItkVtkGlue option. I attached what I have in CMake. >> >> You need to click the Advanced checkbox. I would also click the >> Grouped box as well. >> >> John >> > > -------------- 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 abdul.sw84 at gmail.com Thu Oct 30 17:48:50 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Thu, 30 Oct 2014 22:48:50 +0100 Subject: [ITK] [ITK-users] LINK : fatal error LNK1181 Message-ID: Hello, I'm trying to run this program: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue But, get the following in Visual Studio: LINK : fatal error LNK1181: cannot open input file 'C:\VTKBin\lib\Release\vtkalglib-6.1.lib' 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Release Win32 ---- Do you know why is that? I know that I can run that from the command line and pass an image, but, I don't have the release of the program. Thanks. -------------- 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 drescherjm at gmail.com Thu Oct 30 17:51:19 2014 From: drescherjm at gmail.com (John Drescher) Date: Thu, 30 Oct 2014 17:51:19 -0400 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: On Thu, Oct 30, 2014 at 5:47 PM, Abdul Abdul wrote: > I was able to do the configuration and generation successfully. > > I'm using Visual Studio to run the program. > > I got the following when trying to do so: > > LINK : fatal error LNK1181: cannot open input file > 'C:\VTKBin\lib\Release\vtkalglib-6.1.lib' > 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Release Win32 > ---- > > Do you know why is that? I know that I can run that from the command line > and pass an image, but, I don't have the release of the program. I am not so familiar with vtk-6.1 specifics so someone else may have to help. Which project are you building when you get this error? Did you verify that there were no errors on the vtk build? John _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 cory.quammen at kitware.com Thu Oct 30 17:52:23 2014 From: cory.quammen at kitware.com (Cory Quammen) Date: Thu, 30 Oct 2014 17:52:23 -0400 Subject: [ITK] [ITK-users] LINK : fatal error LNK1181 In-Reply-To: References: Message-ID: I suspect you built only the Debug version of VTK, but you are trying to build your example in Release mode. Build your example in Debug mode instead. On Thu, Oct 30, 2014 at 5:48 PM, Abdul Abdul wrote: > Hello, > > I'm trying to run this program: > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue > > But, get the following in Visual Studio: > > LINK : fatal error LNK1181: cannot open input file > 'C:\VTKBin\lib\Release\vtkalglib-6.1.lib' > 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Release Win32 > ---- > > Do you know why is that? I know that I can run that from the command line > and pass an image, but, I don't have the release of the program. > > Thanks. > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 abdul.sw84 at gmail.com Thu Oct 30 17:52:41 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Thu, 30 Oct 2014 22:52:41 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: This is the project I'm trying to run: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader On Thu, Oct 30, 2014 at 10:51 PM, John Drescher wrote: > On Thu, Oct 30, 2014 at 5:47 PM, Abdul Abdul wrote: > > I was able to do the configuration and generation successfully. > > > > I'm using Visual Studio to run the program. > > > > I got the following when trying to do so: > > > > LINK : fatal error LNK1181: cannot open input file > > 'C:\VTKBin\lib\Release\vtkalglib-6.1.lib' > > 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Release Win32 > > ---- > > > > Do you know why is that? I know that I can run that from the command line > > and pass an image, but, I don't have the release of the program. > > I am not so familiar with vtk-6.1 specifics so someone else may have > to help. Which project are you building when you get this error? Did > you verify that there were no errors on the vtk build? > > John > -------------- 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 abdul.sw84 at gmail.com Thu Oct 30 17:54:30 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Thu, 30 Oct 2014 22:54:30 +0100 Subject: [ITK] [ITK-users] LINK : fatal error LNK1181 In-Reply-To: References: Message-ID: I got the following when in Debug mode for the example: 2>LINK : fatal error LNK1104: cannot open file 