Changesets: Import 2017-06-07 23:51:09
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master 0dad5332 2015-01-16 01:01:24 Details Diff |
ENH: Allow SurfaceToolbox to use higher than 0.9 decimation reduction git-svn-id: http://svn.slicer.org/Slicer4/trunk@23879 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Scripted/SurfaceToolbox/SurfaceToolbox.py | Diff File | ||
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master 4548292c 2015-01-15 11:26:16 naucoin Details Diff |
STYLE: : update Markups documentation with new features Add information about measuring with fiducials, showing the transformed coordinates, hiding the coordinates in the table, refocussing the 3D view. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23878 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Markups/Documentation/Markups.xml | Diff File | ||
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master 05d464b3 2015-01-12 16:53:41 Details Diff |
STYLE: adding comments to multivolume changes to ProcessReadData() From: Jim Miller <millerjv@ge.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23877 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Base/Logic/vtkSlicerApplicationLogic.cxx | Diff File | ||
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master 9c6506ce 2015-01-12 16:53:39 Details Diff |
BUG: fix loading multivolumes produced by CLIs This addresses Slicer issue http://www.na-mic.org/Bug/view.php?id=3382. The patch has been suggested by Jim Miller (see the Slicer issue). Jim wants to add more comments before this is merged with the Slicer master. From: Andrey Fedorov <fedorov@bwh.harvard.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23876 3bd1e089-480b-0410-8dfb-8563597acbee |
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master 54937ce3 2015-01-09 20:05:54 Details Diff |
BUG: Update ITKv4 to fix Resample DTIVolume/ScalarVectorDWIVolume tests This commit fixes a regression introduced by the update of ITK in r23858 // ---------------- BUG: Clear TransformIO's list of transforms in TransformFileReader. Since TransformFileReaderTemplate and TransformIO do not have very good const correctness and encapsulation, it is possible to manipulate their members and change their state in a way they might not expect. In InsightSoftwareConsortium/ITK@81faafe29, a m_TransformIO member was added. This is used in TransformFileReaderTemplate's Update() step instead of creating a new TransformIOBase instance on every Update. To keep completely consistent with the previous behavior, we must clear the TransformIOBase's internal transform list at the time the class was previously instantiated. Thanks to Jean-Christophe Fillion-Robin and the Slicer community for identifying this regression. Change-Id: If5dfd03b32b31ba765c6781d689e91edb944be3f // ---------------- git-svn-id: http://svn.slicer.org/Slicer4/trunk@23875 3bd1e089-480b-0410-8dfb-8563597acbee |
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master e7325e85 2015-01-09 12:23:53 Details Diff |
BUG: Update EMSegment to avoid using invalid BRAINSFit argument. Fixes 0003939 // --------------------- BUG: Remove invalid BRAINSFit argument This commit removes deprecated (and unused for a long time) command line options from the most recent version of BRAINSTools. These command line options have been NO-OP operations for a long time. They have been removed in the version of BRAINSTools now used in Slicer r23872. Thanks to "Hans Johnson <hans-johnson@uiowa.edu>" for providing the patch. // --------------------- git-svn-id: http://svn.slicer.org/Slicer4/trunk@23874 3bd1e089-480b-0410-8dfb-8563597acbee |
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master 5f987eed 2015-01-09 11:41:54 Details Diff |
COMP: Fix linux package using correct teem library folder in launcher settings Thanks to "Francois Budin <fbudin@unc.edu>" for reporting the problem. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23873 3bd1e089-480b-0410-8dfb-8563597acbee |
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master bbc84663 2015-01-09 09:15:36 Details Diff |
ENH: Update BRAINTools Ali Ghayoor (50): BUG: fix BRAINSFitTest_ROIBSpline test failure BUG: increase the tolerance for BRAINSFitTest_ROIBSpline BUG: Symmetric bounding box in training and detection phases of BCD ENH: perform the local search of BCD in Freq domain ENH: Add version number to input template and LLS model files ENH: add the new template files to ReferenceAtlas/20140916_BCD directory ENH: Update the current address of BCD model files to the new one ENH: Remove irrelevent parameters from BRAINSFit ENH: add the new template files to ReferenceAtlas/20141004_BCD directory ENH: Remove wrong model files and update AutoWorkup scripts ENH: Update the BCD model files for internal TestSuite ENH: Integration of ANTs Multimodal Registration into BRAINSFitHelper ENH: Add multi-modal capsbilities to BRAINSFit ENH: Change the classifier in BRAINSABC ENH: Update the ITK tag ENH: Write different posteriors for EM and KNN BUG: Fix BCD test failures BUG: Initialized m_UseKNN member variable on constructor ENH: Add itkCompensatedSummation for MSP estimation BUG: Fix 23 BCD test failures on medusa ENH: Avereged warped intra subjects ENH: Write debug warped intra subject images to the disk ENH: InitializeTransformsPerStage is set on BFit BUG: save-state transform should be cloned from the result transform in BFit BUG: Update ITK tag and a temporary tag for ANTs so BTools can be compiled BUG: Update save-state in BFit based on the last changes to ANTs BUG: Update temporary tags for ITK and ANTs based on bia versions BUG: Fix a bug in BABC when intial atlasToSubjectTx is missing BUG: Avoid writing the inverse of the state file ENH: Convert savedState file to the restored forward and inverse composites BUG: Fix BRAINSABC Failure for single modal images BUG: Fixed some bugs in BRAINSTransformConvert and verified its outputs ENH: BRAINSLandmarkInitializer works with multiple transformTypes BUG: No limit on usage of CompositeTransform for intialization