'C:\ITK\build\lib\Debug\itkdouble-conversion-4.6.lib' 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Debug Win32 ------ 3>Project not selected to build for this solution configuration ========== Build: 1 succeeded, 1 failed, 0 up-to-date, 1 skipped ========== I'll try to build ITK and VTK in release or debug mode once again and see what happens. Thanks. On Thu, Oct 30, 2014 at 10:52 PM, Cory Quammen wrote: > I suspect you built only the Debug version of VTK, but you are trying to > build your example in Release mode. Build your example in Debug mode > instead. > > On Thu, Oct 30, 2014 at 5:48 PM, Abdul Abdul wrote: > >> Hello, >> >> I'm trying to run this program: >> http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader#ItkVtkGlue >> >> But, get the following in Visual Studio: >> >> LINK : fatal error LNK1181: cannot open input file >> 'C:\VTKBin\lib\Release\vtkalglib-6.1.lib' >> 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Release Win32 >> ---- >> >> Do you know why is that? I know that I can run that from the command line >> and pass an image, but, I don't have the release of the program. >> >> Thanks. >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 drescherjm at gmail.com Thu Oct 30 17:54:24 2014 From: drescherjm at gmail.com (John Drescher) Date: Thu, 30 Oct 2014 17:54:24 -0400 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: On Thu, Oct 30, 2014 at 5:52 PM, Abdul Abdul wrote: > This is the project I'm trying to run: > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader I thought you had the error building ITK again.. Anyways I would try Cory's answer.. John _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the 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 cory.quammen at kitware.com Thu Oct 30 17:55:35 2014 From: cory.quammen at kitware.com (Cory Quammen) Date: Thu, 30 Oct 2014 17:55:35 -0400 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: Abdul, Please try to ask your questions in only one email thread. That will make it easier for others to follow along now and in the future if they search the archives. I just answered a question you posted in this thread that you duplicated in a new thread. Thanks, Cory On Thu, Oct 30, 2014 at 5:52 PM, Abdul Abdul wrote: > This is the project I'm trying to run: > http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader > > On Thu, Oct 30, 2014 at 10:51 PM, John Drescher > wrote: > >> On Thu, Oct 30, 2014 at 5:47 PM, Abdul Abdul >> wrote: >> > I was able to do the configuration and generation successfully. >> > >> > I'm using Visual Studio to run the program. >> > >> > I got the following when trying to do so: >> > >> > LINK : fatal error LNK1181: cannot open input file >> > 'C:\VTKBin\lib\Release\vtkalglib-6.1.lib' >> > 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Release Win32 >> > ---- >> > >> > Do you know why is that? I know that I can run that from the command >> line >> > and pass an image, but, I don't have the release of the program. >> >> I am not so familiar with vtk-6.1 specifics so someone else may have >> to help. Which project are you building when you get this error? Did >> you verify that there were no errors on the vtk build? >> >> John >> > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the 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 abdul.sw84 at gmail.com Fri Oct 31 03:11:07 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 31 Oct 2014 08:11:07 +0100 Subject: [ITK] [ITK-users] Running an ITK program In-Reply-To: References: <5450F675.5010404@neuro.ma.uni-heidelberg.de> <5451042B.9060102@neuro.ma.uni-heidelberg.de> Message-ID: Yes, got what you mean Cory. Thanks all for your kind replies. I have built ITK with the itkVtkGlue module checked, and have build VTK, both on release mode. I could then configure and generate the program successfully. Thanks. On Thu, Oct 30, 2014 at 10:55 PM, Cory Quammen wrote: > Abdul, > > Please try to ask your questions in only one email thread. That will make > it easier for others to follow along now and in the future if they search > the archives. I just answered a question you posted in this thread that you > duplicated in a new thread. > > Thanks, > Cory > > On Thu, Oct 30, 2014 at 5:52 PM, Abdul Abdul wrote: > >> This is the project I'm trying to run: >> http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader >> >> On Thu, Oct 30, 2014 at 10:51 PM, John Drescher >> wrote: >> >>> On Thu, Oct 30, 2014 at 5:47 PM, Abdul Abdul >>> wrote: >>> > I was able to do the configuration and generation successfully. >>> > >>> > I'm using Visual Studio to run the program. >>> > >>> > I got the following when trying to do so: >>> > >>> > LINK : fatal error LNK1181: cannot open input file >>> > 'C:\VTKBin\lib\Release\vtkalglib-6.1.lib' >>> > 3>------ Skipped Build: Project: ALL_BUILD, Configuration: Release >>> Win32 >>> > ---- >>> > >>> > Do you know why is that? I know that I can run that from the command >>> line >>> > and pass an image, but, I don't have the release of the program. >>> >>> I am not so familiar with vtk-6.1 specifics so someone else may have >>> to help. Which project are you building when you get this error? Did >>> you verify that there were no errors on the vtk build? >>> >>> John >>> >> >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the 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 abdul.sw84 at gmail.com Fri Oct 31 03:22:07 2014 From: abdul.sw84 at gmail.com (Abdul Abdul) Date: Fri, 31 Oct 2014 08:22:07 +0100 Subject: [ITK] [ITK-users] Message when trying to run an ITK program Message-ID: Hello, I'm trying to run this program through Visual Studio 2013: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader When I do that, I get the following message: *unable to start program 'C:\itk-example\build\Release\ALL_BUILD'.* *The system cannot find the file specified.* How can I solve this issue? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.bogle at auckland.ac.nz Fri Oct 31 03:28:06 2014 From: g.bogle at auckland.ac.nz (Gib Bogle) Date: Fri, 31 Oct 2014 07:28:06 +0000 Subject: [ITK] [ITK-users] Message when trying to run an ITK program In-Reply-To: References: Message-ID: In Solution Explorer, right-click on the program you are building and then Set as Startup Project. By default VS treats ALL_BUILD as the startup project, which is what it tries to execute when you do Debug > Start Without Debugging. Gib ________________________________ From: Insight-users [insight-users-bounces at itk.org] on behalf of Abdul Abdul [abdul.sw84 at gmail.com] Sent: Friday, 31 October 2014 8:22 p.m. To: ITK Subject: [ITK-users] Message when trying to run an ITK program Hello, I'm trying to run this program through Visual Studio 2013: http://www.itk.org/Wiki/ITK/Examples/IO/ImageFileReader When I do that, I get the following message: unable to start program 'C:\itk-example\build\Release\ALL_BUILD'. The system cannot find the file specified. How can I solve this issue? Thanks. -------------- 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 tanghui.seu at gmail.com Fri Oct 31 04:53:53 2014 From: tanghui.seu at gmail.com (Hui Tang) Date: Fri, 31 Oct 2014 16:53:53 +0800 Subject: [ITK] [ITK-users] BinaryDilateImageFilter has an issue? Message-ID: Dear all, I can not get dilation or erosion from BinaryDilateImageFilter or BinaryErodeImageFilter I mostly copied from the example and thought it should work without any problems. Here is my code. Anyone knows what is wrong here? Thanks a lot in advance ! unsigned int radius = 7; typedef itk::BinaryBallStructuringElement StructuringElementType; StructuringElementType structuringElement; structuringElement.SetRadius(radius); structuringElement.CreateStructuringElement(); typedef itk::BinaryDilateImageFilter BinaryDilateImageFilterType; BinaryDilateImageFilterType::Pointer dilateFilter = BinaryDilateImageFilterType::New(); dilateFilter->SetInput(readerint->GetOutput()); dilateFilter->SetKernel(structuringElement); dilateFilter->Update(); Best, Hui -------------- 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 indianzeppelin at gmail.com Fri Oct 31 06:44:32 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Fri, 31 Oct 2014 10:44:32 +0000 Subject: [ITK] [ITK-users] BinaryDilateImageFilter has an issue? In-Reply-To: References: Message-ID: Hi Hui, Could you describe what exactly the problem is? Also, couId you also paste the earlier part of your code (where Image3DIntType and readerint are defined)? On Fri, Oct 31, 2014 at 8:53 AM, Hui Tang wrote: > Dear all, > > I can not get dilation or erosion from BinaryDilateImageFilter or > BinaryErodeImageFilter > > I mostly copied from the example and thought it should work without any > problems. > > Here is my code. > Anyone knows what is wrong here? Thanks