in BABC BUG: MultiModal registration bug in BRAINSABC and BRAINSFit ENH: Add a GenerateCLP command line for GenerateAverageLmkFile BUG: Fixed BCD Test failures on Dashboard BUG: Fix BRAINSFitTest_ROIBSpline test failure BUG: Replace the baselines of BCD tests based on CDash build BUG: Fix a bug in BRAINSFit SyN registration BUG: Fixed a bug in GenericTransformImage BUG: Fixed output origin in ResampleInPlaceImageFilter ENH: Add a regression test to BRAINSResample for ResampleInPlace BUG: ReadTransformFromDisk can process a list of transforms now BUG: Fixed a bug in gtractResampleDWIInPlace ENH: Add a test for gtractResampleDWIInPlace BUG: Fixed a bug BRAINSHoughEyeDetector ENH: add reading from landmark file to BRAINSTalairach ENH: Add a python script to create inputLmkFile for BTalairach BUG: Fix BFit crash when only one value is set for splineGridSize Hans Johnson (86): ENH: Update to include ITKv4 Mattes Performance fixes. ENH: Per requests of the slicer community, defaults changed. ENH: Added --dry-run feature WIP: Needs more work on SEM tools. DO NOT SUBMIT THIS. COMP: ITK Components needed for build. WIP: Removed BRAINSSurface building. ENH: Updated SEMTools to new command line usage. BUG: Filenames needed to change from hdf5 to h5 extension in autoworkup. BUG: Eliminate unnecessary handling of version COMP: Remove compiler warning ENH: Added UseKNN on the command line. STYLE: Remove unnecessary CLUSTER tag from config file ENH: Improve SyN registration in BABC ENH: Trying to add sqrt of multiplied posteriors ENH: Automatically calculate the number of sampels to use ENH: Add initial masking to Averaged images ENH: Update to include SEM generated interfaces. ENH: Fix BRAINSABC for AutoWorkup. ENH: Improved fine grained control of processing ENH: Added fixes for ITK FixedParameters. ENH: Cleaned up logic for isolating separate processing steps ENH: Added new command line for ANTS BUG: Fixed order of imports ENH: Updated Workflow for ANTs state saving. ENH: Add saveState and storeState to BFit and BABC ENH: Added stub restoring ANTs registration ENH: Improved linkage of SyN to BRAINSABC. ENH: Testing new ANTs registration values. ENH: Provide consistent registration for ANTs. ENH: ANTs testing with separate stages. ENH: Remove requirement for atlasToSubjectIntialTransform flag. ENH: Added cluster flags and remove debugging. ENH: Fixed segmentation phase of processing BUG: Need to ensure range of threads are integer values. ENH: Improved registration parameters for optimization. STYLE: Remove aliasing that was confusing ENH: Added debugging info. BUG: Missing update on averaging filter STYLE: ::Zero and ::One have been deprecated since 2012 ENH: Syncronize with NAMICExternalProjects. ENH: Improve logic for choosing registration mode. ENH: Improve T1 only segmentations ENH: Optimize registration parameters for ANTs template building. BUG: Command line to limit subjects to process was incorrect. STYLE: Hide debugging information. ENH: Fine tuning ANTs registration to take less time ENH: Limit the number of iterations for full size SyN BUG: matplotlib is not a requirement. ENH: Conversion to composite files continued ENH: Provide skipping logic for template building phase. ENH: FIXING BUGS IN template use for phase 3. ENH: Added GenerateAverageLmkFile interface. ENH: Split required and optional items from datagrabber. BUG: Incorrect syntax for custom pipeline arguments ENH: Try to fix Brainstem segmentations. BUG: Connections to Segmentation were incorrect ENH: Make segmentation connection. ENH: Add feature for using ROIAuto for registration masking ENH: Add r/l hemisphere separation. COMP: Improve Compilation for ITK modules ENH: Adding MALF label fusion to autoworkup COMP: Fix compilation linkage errors. ENH: Initial code copied directly from BRAINS3/src/iplProg/GenusZero STYLE: Clean code for easier maintenance. ENH: Copy vtkITK from Slicer ENH: Migrate to Slicer version of vtkITK, and update to VTK version 6 COMP: Remove compilation warning of returning without value. COMP: Fixed compilation problems ENH: Improve quality of MALF outputs ENH: Update ITKv4 to include performance fixes. COMP: Incorrect function signature. ENH: Lastest alpha ITK 4.7 release. COMP: Consolidated duplicate code, fix include directory ENH: Merged fusion and other knowlege ENH: Update external packages. COMP: C++11 style nullptr usage COMP: Use C++11 keyword override for code maintenance COMP: Remove unused typedefs ENH: Updated VTK. COMP: Improve VTK compilation options. BUG: Changes to Fix 'space directions' field in the NRRD Header BUG: Prevent infiinte loop for bad cases in BABC COMP: Missing ITK_OVERRIDE substitution. COMP: Fix VTK QT relationship builds. ENH: Syncronized with NAMICExternalProjects. ENH: Deprecate ::Zero and ::One Kent Williams (14): COMP: remove ITKV3_COMPATIBILITY entireley COMP: Removed deprecated V3 filters COMP: Remove shadow declaration warnings COMP: fix core dump due to premature object destruction COMP: Replace Rigod{2,3}Transform with derived classes COMP: Initialize m_AtlasToSubjectInitialTransform COMP: Turn off ITKV3Compatibility and ITKDeprecated BUG: Fix scaling of vectors by b-values COMP: fix some gcc 4.9.2 warnings COMP: gcc4.9.1 warnings for ANTs COMP: Enable BRAINSSurfaceTools by default COMP: Fix warningsCOMP: get BRAINSSurfaceTools to build. COMP: Remove gcc 4.9 warnings COMP: Remove more gcc 4.9 warnings Regina Kim (9): ENH: BRAINSABC multimodal functionality WIP: BRAINSABC multimodal functionality WIP: working version with the local option WIP: SyN Registration parameter tunning BUG: Fix the bug introduced by merging BUG: Multimodal registration into BABC BUG: kNN output were improperly propagated. Fixed ENH: By pass denoising for BCD failures BUG: BRAINSCut DG move and template building fix BRAINSCut probablity DataGrabber were placed into segmentation section instead of default section. eunyoung regina kim (2): Update README Create MALFLabel_neuromorphometrics_colortable.txt fbudin69500 (1): ENH: Addition of an option in DWIConvert to read input BVector files that are transposed when converting FSL images to NRRD images. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23872 3bd1e089-480b-0410-8dfb-8563597acbee |