a lot in advance ! > > > unsigned int radius = 7; > > typedef itk::BinaryBallStructuringElement StructuringElementType; > > StructuringElementType structuringElement; > > structuringElement.SetRadius(radius); > > structuringElement.CreateStructuringElement(); > > > > typedef itk::BinaryDilateImageFilter StructuringElementType> BinaryDilateImageFilterType; > > BinaryDilateImageFilterType::Pointer dilateFilter = > BinaryDilateImageFilterType::New(); > > dilateFilter->SetInput(readerint->GetOutput()); > > dilateFilter->SetKernel(structuringElement); > > dilateFilter->Update(); > > > > Best, > > > > Hui > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > > -- Regards, Girish -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From c.metz at quantib.com Fri Oct 31 11:17:30 2014 From: c.metz at quantib.com (Coert Metz) Date: Fri, 31 Oct 2014 16:17:30 +0100 Subject: [ITK] Direction matrix and LPS system Message-ID: Dear all, We are currently writing a conversion from a third party image format to the ITK format. For that we need to correctly set the image origin and direction matrix. When directly reading DICOM images in ITK, (according to the code) they are ordered in such a way that the coordinate system is right handed, i.e. the columns of the direction matrix form a right handed coordinate system. Also the Doxygen of SetDirection says the direction matrix columns should form a right handed coordinate system. In the image we get from the third party system (in memory) the DICOM slices are not reordered, which means the coordinate system might be left handed instead of right handed. We currently accommodate for this by setting the right direction matrix, which seems to work fine, but also seems to be illegal according to the Doxygen comment of SetDirection. Is there any issue that can occur when following our approach? We would rather not reorder the data, but just use the voxel data from the third party system as is. Kind regards, -- Coert Metz, PhD Research & Development Engineer | Quantib B.V. c.metz at quantib.com | +31 650 68 60 28 -- This message may contain confidential or privileged information. If you are not the addressee, please notify the sender and delete it from your files. -------------- next part -------------- An HTML attachment was scrubbed... URL: From norman-k-williams at uiowa.edu Fri Oct 31 11:18:54 2014 From: norman-k-williams at uiowa.edu (Williams, Norman K) Date: Fri, 31 Oct 2014 15:18:54 +0000 Subject: [ITK] [ITK-dev] Patch for SpatialObject -- fixed regressions, testing with BRAINSTools Message-ID: This doesn?t fix the general problem with thread safety that your patch to Transform::GetInverse exposed, but I believe it will fix the problem with BRAINSTools test regressions. I?m testing that now. It addresses (partially) the thread safety issue in the specific case of using a SpatialObject as a mask in the registration framework. Instead of computing the inverse at every invocation of SpatialObject::IsInside, it only computes it when the transform it depends on (the IndexToWorldTransform) . Since a mask object (or any SpatialObject) is will not change its WorldToIndex transform during registration, the patch remove the crash due to more than one thread modifying the transform at the same time. It also removes potentially hundreds of thousands of calls to Transform::GetInverse() which can only improve performance. I wonder why this simple-minded optimization never showed up on anyone?s radar before. The topic in Gerrit is here: http://review.source.kitware.com/#/c/17779/ It is also in the BRAINSia git fork of ITK: https://github.com/BRAINSia/ITK/tree/SpatialObjectInternalInverse ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________ -------------- 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 indianzeppelin at gmail.com Fri Oct 31 12:56:26 2014 From: indianzeppelin at gmail.com (Girish Mallya Udupi) Date: Fri, 31 Oct 2014 16:56:26 +0000 Subject: [ITK] [ITK-users] BinaryDilateImageFilter has an issue? In-Reply-To: References: Message-ID: Hi Hui, Here's an explanation (someone more knowledgeable can correct me or explain it in a better way). See [1]. The dilate (as well as the erode) filter considers as foreground those pixels which have a "DilateValue". If this value is not set, it defaults to the maximum possible value of the *PixelType *which in your case is the maximum value of the *signed int* type. So, if you know the foreground value of your binary image, you might want to try setting this "DilateValue", by using *dilateFilter->SetDilateValue(). *You can also use the MinimumMaximumImageCalculator to find the maximum value (see [2]). As an aside, wouldn't it be better to use *unsigned char* instead of *int *in this case, since the image is binary? [1] http://www.itk.org/Doxygen/html/classitk_1_1BinaryDilateImageFilter.html [2] http://www.itk.org/Doxygen/html/classitk_1_1MinimumMaximumImageCalculator.html#a39a9bfc33090e47df71d5b9cd6665ccb On Fri, Oct 31, 2014 at 10:58 AM, tanghui.seu wrote: > Hi Grish > > Thanks a lot for your reply! > The dilate Filter outputs the same as the input image. > > Image3DIntType is itk?:image > I correctly read in a binary image. > > Sorry that i can not provide the code now..... it is in my workstation. > Thanks a lot again! > > > ???????? > > > Girish Mallya Udupi wrote: > > Hi Hui, > > Could you describe what exactly the problem is? Also, couId you also paste > the earlier part of your code (where Image3DIntType and readerint are > defined)? > > > On Fri, Oct 31, 2014 at 8:53 AM, Hui Tang wrote: > >> Dear all, >> >> I can not get dilation or erosion from BinaryDilateImageFilter or >> BinaryErodeImageFilter >> >> I mostly copied from the example and thought it should work without any >> problems. >> >> Here is my code. >> Anyone knows what is wrong here? Thanks a lot in advance ! >> >> >> unsigned int radius = 7; >> >> typedef itk::BinaryBallStructuringElement StructuringElementType; >> >> StructuringElementType structuringElement; >> >> structuringElement.SetRadius(radius); >> >> structuringElement.CreateStructuringElement(); >> >> >> >> typedef itk::BinaryDilateImageFilter > StructuringElementType> BinaryDilateImageFilterType; >> >> BinaryDilateImageFilterType::Pointer dilateFilter = >> BinaryDilateImageFilterType::New(); >> >> dilateFilter->SetInput(readerint->GetOutput()); >> >> dilateFilter->SetKernel(structuringElement); >> >> dilateFilter->Update(); >> >> >> >> Best, >> >> >> >> Hui >> >> _____________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://www.kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-users >> >> > > > -- > Regards, > Girish > -- Regards, Girish -------------- 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 rogerbramon at gmail.com Fri Oct 31 13:55:24 2014 From: rogerbramon at gmail.com (Roger Bramon Feixas) Date: Fri, 31 Oct 2014 18:55:24 +0100 Subject: [ITK] [ITK-users] Error compiling msvc2010 + ITK4.6 + Qt In-Reply-To: References: <5446873A.7070500@imnc.in2p3.fr> <930E7D31-ACFE-4ECF-8EAD-E8D3B6081B92@mail.nih.gov> <54475B84.5020906@imnc.in2p3.fr> <54492AB3.2030006@imnc.in2p3.fr> <544A073B.4080905@imnc.in2p3.fr> Message-ID: Hi, I also have this link problem trying to build using msvc2013_opengl + ITK 4.6.1 + VTK 6.1 + GDCM 2.4.4 + Qt 5.3.2. We are using qmake as well. Any suggestion will be appreciated. Many thanks, Roger On Fri, Oct 24, 2014 at 4:57 PM, Matt McCormick wrote: > Hi Fran?oise, > > > CMake is recommended -- it will avoid this problem and others. It > works well with Qt. > > Thanks, > Matt > > On Fri, Oct 24, 2014 at 4:00 AM, Fran?oise Lefebvre > wrote: > > > > No, I'm not. I have always used a .pro file and qmake. > > > > Le 23/10/2014 23:37, Matt McCormick a ?crit : > > > >> Hi, > >> > >> Are you using CMake to configure your project? > >> > >> Matt > >> > >> On Thu, Oct 23, 2014 at 12:20 PM, Fran?oise Lefebvre > >> wrote: > >>> > >>> Hi, > >>> > >>> I also tried on Windows 8,msvc2012_opengl and Qt5.3. I get exactly the > >>> same > >>> link error. > >>> > >>> FL > >>> > >>> > >>> Le 22/10/2014 09:23, Fran?oise Lefebvre a ?crit : > >>> > >>>> Yes I did. > >>>> > >>>> Le 21/10/2014 19:18, Bradley Lowekamp a ?crit : > >>>>> > >>>>> Did you try the latest 4.6.1 release? > >>>>> > >>>>> Brad > >>>>> > >>>>> On Oct 21, 2014, at 12:18 PM, Fran?oise Lefebvre > >>>>> > >>>>> wrote: > >>>>> > >>>>>> Hi, > >>>>>> > >>>>>> ITK 4.6 was succesfully build using cmake2.8.10.2, the default > >>>>>> parameters and the Module_ITKReview on. > >>>>>> > >>>>>> I am now trying to compile a program developed in C++ using Qt5.1.1 > >>>>>> and > >>>>>> Microsoft Visual C++ express 2010 on Windows 7. > >>>>>> > >>>>>> I get the following link error : > >>>>>> > >>>>>> 1>itksys-4.6.lib(EncodingCXX.obj) : error