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master ecfcf047 2015-01-09 02:29:43 Details Diff |
BUG: Update CTK so that platform specific end-of-line is used in ctkFileLogger $ git shortlog 07222d0..e47ac49 --no-merges Andras Lasso (1): ENH: Use platform-specific EOL character in log file Sascha Zelzer (2): Use modern CMake features in plugin build macro. Bumped the number of max degrees. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23871 3bd1e089-480b-0410-8dfb-8563597acbee |
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master f7365e81 2015-01-09 02:09:40 Details Diff |
ENH: Split camera refocus on markup into two levels. Fixes 0003683 Add method to refocus one camera and call it from the method that refocuses all 3D cameras. Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> From: Nicole Aucoin <nicole@bwh.harvard.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23870 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Markups/Logic/vtkSlicerMarkupsLogic.cxx | Diff File | ||
| mod - Modules/Loadable/Markups/Logic/vtkSlicerMarkupsLogic.h | Diff File | ||
| mod - Modules/Loadable/Markups/Testing/Python/MarkupsInViewsSelfTest.py | Diff File | ||
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master a782f736 2015-01-09 02:09:36 Details Diff |
ENH: Add ability to refocus 3d cameras on a fiducial. Fixes 0003683 Added a right click context menu option to refocus the 3D camera to the first selected fiducal. This can help localise the fiducial in a large scene. Added logic method to get all camera nodes and set the focal point on them. Added the call to a self test. From: Nicole Aucoin <nicole@bwh.harvard.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23869 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Loadable/Markups/Logic/vtkSlicerMarkupsLogic.cxx | Diff File | ||
| mod - Modules/Loadable/Markups/Logic/vtkSlicerMarkupsLogic.h | Diff File | ||
| mod - Modules/Loadable/Markups/Testing/Python/MarkupsInViewsSelfTest.py | Diff File | ||
| mod - Modules/Loadable/Markups/qSlicerMarkupsModuleWidget.cxx | Diff File | ||
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master 31d496ad 2015-01-09 01:50:09 Details Diff |
BUG: Fixed loading of DICOM image from files containing special characters Got some DICOM files that contained a special character in the file names and in the patient name. Slicer failed to load them because lack of proper encoding before using them. Solution: * Encode strings to latin1 before using them in VTK set functions. * Encode file names to a byte stream before sending them to hashlib. From: Andras Lasso <lasso@queensu.ca> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23868 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Scripted/DICOMLib/DICOMPlugin.py | Diff File | ||
| mod - Modules/Scripted/DICOMPlugins/DICOMScalarVolumePlugin.py | Diff File | ||
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master 1413b7c7 2015-01-09 01:50:05 Details Diff |
ENH: Re-factor code introducing "slicer.util.toVTKString" Co-authored-by: Andras Lasso <lasso@queensu.ca> From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23867 3bd1e089-480b-0410-8dfb-8563597acbee |
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| mod - Modules/Scripted/DICOMLib/DICOMPlugin.py | Diff File | ||
| mod - Modules/Scripted/DICOMPlugins/DICOMScalarVolumePlugin.py | Diff File | ||
| mod - Modules/Scripted/DataProbe/DataProbeLib/SliceViewAnnotations.py | Diff File | ||
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master b0e10b34 2015-01-09 01:45:26 Details Diff |
COMP: Remove ITKv3Compatibility dependency from EMSegment // --------------- ENH: Remove dependency on ITKv3Compatibility module. Thanks to "Bradley Lowekamp <blowekamp@mail.nih.gov>" for providing the patch. See http://itk.org/migrationv4/index.php?action=artikel&cat=3&id=143&artlang=en for more details // --------------- From: Bradley Lowekamp <blowekamp@mail.nih.gov> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23866 3bd1e089-480b-0410-8dfb-8563597acbee |
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master b9b6d168 2015-01-08 19:58:22 Details Diff |
COMP: Update teem to fix MacOSX packaging issue $ git shortlog 93ba14a..71e15b1 --no-merges Jean-Christophe Fillion-Robin (1): COMP: Restore library output path to "lib" folder From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23865 3bd1e089-480b-0410-8dfb-8563597acbee |
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master 85d06ce5 2015-01-08 19:58:20 Details Diff |
BUG: Update teem to fix issue 0003455 $ git shortlog 9142f9a..93ba14a Jean-Christophe Fillion-Robin (1): COMP: Associate component with teem install rules From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23864 3bd1e089-480b-0410-8dfb-8563597acbee |
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master 862b7eed 2015-01-08 19:58:17 Details Diff |
ENH: Update teem version from 1.10.0 to 1.12.0 with Slicer specific changes The list of contributors for this update: $ git shortlog -s 1.10.0..9142f9a 8 Hans Johnson 3 Kent Williams 3 MichelKitware 1 bigler 9 blezek 3 chaircrusher 5 dlrdave 2 dmwsci 5 jbm139 1 jefferis 2 jorikb 1847 kindlmann 2 matthewbrett 20 michaelcallahan 28 michelkitware 1 olduvaihand 1 rchoudhury 15 rjosest 14 samquinan 60 tststs The list of all changes can be visualized here: https://github.com/Slicer/teem/compare/1.10.0...9142f9a Co-authored-by: Hans Johnson <hans-johnson@uiowa.edu> Co-authored-by: Alex Yarmarkovich <alexy@bwh.harvard.edu> From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23863 3bd1e089-480b-0410-8dfb-8563597acbee |
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master 7292bef0 2015-01-08 19:58:14 Details Diff |
STYLE: Improve error message associated with _fixup_paths_append macro From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23862 3bd1e089-480b-0410-8dfb-8563597acbee |
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master f5f25071 2015-01-08 17:23:50 Details Diff |
COMP: Update VTK to fix build error on Debian "Jessie". Fixes 0003906 Co-authored-by: "Sharp, Gregory C." <GCSHARP@mgh.harvard.edu> This commit fixes the following build error: // ---------------- [ 35%] Building CXX object Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGLObjects.dir/vtkXOpenGLRenderWindow.cxx.o In file included from /usr/include/GL/glx.h:333:0, from /home/gsharp/build/slicer-4/Slicer-build/VTKv6/Rendering/OpenGL/vtkXOpenGLRenderWindow.cxx:30: /usr/include/GL/glxext.h:480:143: error: ‘GLintptr’ has not been declared typedef void ( *PFNGLXCOPYBUFFERSUBDATANVPROC) (Display *dpy, GLXContext readCtx, GLXContext writeCtx, GLenum readTarget, GLenum writeTarget, GLintptr readOffset, GLintptr writeOffset, GLsizeiptr size); // ---------------- $ git shortlog ea7cdc4..563cc62 --no-merges Marcus D. Hanwell (1): Actually define GLX_GLXEXT_LEGACY to prevent the include git-svn-id: http://svn.slicer.org/Slicer4/trunk@23861 3bd1e089-480b-0410-8dfb-8563597acbee |
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master 1b75eefd 2015-01-08 17:23:47 Details Diff |
BUG: SliceViewAnnotation: Show scalarbar for windows < 1.0. Fixes 0003881 This will fix the bug which hides the sliceview annotations scalarbar for window width values less than 1. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23860 3bd1e089-480b-0410-8dfb-8563597acbee |
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master 4e1616ba 2015-01-08 14:59:49 Details Diff |
BUG: Don't explicitly set the OSX_DEPLOYMENT_TARGET Setting the OSX_DEPLOYMENT_TARGET implicitly controls which C++ standard library is used libstdc++ vs libc++. Mixing the two in binaries can result in unstable behavior. We now implicitly configure the OSX_SYSROOT to the latest SDK, but require the user to explicitly set the OSX_DEPLOYMENT_TARGET to ensure compatibility with the build environment. Co-authored-by: Hans Johnson <hans-johnson@uiowa.edu> Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> From: Bradley Lowekamp <blowekamp@mail.nih.gov> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23859 3bd1e089-480b-0410-8dfb-8563597acbee |
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master 90af607c 2015-01-08 14:52:08 Details Diff |
ENH: Update ITKv4, SimpleITK and Swig Co-authored-by: Hans Johnson <hans-johnson@uiowa.edu> // ------------------------------ ITKv4 changes: Alexander Schmidt-Richberg (1): ENH: Updated Remote Module VariationalRegistration to new git tag Ali Ghayoor (11): ENH: Make ITKv4 compatible with ITKSoftwareGuide ENH: Add GetCurrentStepLength to RegularStepGradDescentOptv4 ENH: Convert three ImageRegistration Examples to ITKv4 ENH: Add multi-Res and multistage registration Examples to ITKv4 ENH: Convert DeformableReg examples to ITKv4 reg framework BUG: Expand a test to reflect multi-metric registration bug BUG: Fix multi metric point sampling bug in ImageRegistrationMethodv4 ENH: Add direct initialization to SyN registration ENH: Direct initialization of SyN by restoring the state ENH: LandmarkBasedTransformInitializer supports BSplineTransformType DOC: Revise the registration examples of ITKSoftwareGuide Arnaud Gelas (15): COMP: use find_package(VTK COMPONENTS) for LevelSetsv4Visualization ENH: Importing Laplacian Deformation for QuadEdgeMesh DOC: Add more explanation about SmoothingQuadEdgeMeshFilter's usage ENH: SmoothingQuadEdgeMeshFilter::SetCoefficientMethod calls Modified() ENH: Add progress report in itk::SmoothingQuadEdgeMeshFilter COMP: missing cast when calling gdcm::DataElement::SetByteValue ENH: increase LaplacianDeformation code coverage STYLE: use typedef rather than inheritance BUG: split include directories into appropriate cmake variables HDF5 BUG: missing gdcm libraries when using system GDCM DOC: fix doxygen documentaiton for itk::LaplacianDeformationQuadEdgeMeshFilter ENH: Add one method to erase a tag into MetaDataDictionary ENH: Adding SubdivisionQuadEdgeMeshFilters to ITK as remote module COMP: address clang -Winconsistent-missing-override in ITKQuadEdgeMesh COMP: fix warnings on dashboard for Subdivision remote module Bill Lorensen (5): ENH: Specify required VTK modules COMP: Wiki examples require additional vtk modules ENH: Modify WikiExamples remote config COMP: Bad test signature COMP: Update tag for wiki examples Brad King (5): ENH: Use if(DEFINED) to simplify conditions COMP: Fix vxl_config_macros checks broken by refactoring COMP: Fix one more vxl_config_macros check broken by refactoring BUG: Fix itk_module_config for repeated calls BUG: Fix itk_module_config for repeated calls Bradley Lowekamp (51): PERF: Remove dynamically allocated temporary in evaluate method BUG: Implement ITK Style Singleton design pattern ENH: Add no throw exception specification for UnRegister methods COMP: Must specify order as "noexcept override" BUG: Add GetInverse for IdentityTransform ENH: Adding SetIdentity method to base DisplacementField class BUG: Remove unused redefinition of NULL BUG: Don't print to std::cout in PrintSelf ENH: Prefer the PrintSelfObjectMacro for printing nested objects BUG: Use METER of sCAL scale unit BUG: Use PNG_SCALE_METER for PNG sCAL unit COMP: Fix signed to unsigned int comparison ENH: Extract TiffReaderInternal to separate file ENH: Refactor ReadTwoSamplePerPixelImage into template function ENH: Refactor GenericReadImage into template function BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO ) ENH: Refactor method to convert RGBA image to output buffer ENH: Refactor duplicated code to read a page BUG: Fix right oriented tiff images BUG: Remove dead separated plannar code, add test STYLE: Fix minor kwstyle defects in test and test results BUG: Use array delete operator for array new allocations ENH: add arbitrary TIFF TAGs to meta-data dictionary ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage BUG: Address Coverity warning about null pointer dereferences ENH: Remove support for TIFF tile as 3D and dead code ENH: RGBA read images should stay unchanged. BUG: Override method to MakeOutput by name ENH: Refactor per pixel conversion function to per scan-line method PERF: Refactor color table lookup BUG: Adding missing parentheses around boolean expression ENH: adding TIFFImageIO test for RGB palette images PERF: Improve recursive Gaussian perfromance with VectorImages ENH: Query libtiff to determine compression support BUG: Support TIFF tiled image with TIFFReadRGBAImage BUG: Use SizeValueType for length of scanline PERF: Store causal results directly in output buffers COMP: Add explicit conversion to const char COMP: Explicitly add override to GetNameOfClass method COMP: Address internal segmentation fault with Intel compiler ENH: Adding method to set global physical space tolerance COMP: Explicitly add override to GetNameOfClass method BUG: Add new TypeMacro for non-overloaded classes BUG: Fix obscure race condition on access thread pool initialization BUG: Updating FDFImageIO remote module BUG: Fix segfault when setting displacement field as null BUG: Don't enable SSE rounding with OSX and gccxml BUG: Add portable access to Tiff field name BUG: Fix conversion compilation error BUG: Rename remote module FDFImageIO -> IOFDF BUG: IOFDF remote module should stay with InsightConsortium repo Christopher Mullins (22): COMP: Allows latex to compile for ITKSoftwareGuide COMP: Wrap MeshBase templates COMP: Fix warning in BlockMatchingImageFilter STYLE: Line lengths in examples should be no longer than 80 chars. COMP: Wrap the remaining MeshBase and MeshToMeshFilter types. COMP: Fix LaTeX warnings. STYLE: Fix formatting/punctuation errors. STYLE: Formatting and punctuation fixes. DOC: Edits for Book 2 Chapter 1 documentation in the Examples. DOC: Edits for book 2 chapter 2. DOC: More chapter 2 edits DOC: Book 2 Chapter 3 edits (part 1) DOC: book 2 chapter 4 Segmentation edits STYLE: Fix line length in OpenJPEG license for 80 character. DOC: Finish the ImageLinearIteratorWithIndex example. DOC: Text and picture problems, book2 BUG: Fix text in margin issues DOC: Edits for the beginning of chapter 5, Statistics DOC: Fix empty code block. DOC: Fix code overlapping figure STYLE: Keep the text in the margins STYLE: Put newline before long doxygen reference Cory Quammen (2): COMP: Avoid including VTK_USE_FILE within ITK BUG: Fix segfaults in ITKExamples Danny Perry (2): BUG: adding test for vnl_sparse_matrix::mult() BUG: size of q buffer should actually be (this->rows())*pcols. Dirk Padfield (1): BUG: Corrected processing of last sigma GCC-XML Upstream (1): ENH: pygccxml v1.6.2 (reduced) Hans Johnson (12): COMP: Add tolerance for comparing floating point PERF: Remove non-threadable algorithm components BUG: Syntax error in comment PERF: Add non-blocking mutex locking. ENH: Use TryLock minimize thread stalls BUG: ThreadedIndexedContainerPartitioner is inclusive STYLE: Remove include_regular_expression from Examples BUG: Demonstrate Inv(Inv(T)) != T BUG: Ensure Inv(Inv(T)) == T for transforms COMP: Valgrind detects uninitialized memory read COMP: Missing required base class API component ENH: Expand interface for selecting threadpool Ismael Belghiti (1): DOC: Spelling Error in PatchBasedDenoisingBaseImageFilter Jean-Christophe Fillion-Robin (1): Ensure ITKDeprecated is always excluded from the default module list. Jim Miller (1): STYLE: Removing what appears to be a temporary file Johan Andruejol (1): ENH: Fix normalization for null vectors and return the norm Jon Haitz Legarreta (1): ENH: New test for itkLabelShapeOpeningImageFilter KWSys Robot (3): KWSys 2014-09-08 (80e852f6) KWSys 2014-10-31 (88c8cc7f) KWSys 2014-11-12 (5843f590) Kent Williams (10): COMP: use find_package(VTK COMPONENTS) to specify just needed VTK Components BUG: ImageSources/test/CMakeLists.txt incorrect library var reference COMP: Fix coverity defects related to RegistrationV4 examples COMP: silence warning of vnl_vector_fixed_ref::assert_size COMP: Fix various Coverity warnings COMP: Fix a typo in an error message print statement. COMP: itk::Command-derived class used pointless dynamic_cast. PERF: Don't recompute InternalInverse repeatedly COMP: Correct orientation/spacing for Philips MultiFrame ENH: Add test to exercise issue with Transform::GetInverse Mark Hiner (2): ENH: Update SCIFIO remote module hash BUG: Fix duplicate variables in Windows Matthew McCormick (90): DOC: Fix itkSetGetDecoratedInputMacro Doxygen macro. ENH: Move FFTComplexToComplexImageFilter out of Review. ENH: Add VnlComplexToComplexFFTImageFilter. BUG: Use fixed seed for Vnl FFT tests for repeatibility. ENH: Bump CMakeLists.txt version to 4.7.0. BUG: Do not run vnl_test_na with broken libc++. DOC: Fix Software Guide page overruns in IterativeClosestPoint{1,2}.cxx. DOC: Remove duplicate text in LaplacianRecursiveGaussian example. BUG: Uninitialized m_TransformDirection in ComplexToComplexFFTImageFilter. BUG: Fix offset[2] in PointSetToSpatialObjectDemonsRegistrationTest. STYLE: Fix style in VoronoiDiagram2D. BUG: Fix invalid assignment of second VoronoiBoundaryOrigin. BUG: Remove unused m_{SplitEpsilon,SigmoidPrimeOffset}. BUG: Fix Win MultiThreader check for successful process creation. BUG: Fix VTKPolyDataMeshIO writing for 2D second rank tensor. COMP: Fix ImageRegistration8RegisteredSlice.png baseline name. DOC: itk::statistics -> itk::Statistics. COMP: Fix transform type for ITKv3/IterativeClosestPoint2. COMP: Improve const correctness of GradientRecursiveGaussianImageFilter. COMP: ThreadJob NULL not defined. COMP: Remove unused typedefs in LevelSetsv4Visualization. COMP: Remove unused typedef's in VtkGlue. ENH: Mark BSplineWarping2Test as RUNS_LONG. COMP: Remove call for non-existent variable in Nifti debugging. BUG: Close the file on Read and Write in HDF5TransformIO. BUG: Remove InsightLegacy test code from TransformHDF5Test. ENH: Add {Set,Get}TransformIO for TransformFile{Reader,Writer}. STYLE: Use SeriesUIDContainerType and FileNamesContainerType ENH: Allow specification of orthogonality tolerance in rigid transforms. BUG: TransformFileReader does not clear its TransformList. BUG: Prevent dangling pointer in HDF5TransformIO. COMP: Do not use _stat64 with MinGW-32. COMP: Address LaplacianDeformation Doxygen warnings. COMP: Do not wrap the FixedArray of Image SmartPointer's. COMP: Add missing wrapping for TransformIOBaseTemplate. COMP: Mark DeformableRegistration6Test as RUNS_LONG. BUG: Use -py3 when building wrapping for Python 3. DOC: Improve ImageRegistration4 grammar. ENH: Add IOTransformDCMTK Remote module. DOC: Add migration guide for GDCM Rescale slope intercept apply on write. COMP: Remove unused typedef's in GPU code. STYLE: Improve style of HoughTransform2DLinesImageFilter example. COMP: Use ConceptChecking for IterativeInverse dimension check. COMP: Wrap TransformIOBaseTemplate for const SmartPointer. COMP: Add warning exceptions for third party pcre, swig, gccxml. ENH: Bump ITK version to 4.6.1. BUG: Add missing ITK_OVERRIDE to ITKImageeSources module. BUG: Remove GaussianImageSource members shadowing GenerateImageSource. STYLE: Style fixes to ITKImageSources module. BUG: GaussianSpatialFunction and GaborImageSource use SpacePrecisionType. BUG: Do not perform itk_download_attempt_check when not building ITK. DOC: Update GDCMImageIO rescale slope intercept doc. BUG: Only register requestion IO COMPONENT modules. BUG: Fix wrapping .i, .idx CMake dependencies. COMP: Add VTK Python module when wrapping ITKVtkGlue. STYLE: Remove NULL definition in itkVoronoiDiagram2DGenerator. STYLE: VoronoiDiagram2DGenerator defines a VoronoiDiagramType typedef. COMP: Add missing VTK module dependency for LevelSetsv4Visualization. BUG: By default, do not create any fixed parameters. STYLE: Remove trivial method comments in itkTransform.hxx. BUG: PolylineMask Filter's GenerateData is protected / virtual. ENH: Add HigherOrderAccurateGradient Module. BUG: Use input RequestedRegion Index in SliceBySliceImageFilter internal. COMP: Remove extra semi-colon, variable scope in DCMTKFileReader. STYLE: Style fixes for Transform classes. DOC: Increase Doxygen LOOKUP_CACHE_SIZE. BUG: MatrixOffsetTransformBase::GetFixedParameters not thread safe. DOC: Index Wiki examples with Doxygen. COMP: Bump SphinxExamples remote module. DOC: Index Sphinx examples in Doxygen. COMP: Remove old java examples. COMP: Remove duplicate DiffusionTensor3DReconstruction example reference. COMP: Address GradientAnisotropicDiffusionImageFilter example settings. COMP: Bump Sphinx Examples remote. COMP: Bump WikiExamples remote. BUG: Register AzimuthElevationToCartesianTransform to factories. DOC: Update texture feature class references. BUG: Fix texture feature correlation computation for constant image. STYLE: Put ImageToImageFilterCommon in its own file. BUG: Wrap ImageToImageFilterCommon. STYLE: Put ImageSourceCommon in its own file. COMP: Add missing itkImageRegionSplitterBase to ImageSourceCommon. BUG: Reset ITK_MODULES_REQUESTED to all modules with multiple calls. BUG: Configure against VTK 5. COMP: Add ITK_SOURCE_DIR to doxygen EXAMPLE_PATH. COMP: Increase DOT_GRAPH_MAX_NODES. DOC: Add Doxygen macros for itkSetGetDecoratedObjectMacro. ENH: Warning when reading a PNG with UNKNOWN unit and non-unit spacing. BUG: Fix VTK5 module export code. BUG: Fix LevelSetsv4Visualization VTK variable names. Michka Popoff (38): ENH: Fixes for python 3 support BUG: Add VTK_VERSION for older VTK versions BUG: Improve SWIG version check COMP: Add wrapping for ThreadPool and ThreadJob COMP: Remove unimplemented DestroyPool method COMP: Fix itkVnlComplexToComplexFFTImageFilter wrapping COMP: Do not hide pygccxml warnings ENH: Update links in readme file STYLE: Remove trailing whitespaces STYLE: Set ITK_USE_SYTEM_ZLIB and ITK_USE_SYTEM_SZIP BUG: Fix memory leak in MetaImageIO after exception ENH: Add script to update pygccxml from upstream ENH: Remove Sun OS compatibility for the wrappings COMP: Fix for conversion to non-pointer like type warning STYLE: LabelObject style DOC: Remove broken link from LabelObject class description ENH: Do not setup the python tests if not asked ENH: Add new GetTypes() and GetTypesAsList() methods to the template class COMP: Fix CMP0054 warnings in wrappings STYLE: Remove old cmake < 2.8.4 specific code STYLE: Remove old cmake < 2.8.5 specific code ENH: Update to PCRE 8.36 COMP: Refactor Wrapping setup and fix legacy warnings ENH: Add wrapping configuration to ITKConfig.cmake STYLE: Some minor code cleanup in the wrapping setup DOC: Fix typo in RelabelComponentImageFilter ENH: Deprecate VectorResampleImageFilter DOC: Add migration guide for ::Zero and ::One ENH: Deprecate ::Zero and ::One ENH: Add option to disable sorting by size in itkRelabelComponentImageFilter ENH: Add Vector and RGB wrapping to linear interpolator STYLE: Remove SORT macro in wrappings COMP: Fix warning for InterpolateImageFunction wrapping COMP: Add a check for Blocks in GPU module COMP: Bump SCIFIO to fix test build warnings COMP: Fix wrapping of itkImageFunctionBase ENH: Add CVD and CVF types to VectorIndexSelectionCastImageFilter wrappings DOC: Improvements for Book1, Chap4 Nick Tustison (7): BUG: Need to explicitly specify spline order. ENH: Initializing the transform center. BUG: Need to check the dynamic cast before any calls. ENH: Adding modifications for point set metrics. BUG: Need to specify TInternalComputationValueType for default metric. ENH: Adding sparse points to B-spline field estimate. BUG: Uninitialized variables. Richard Beare (1): ENH: Include TIFF tags in the MetaDataDictionary Taylor Braun-Jones (1): BUG: Fix SliceBySliceImageFilter doesn't propagate information internally Umang B (1): ENH: Use thread pool to dispatch multithreading tasks Vivien Delmon (2): BUG: ExtractImageFilter::CollapseToSubMatrix fix ENH: Add a test on extracted directions in CollapseToSubMatrix mode Vladimir S. FONOV (1): BUG: Fixing incorrect MINC style inverse transform Ziv Yaniv (1): COMP: fixed warnings from gcc4.1.2, made implicit casts explicit // ------------------------------ SimpleITK changes: $ git shortlog f2241a13..57e6a526 --no-merges Bradley Lowekamp (199): Adding ANTS neighborhood correlation to registration method BUG: UseHistograms was not getting set on ITK filter Updating ITK tag along 4.6.0 release Hide visibility warnings Adding Compare class for transform classes. Adding basic comparison driver to compare a transformation Adding basic test of the transform compare driver Don't automatically convert to md5 hashes for files. Moving Python tests to the AdditionalTests file Update Python Examples and manual unit tests with standard DATA{} Remove the fixed image used for reference Adding TRANSFORM_COMPARE option to sitk_add_test rename cmake support file with sitk prefix Moving sitk custom add test function to separate cmake file rename variable SITK_DATA_ROOT to SimpleITK_DATA_ROOT Move python add_test wrapper to separate cmake file Moving CXX Example testing to examples directory Moving python example tests to example directory Moving Ruby Lua and TCL example tests to example directory remove check for build examples from add tests Use if COMMAND to detect if a function is defined Move Java test examples to example directory Moving R add test wrapper to common cmake file Adding missing R SimpleGaussian example Moving CSharp examples test to example directory Always allow sitk_add_?_test In test assert array is not empty Adding comparison for ImageRegistrationMethod1 example Improve CXX ImageRegistration2 Switching to JointHistogram MI metric Adding verification of for python ImageRegistrationMethod2 Adding baseline image for demons registration examples Always print dart measurement for RMSDifference Use "true" for bool values to avoid int to bool comparison warnings Adding initial Euler3DTransform class Adding Euler3DTransform to header and wrapping BUG: Add check for correct size of parameters to transforms Add virtual method to set pimple transform Core improvements to Euler3DTransform Adding comprehensive test of the Euler3DTransform. Fix some style issues with EulerTransform interface Adding specific translation transform interface Adding specific interface for the affine transform Adding specific interface for Euler2D transform Adding specific versor transform interface Adding transform interfaces for 2d and 3d similarity transforms Fix PatchBasedDenoising warning for double to in conversion Fix unused variable warning Set Scale function pointer to null Use setter methods for Euler3D constructor with values Adding skeleton test place holders for transforms Using const vector & for function object parameters Fix wrong function called for GetCenter COMP: VS11+ requires C++11 nullptr for assignment to std::function Detect C++11 nullptr keyword define SITK_NULLPTR as it or NULL Adding testing for affine transformation Adding gtest predicate and macro for tolerant vector compares completed testing for affine transformation Adding comprehensive testing for euler2d transform Fix default argument to euler2d constructor Set old function pointers to null before initializing Adding Set/GetTranslation method to Similarity3D Adding comprehensive test for Similarity3D Transform Remove reference to double for Scale variable Adding comprehensive test for similarity 2d transform Remove extra Translate method from Versor transform Adding specific interface for VersorRigid3D transform Adding tests for the versor rigid3d transform Remove pre argument for Translate methods Adding more testing for transforming points COMP: Fix operator<< for std:vector in custom gtest predicate Adding missing header files for testing Refine logic of using c++11 nullptr Adding testing for Similarity2D constructor Adding rough json file to generate initial code Adding initial generated code from json Rename CenterVersorTransformInitializer to add Filter Suffix Correct the Versor Initialization wrapping code Print parent process object and minor documentation tweaks Adding initial testing for Versor transform initializer Fixing conversion double to uint8_t conversion warning in test Improve error message for transform initializers Adding explicit constructor from base transform to vesor Moving vector testing facilities to SimpleITKTestHarness Must include test harness before gtest Moving VectorDoubleRMS Predicate to cxx file Adding inline keyword to functions in anonymous namespace Adding explicit conversion constructor to transform from base class Adding comprehensive testing for the versor initializer Explicitly use Self qualifier for virtual method in constructor Adding wrapping for ScaleSkewVersorTransform Adding comprehensive testing for ScaleSkewVersorTransform Don't take address of zero sized std::vector Move Matrix/Direction conversion function to TemplateFunctions header Adding protected constructor for derived classes to construct pimple Adding transform specific interface for bspline transforms Adding basic testing for BSplineTransform Adding testing of point transform and skew setter Adding rough json file to generate initial code Adding initial generate code from json Rename initial generated files Modify generate code for BSplineTransformInitializerFilter Adding testing for the BSplineTransfromInitalizerFilter Correct skewed point expected value Updated ITK super build to tag v4.6.0 Updating to the official ITK v4.6.0 tag Adding GetCoefficientImages method Convert <sp\> tag to a space Updating JSON doc string from ITK 4.6 with spacing corrections. Fix errors in the BSpline test Setting BSpline functions pointers to null before initialization ENH: Adding masking of fixed and moving image for registration BUG: exit with failure code when not enough arguments are specified. Adding BSpline registration examples based on ITK DeformableRegistration4 ITKv4.6 changes the results, renaming old baseline Update FFTConvolution baseline for change in origin Rename the registration tests file to sitkMethodRegistrationTests Create itk SpatialObject from image with conversion Move the logic for checking the dimensions of mask match Adding testing of mask with registration Fix miss matched parenthesizes. Fix logic in assert statement. Add basic filters library to registration ENH: Adding MultiResolutionIterationEvent Adding a Python example for multi-resolution BSpline registration Adding baseline for new bspline example Add SetIdentity method to transform interface Adding comprehensive testing for SetIdentity. Fix test not clearing string Add Transform IO support for BSpline of order 1,2,4 Addd BSpline::GetOrder method Support creation of bspline of order 1,2,3,4 Adding testing for bspline order BSplines of order 0,1,2,3 are support, not 4 Use unsigned int for bspline order type Add support for different bspline order in the initializer. Adding GetInverse method to transforms Adding doxygen comment for SetInverse Adding comprehensive testing for GetInverse method Adding missing declaration of GetInverse in PimpleTransform base Adding Transform::IsLinear method BUG: Use fix image as reference image for bspline transform Rename registration SetTransform to SetInitialTransform Adding testing for registration transform inplace option Adding documentation for SetInitialTransform method Adding new registration methods to set moving and fixed transforms Adding testing for the initial transforms Adding doxygen documentation for initialize transform methods. Fix header guarder name to match file Use helper macro to set member function pointers BUG: Delete pimple before setting Remove extra std::auto_ptr in transform pimple Adding ScaleVersorTransform interface. Adding Get/Set Matrix method to affine transform Use the transform helper set macro in versor transforms too Add GetMatrix method to matrix offset based transforms Adding implementation of GetInverse method for transform class. Adding doxygen documentation to the GetInverse method. Adding testing for transform's GetInverse method Adding testing for GetMatrix method Adding testing for transform SetMatrix method Add accessor method to get the optimizer scales. Adding doxygen documentation for the GetOptimizerScales method Adding example which utilizes center estimator and scales estimator Adding baseline images and testing for the registration3 example Adjust RMS error for displacement field for IRM3 test Updating generated documentation strings for SWIG. Manually updating R package version. Update BugReports URL for R wrapping Updating ITK Superbuild version to 4.6.1 BUG: Pass system search paths from system build to external builds Do a try import on setuptools then fall back to distutils Add setupegg.py which uses ez_setup to get setuptools When installing the wheel package use ez_setup Fix Python Download URL BUG: Adding missing cmake error variable for wheel process Replaced python execfile with python 3 compatible code Update ITK External superbuild to ITK 4.7rc01 Add export specification for instantiated Transform::InternalInitialization Fix Registration library's dependency on library with Cast filter Make BasicFilters1 library manually specified. Correctly do explicit instantiation of member function with specified linkage. Updating ITK superbuild towards 4.7rc2 Fixing conversion double to uint8_t conversion warning in test ENH: Updating JSON from ITK doxygen Revert "Updating generated documentation strings for SWIG." Add Doygen grouping to overloaded procedural methods Adds space before for ulink doxygen nodes to SWIG Updating SWIG doc strings from latest updated json files. Updating Lua Example to latest registration Update to v4.7rc01 tag for ITK superbuild Fix png inputs sCal flag Fixing png sCal field to METER Update ITK superbuild to the official 4.7.0 release Updating SimpleITK version to v0.8.1 Updating PythonDownloadPage with 0.8.1 eggs BUG: Correct check for empty string for CMake variable type Explicitly use DEFINED to check if variable is set BUG: Apply escape sequence to problematic characters. Dave Chen (3): Patch to remote -k flag for gzip Added missing commas in new JSON files DOC: Fixed spacing in the XML to JSON script David T. Chen (4): ENH: Perform download of ITK tag file during build time Changed useSeriesDetails default to false Fixed for Python 3 Added ImageRegistrationMethod1 example Ziv Yaniv (1): COMP: CMake change that ensures ITK required modules are on. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23858 3bd1e089-480b-0410-8dfb-8563597acbee |
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master 0aa1a69c 2015-01-08 12:49:00 Details Diff |
COMP: Deprecate ITK function ::Zero and ::One to fix clang link error These were deprecated in 2012; just before the ITK 4.2 release. ZeroValue() and OneValue() should be used instead. -- This coforms to ITKv4 changes made in InsightSoftwareConsortium/ITK@6c23e1da InsightSoftwareConsortium/ITK@3f712cd0 When building with clang on 10.9 where ITKv4 is a shared library, a linking error occured for unfound symbols: NumericTraits< OutputPixelType >::Zero but using the NumericTraits< OutputPixelType >::ZeroValue() allows linkage to occur properly. From: Hans Johnson <hans-johnson@uiowa.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23857 3bd1e089-480b-0410-8dfb-8563597acbee |
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master f8cb1f53 2015-01-08 00:20:22 Details Diff |
ENH: update DICOMMultiVolumePlugin Include TR and TE attributes for FA-separated multivolume nodes, as these are necessare for T1 calculation git-svn-id: http://svn.slicer.org/Slicer4/trunk@23856 3bd1e089-480b-0410-8dfb-8563597acbee |
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master f877587c 2015-01-07 18:23:53 Details Diff |
BUG: Fix Models module scrolling. Fixes 0003927 This commit partially reverts the changes to the models UI file introduced in r23788 and restore the proper functioning of the scrolling ensuring the "orientations" property of the ctkExpandableWidget is set. Co-authored-by: Alex Yarmarkovich <alexy@bwh.harvard.edu> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23855 3bd1e089-480b-0410-8dfb-8563597acbee |
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