LNK2019: symbole externe > non > >>>>>> r?solu __imp__CommandLineToArgvW at 8 r?f?renc? dans la fonction > "public: > >>>>>> static class itksys::Encoding::CommandLineArguments __cdecl > >>>>>> itksys::Encoding::CommandLineArguments::Main(int,char const * const > >>>>>> *)" > >>>>>> (?Main at CommandLineArguments@Encoding at itksys@@SA?AV123 at HPBQBD@Z) > >>>>>> > >>>>>> I didn't get this error when compiling with itk4.3 . > >>>>>> > >>>>>> Any hint ? > >>>>>> > >>>>>> Thank you for your help, > >>>>>> > >>>>>> F. Lefebvre > >>>>>> > >>>>>> _____________________________________ > >>>>>> Powered by www.kitware.com > >>>>>> > >>>>>> Visit other Kitware open-source projects at > >>>>>> http://www.kitware.com/opensource/opensource.html > >>>>>> > >>>>>> Kitware offers ITK Training Courses, for more information visit: > >>>>>> http://www.kitware.com/products/protraining.php > >>>>>> > >>>>>> Please keep messages on-topic and check the 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 > > > > > > -- > > Fran?oise LEFEBVRE > > IMNC (Imagerie et Mod?lisation en Neurobiologie et Canc?rologie) > > Campus d'Orsay - B?t 440 > > 91405 ORSAY Cedex > > 01 69 15 51 87 > > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/insight-users From g.lemaitre58 at gmail.com Fri Oct 31 19:03:36 2014 From: g.lemaitre58 at gmail.com (=?UTF-8?Q?Guillaume_Lema=C3=AEtre?=) Date: Sat, 1 Nov 2014 00:03:36 +0100 Subject: [ITK] [ITK-users] SimpleITK - Reading different DICOM serie Message-ID: Hi all, I am currently using SimpleITK with python to read directly some DICOM data. My dataset is corresponding to an MRI modality composed of 40 series. Each serie is a 3D volume. I would like to read the serie one-by-one. As a minimal example, I can post the following code: reader = sitk.ImageSeriesReader() # For each serie found for serie in reader.GetGDCMSeriesIDs(path_to_data): # Get the dicom filename corresponding to the current serie dicom_names = reader.GetGDCMSeriesFileNames(path_to_data, serie) reader.SetFileNames(dicom_names) image = reader.Execute() I got the following error: WARNING: In /home/lemaitre/anaconda/conda-bld/work/build/ITK/Modules/IO/GDCM/src/itkGDCMSeriesFileNames.cxx, line 138 GDCMSeriesFileNames (0x3078840): No Series were found However, the output of reader.GetGDCMSeriesIDs(path_to_data) seems ok: ('1.2.826.0.1.3680043.2.1125.1.12083572272639445972057901411530444', ............................ 40 lines ........................... '1.2.826.0.1.3680043.2.1125.1.98804240625293208256969403455867278') So my question is the following. What is the right way to passing the serieID to the GetGDCMSeriesFileNames() function. Thanks in advance, Best regards, -- *LEMA?TRE GuillaumePhD CandiateMSc Erasmus Mundus ViBOT (Vision-roBOTic)MSc Business Innovation and Technology Management* g.lemaitre58 at gmail.com *ViCOROB - Computer Vision and Robotic Team* Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona Tel. +34 972 41 98 12 - Fax. +34 972 41 82 59 http://vicorob.udg.es/ *LE2I - Le Creusot*IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot Tel. +33 3 85 73 10 90 - Fax. +33 3 85 73 10 97 http://le2i.cnrs.fr https://sites.google.com/site/glemaitre58/ Vice - Chairman of A.S.C. Fours UFOLEP Chairman of A.S.C. Fours FFC Webmaster of http://ascfours.free.fr -------------- 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 rahmodi at gmail.com Wed Oct 29 11:52:52 2014 From: rahmodi at gmail.com (rahul modi) Date: Wed, 29 Oct 2014 15:52:52 -0000 Subject: [ITK] Reading old Philips DICOM Message-ID: Hi, This is in reference to a a messsage [ITK] Reading old Philips DICOM ( http://public.kitware.com/pipermail/community/2014-March/001860.html) I am facing a similar problem reading an old Philips dicom (scanner parnaroma 0.23t) ITK-Snap ver 3.2 crashes when reading this dicom. I also tried reading the file using ITK ver 4.2 The crash occurs while running the Update() function for ImageSeriesReader The error I get is: Assertion failed: pixeltype <= outputpt, file C:\Temp\ITK\InsightToolkit-4.2.0\Modules\IO\GDCM\src\itkGDCMImageIO.cxx, line 352 I can read this file with all gdcm command line tools Is this a known issue? Thanks in advance for any help. The dicom file is attached with this post. Best, Rahul Modi -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: I0 Type: application/octet-stream Size: 230004 bytes Desc: not available URL: