Changesets: Import 2017-06-07 23:51:09

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master 5fd54c6d

2016-01-08 13:53:27

jcfr

Details Diff 		ENH: Add SlicerDMRI remote module

See http://slicerdmri.github.io/

The goal is to make Slicer core leaner and ultimately create a
SlicerDMRI extension

This remote module provides the following modules removed in previous
commits:

FiberBundleToLabelMap (Scripted)
DICOM2FullBrainTractography (Scripted)

TractographyDisplay (Loadable)
TractographyInteractiveSeeding (Loadable)

DiffusionTensorScalarMeasurements (CLI)
DiffusionWeightedVolumeMasking (CLI)
DWIJointRicianLMMSEFilter (CLI)
DWIRicianLMMSEFilter (CLI)
DWIToDTIEstimation (CLI)
DWIUnbiasedNonLocalMeansFilter (CLI)
DTIImportExport (CLI)
TractographyLabelMapSeeding (CLI)
FiberBundleLabelSelect (CLI)
FiberTractMeasurements (CLI)

Note that the following plugins and modules are not yet integrated
into SlicerDMRI:

ResampleDTIVolume (CLI)
ResampleScalarVectorDWIVolume (CLI)
DICOMDiffusionVolumePlugin (DICOM plugin)

Additionally, the following MRML nodes are still living in Slicer core,
they will ultimately be moved out when the infrastructure will support
it:
vtkMRMLDiffusionImageVolumeNode
vtkMRMLDiffusionTensorDisplayPropertiesNode
vtkMRMLDiffusionTensorVolumeDisplayNode
vtkMRMLDiffusionTensorVolumeNode
vtkMRMLDiffusionTensorVolumeSliceDisplayNode
vtkMRMLDiffusionWeightedVolumeDisplayNode
vtkMRMLDiffusionWeightedVolumeNode

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Isaiah Norton <inorton@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24855 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/CMakeLists.txt Diff File
mod - Modules/Loadable/CMakeLists.txt Diff File
mod - SuperBuild.cmake Diff File

master 71aa703c

2016-01-08 13:53:25

jcfr

Details Diff 		ENH: Remove FiberBundleToLabelMap Scripted module.

It will be re-added as part of SlicerDMRI remote module.

See See http://slicerdmri.github.io/

From: Isaiah Norton <inorton@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24854 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/CMakeLists.txt Diff File
rm - Modules/Scripted/FiberBundleToLabelMap/CMakeLists.txt Diff File
rm - Modules/Scripted/FiberBundleToLabelMap/FiberBundleToLabelMap.py Diff File

master 37860919

2016-01-08 13:53:23

jcfr

Details Diff 		ENH: Remove DICOM2FullBrainTractography Scripted module.

It will be re-added as part of SlicerDMRI remote module.

See See http://slicerdmri.github.io/

From: Isaiah Norton <inorton@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24853 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/CMakeLists.txt Diff File
rm - Modules/Scripted/DICOM2FullBrainTractography/CMakeLists.txt Diff File
rm - Modules/Scripted/DICOM2FullBrainTractography/DICOM2FullBrainTractography.py Diff File
rm - Modules/Scripted/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/Resources/UI/dicom2nrrd.ui Diff File
rm - Modules/Scripted/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/Resources/UI/done.ui Diff File
rm - Modules/Scripted/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/Resources/UI/dti2fibers.ui Diff File
rm - Modules/Scripted/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/Resources/UI/dwi2dti.ui Diff File
rm - Modules/Scripted/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/__init__.py Diff File
rm - Modules/Scripted/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/full_tractography_workflow.py Diff File
rm - Modules/Scripted/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/workflow_support.py Diff File
rm - Modules/Scripted/DICOM2FullBrainTractography/Testing/CMakeLists.txt Diff File
rm - Modules/Scripted/DICOM2FullBrainTractography/Testing/Python/CMakeLists.txt Diff File

master ae3b9cdc

2016-01-08 13:53:18

jcfr

Details Diff 		ENH: Remove TractographyDisplay Loadable module.

It will be re-added as part of SlicerDMRI remote module.

See See http://slicerdmri.github.io/

From: Isaiah Norton <inorton@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24852 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/CMakeLists.txt Diff File
rm - Modules/Loadable/TractographyDisplay/CMakeLists.txt Diff File
rm - Modules/Loadable/TractographyDisplay/Documentation/TractographyDisplay.dox Diff File
rm - Modules/Loadable/TractographyDisplay/Logic/CMakeLists.txt Diff File
rm - Modules/Loadable/TractographyDisplay/Logic/vtkSlicerFiberBundleLogic.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/Logic/vtkSlicerFiberBundleLogic.h Diff File
rm - Modules/Loadable/TractographyDisplay/MRML/CMakeLists.txt Diff File
rm - Modules/Loadable/TractographyDisplay/MRML/vtkMRMLFiberBundleDisplayNode.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/MRML/vtkMRMLFiberBundleDisplayNode.h Diff File
rm - Modules/Loadable/TractographyDisplay/MRML/vtkMRMLFiberBundleGlyphDisplayNode.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/MRML/vtkMRMLFiberBundleGlyphDisplayNode.h Diff File
rm - Modules/Loadable/TractographyDisplay/MRML/vtkMRMLFiberBundleLineDisplayNode.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/MRML/vtkMRMLFiberBundleLineDisplayNode.h Diff File
rm - Modules/Loadable/TractographyDisplay/MRML/vtkMRMLFiberBundleNode.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/MRML/vtkMRMLFiberBundleNode.h Diff File
rm - Modules/Loadable/TractographyDisplay/MRML/vtkMRMLFiberBundleStorageNode.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/MRML/vtkMRMLFiberBundleStorageNode.h Diff File
rm - Modules/Loadable/TractographyDisplay/MRML/vtkMRMLFiberBundleTubeDisplayNode.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/MRML/vtkMRMLFiberBundleTubeDisplayNode.h Diff File
rm - Modules/Loadable/TractographyDisplay/MRMLDM/CMakeLists.txt Diff File
rm - Modules/Loadable/TractographyDisplay/MRMLDM/vtkMRMLTractographyDisplayDisplayableManager.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/MRMLDM/vtkMRMLTractographyDisplayDisplayableManager.h Diff File
rm - Modules/Loadable/TractographyDisplay/Testing/CMakeLists.txt Diff File
rm - Modules/Loadable/TractographyDisplay/Testing/Cxx/CMakeLists.txt Diff File
rm - Modules/Loadable/TractographyDisplay/Testing/Cxx/qSlicerTractographyDisplayGlyphWidgetTest1.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/Testing/Cxx/vtkMRMLFiberBundleDisplayNodeTest1.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/Testing/Cxx/vtkMRMLFiberBundleGlyphDisplayNodeTest1.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/Testing/Cxx/vtkMRMLFiberBundleLineDisplayNodeTest1.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/Testing/Cxx/vtkMRMLFiberBundleNodeTest1.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/Testing/Cxx/vtkMRMLFiberBundleStorageNodeTest1.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/Testing/Cxx/vtkMRMLFiberBundleTubeDisplayNodeTest1.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/Testing/Data/Input/helix_roi_tract.mrml Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/CMakeLists.txt Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/Resources/UI/qSlicerTractographyDisplayBasicWidget.ui Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/Resources/UI/qSlicerTractographyDisplayGlyphWidget.ui Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/Resources/UI/qSlicerTractographyDisplayModuleWidget.ui Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/Resources/UI/qSlicerTractographyDisplayWidget.ui Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/Resources/UI/qSlicerTractographyEditorROIWidget.ui Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/qMRMLSceneTractographyDisplayModel.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/qMRMLSceneTractographyDisplayModel.h Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/qMRMLTractographyDisplayTreeView.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/qMRMLTractographyDisplayTreeView.h Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/qSlicerTractographyDisplayBasicWidget.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/qSlicerTractographyDisplayBasicWidget.h Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/qSlicerTractographyDisplayGlyphWidget.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/qSlicerTractographyDisplayGlyphWidget.h Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/qSlicerTractographyDisplayModuleWidget.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/qSlicerTractographyDisplayModuleWidget.h Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/qSlicerTractographyDisplayWidget.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/qSlicerTractographyDisplayWidget.h Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/qSlicerTractographyEditorROIWidget.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/Widgets/qSlicerTractographyEditorROIWidget.h Diff File
rm - Modules/Loadable/TractographyDisplay/qSlicerFiberBundleReader.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/qSlicerFiberBundleReader.h Diff File
rm - Modules/Loadable/TractographyDisplay/qSlicerTractographyDisplayModule.cxx Diff File
rm - Modules/Loadable/TractographyDisplay/qSlicerTractographyDisplayModule.h Diff File

master f01c97e9

2016-01-08 13:53:13

jcfr

Details Diff 		ENH: Remove TractographyInteractiveSeeding Loadable module.

It will be re-added as part of SlicerDMRI remote module.

See See http://slicerdmri.github.io/

From: Isaiah Norton <inorton@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24851 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/CMakeLists.txt Diff File
rm - Modules/Loadable/TractographyInteractiveSeeding/CMakeLists.txt Diff File
rm - Modules/Loadable/TractographyInteractiveSeeding/Documentation/TractographyInteractiveSeeding.dox Diff File
rm - Modules/Loadable/TractographyInteractiveSeeding/Logic/CMakeLists.txt Diff File
rm - Modules/Loadable/TractographyInteractiveSeeding/Logic/vtkMRMLTractographyInteractiveSeedingNode.cxx Diff File
rm - Modules/Loadable/TractographyInteractiveSeeding/Logic/vtkMRMLTractographyInteractiveSeedingNode.h Diff File
rm - Modules/Loadable/TractographyInteractiveSeeding/Logic/vtkSlicerTractographyInteractiveSeedingLogic.cxx Diff File
rm - Modules/Loadable/TractographyInteractiveSeeding/Logic/vtkSlicerTractographyInteractiveSeedingLogic.h Diff File
rm - Modules/Loadable/TractographyInteractiveSeeding/Resources/UI/qSlicerTractographyInteractiveSeedingModuleWidget.ui Diff File
rm - Modules/Loadable/TractographyInteractiveSeeding/Testing/CMakeLists.txt Diff File
rm - Modules/Loadable/TractographyInteractiveSeeding/Testing/qSlicerTractographyInteractiveSeedingModuleWidgetTest1.cxx Diff File
rm - Modules/Loadable/TractographyInteractiveSeeding/Testing/qSlicerTractographyInteractiveSeedingModuleWidgetTest2.cxx Diff File
rm - Modules/Loadable/TractographyInteractiveSeeding/qSlicerTractographyInteractiveSeedingModule.cxx Diff File
rm - Modules/Loadable/TractographyInteractiveSeeding/qSlicerTractographyInteractiveSeedingModule.h Diff File
rm - Modules/Loadable/TractographyInteractiveSeeding/qSlicerTractographyInteractiveSeedingModuleWidget.cxx Diff File
rm - Modules/Loadable/TractographyInteractiveSeeding/qSlicerTractographyInteractiveSeedingModuleWidget.h Diff File

master c33065b9

2016-01-08 13:53:09

jcfr

Details Diff 		ENH: Remove DiffusionTensorScalarMeasurements CLI module.

It will be re-added as part of SlicerDMRI remote module.

See See http://slicerdmri.github.io/

From: Isaiah Norton <inorton@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24850 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/CMakeLists.txt Diff File
rm - Modules/CLI/DiffusionTensorScalarMeasurements/CMakeLists.txt Diff File
rm - Modules/CLI/DiffusionTensorScalarMeasurements/DiffusionTensorScalarMeasurements.cxx Diff File
rm - Modules/CLI/DiffusionTensorScalarMeasurements/DiffusionTensorScalarMeasurements.xml Diff File
rm - Modules/CLI/DiffusionTensorScalarMeasurements/Testing/CMakeLists.txt Diff File
rm - Modules/CLI/DiffusionTensorScalarMeasurements/Testing/DiffusionTensorScalarMeasurementsTest.cxx Diff File

master d43ad9e5

2016-01-08 13:53:07

jcfr

Details Diff 		ENH: Remove DiffusionWeightedVolumeMasking CLI module.

It will be re-added as part of SlicerDMRI remote module.

See See http://slicerdmri.github.io/

From: Isaiah Norton <inorton@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24849 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/CMakeLists.txt Diff File
rm - Modules/CLI/DiffusionWeightedVolumeMasking/CMakeLists.txt Diff File
rm - Modules/CLI/DiffusionWeightedVolumeMasking/Data/Baseline/DiffusionWeightedVolumeMaskingTest_EstimatedBaseline.nhdr Diff File
rm - Modules/CLI/DiffusionWeightedVolumeMasking/Data/Baseline/DiffusionWeightedVolumeMaskingTest_EstimatedBaseline.raw.gz Diff File
rm - Modules/CLI/DiffusionWeightedVolumeMasking/Data/Baseline/DiffusionWeightedVolumeMaskingTest_OtsuThresholdMask.nhdr Diff File
rm - Modules/CLI/DiffusionWeightedVolumeMasking/Data/Baseline/DiffusionWeightedVolumeMaskingTest_OtsuThresholdMask.raw.gz Diff File
rm - Modules/CLI/DiffusionWeightedVolumeMasking/DiffusionWeightedVolumeMasking.cxx Diff File
rm - Modules/CLI/DiffusionWeightedVolumeMasking/DiffusionWeightedVolumeMasking.xml Diff File
rm - Modules/CLI/DiffusionWeightedVolumeMasking/Testing/CMakeLists.txt Diff File
rm - Modules/CLI/DiffusionWeightedVolumeMasking/Testing/DiffusionWeightedVolumeMaskingTest.cxx Diff File

master 6ce78500

2016-01-08 13:53:04

jcfr

Details Diff 		ENH: Remove DWIJointRicianLMMSEFilter CLI module.

It will be re-added as part of SlicerDMRI remote module.

See See http://slicerdmri.github.io/

From: Isaiah Norton <inorton@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24848 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/CMakeLists.txt Diff File
rm - Modules/CLI/DWIJointRicianLMMSEFilter/CMakeLists.txt Diff File
rm - Modules/CLI/DWIJointRicianLMMSEFilter/DWIJointRicianLMMSEFilter.cxx Diff File
rm - Modules/CLI/DWIJointRicianLMMSEFilter/DWIJointRicianLMMSEFilter.xml Diff File
rm - Modules/CLI/DWIJointRicianLMMSEFilter/LMMSE.cxx Diff File
rm - Modules/CLI/DWIJointRicianLMMSEFilter/Testing/CMakeLists.txt Diff File
rm - Modules/CLI/DWIJointRicianLMMSEFilter/itkComputeRestrictedHistogram.h Diff File
rm - Modules/CLI/DWIJointRicianLMMSEFilter/itkComputeRestrictedHistogram.txx Diff File
rm - Modules/CLI/DWIJointRicianLMMSEFilter/itkLMMSEVectorImageFilter.h Diff File
rm - Modules/CLI/DWIJointRicianLMMSEFilter/itkLMMSEVectorImageFilter.txx Diff File
rm - Modules/CLI/DWIJointRicianLMMSEFilter/itkOtsuStatistics.h Diff File
rm - Modules/CLI/DWIJointRicianLMMSEFilter/itkOtsuStatistics.txx Diff File
rm - Modules/CLI/DWIJointRicianLMMSEFilter/itkOtsuThreshold.h Diff File
rm - Modules/CLI/DWIJointRicianLMMSEFilter/itkOtsuThreshold.txx Diff File

master 8564603b

2016-01-08 13:53:01

jcfr

Details Diff 		ENH: Remove DWIRicianLMMSEFilter CLI module.

It will be re-added as part of SlicerDMRI remote module.

See See http://slicerdmri.github.io/

From: Isaiah Norton <inorton@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24847 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/CMakeLists.txt Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/CMakeLists.txt Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/DWIRicianLMMSEFilter.cxx Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/DWIRicianLMMSEFilter.xml Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/LMMSE.cxx Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/Testing/CMakeLists.txt Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/itkComputeRestrictedHistogram.h Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/itkComputeRestrictedHistogram.txx Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/itkComputeStatisticsWherePositiveFilter.h Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/itkComputeStatisticsWherePositiveFilter.txx Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/itkExtractVolumeFilter.h Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/itkExtractVolumeFilter.txx Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/itkLMMSEVectorImageFilter.h Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/itkLMMSEVectorImageFilter.txx Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/itkLMMSEVectorImageFilterStep.h Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/itkLMMSEVectorImageFilterStep.txx Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/itkMaskedMeanImageFilter.h Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/itkMaskedMeanImageFilter.txx Diff File
rm - Modules/CLI/DWIRicianLMMSEFilter/itkVectorImageCastFilter.h Diff File

master e9e8e152

2016-01-08 13:52:58

jcfr

Details Diff 		ENH: Remove DWIToDTIEstimation CLI module.

It will be re-added as part of SlicerDMRI remote module.

See See http://slicerdmri.github.io/

From: Isaiah Norton <inorton@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24846 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/CMakeLists.txt Diff File
rm - Modules/CLI/DWIToDTIEstimation/CMakeLists.txt Diff File
rm - Modules/CLI/DWIToDTIEstimation/DWIToDTIEstimation.cxx Diff File
rm - Modules/CLI/DWIToDTIEstimation/DWIToDTIEstimation.xml Diff File
rm - Modules/CLI/DWIToDTIEstimation/Testing/CMakeLists.txt Diff File
rm - Modules/CLI/DWIToDTIEstimation/Testing/DWIToDTIEstimationTest.cxx Diff File

master 5ce74478

2016-01-08 13:52:56

jcfr

Details Diff 		ENH: Remove DWIUnbiasedNonLocalMeansFilter CLI module.

It will be re-added as part of SlicerDMRI remote module.

See See http://slicerdmri.github.io/

From: Isaiah Norton <inorton@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24845 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/CMakeLists.txt Diff File
rm - Modules/CLI/DWIUnbiasedNonLocalMeansFilter/CMakeLists.txt Diff File
rm - Modules/CLI/DWIUnbiasedNonLocalMeansFilter/DWIUnbiasedNonLocalMeansFilter.cxx Diff File
rm - Modules/CLI/DWIUnbiasedNonLocalMeansFilter/DWIUnbiasedNonLocalMeansFilter.xml Diff File
rm - Modules/CLI/DWIUnbiasedNonLocalMeansFilter/Testing/CMakeLists.txt Diff File
rm - Modules/CLI/DWIUnbiasedNonLocalMeansFilter/UNLM.cxx Diff File
rm - Modules/CLI/DWIUnbiasedNonLocalMeansFilter/itkComputeRestrictedHistogram.h Diff File
rm - Modules/CLI/DWIUnbiasedNonLocalMeansFilter/itkComputeRestrictedHistogram.txx Diff File
rm - Modules/CLI/DWIUnbiasedNonLocalMeansFilter/itkOtsuStatistics.h Diff File
rm - Modules/CLI/DWIUnbiasedNonLocalMeansFilter/itkOtsuStatistics.txx Diff File
rm - Modules/CLI/DWIUnbiasedNonLocalMeansFilter/itkOtsuThreshold.h Diff File
rm - Modules/CLI/DWIUnbiasedNonLocalMeansFilter/itkOtsuThreshold.txx Diff File
rm - Modules/CLI/DWIUnbiasedNonLocalMeansFilter/itkUNLMFilter.h Diff File
rm - Modules/CLI/DWIUnbiasedNonLocalMeansFilter/itkUNLMFilter.txx Diff File

master 57cf08a9

2016-01-08 13:52:54

jcfr

Details Diff 		ENH: Remove DTIImportExport CLI module.

It will be re-added as part of SlicerDMRI remote module.

See See http://slicerdmri.github.io/

From: Isaiah Norton <inorton@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24844 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/CMakeLists.txt Diff File
rm - Modules/CLI/DTIImportExport/CMakeLists.txt Diff File
rm - Modules/CLI/DTIImportExport/DTIexport.cxx Diff File
rm - Modules/CLI/DTIImportExport/DTIexport.xml Diff File
rm - Modules/CLI/DTIImportExport/DTIimport.cxx Diff File
rm - Modules/CLI/DTIImportExport/DTIimport.xml Diff File
rm - Modules/CLI/DTIImportExport/Testing/CMakeLists.txt Diff File

master 06f8dd41

2016-01-08 13:52:51

jcfr

Details Diff 		ENH: Remove TractographyLabelMapSeeding CLI module.

It will be re-added as part of SlicerDMRI remote module.

See See http://slicerdmri.github.io/

From: Isaiah Norton <inorton@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24843 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/CMakeLists.txt Diff File
rm - Modules/CLI/TractographyLabelMapSeeding/CMakeLists.txt Diff File
rm - Modules/CLI/TractographyLabelMapSeeding/Testing/CMakeLists.txt Diff File
rm - Modules/CLI/TractographyLabelMapSeeding/Testing/TractographyLabelMapSeedingTest.cxx Diff File
rm - Modules/CLI/TractographyLabelMapSeeding/TractographyLabelMapSeeding.cxx Diff File
rm - Modules/CLI/TractographyLabelMapSeeding/TractographyLabelMapSeeding.xml Diff File

master d8ddc52b

2016-01-08 13:52:49

jcfr

Details Diff 		ENH: Remove FiberBundleLabelSelect CLI module.

It will be re-added as part of SlicerDMRI remote module.

See See http://slicerdmri.github.io/

From: Isaiah Norton <inorton@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24842 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/CMakeLists.txt Diff File
rm - Modules/CLI/FiberBundleLabelSelect/CMakeLists.txt Diff File
rm - Modules/CLI/FiberBundleLabelSelect/Data/Baseline/selectedfibersbaseline.vtk Diff File
rm - Modules/CLI/FiberBundleLabelSelect/Data/Input/mask.nrrd Diff File
rm - Modules/CLI/FiberBundleLabelSelect/Data/Input/tractography.vtk Diff File
rm - Modules/CLI/FiberBundleLabelSelect/Data/Input/tractography.vtp Diff File
rm - Modules/CLI/FiberBundleLabelSelect/FiberBundleLabelSelect.cxx Diff File
rm - Modules/CLI/FiberBundleLabelSelect/FiberBundleLabelSelect.xml Diff File
rm - Modules/CLI/FiberBundleLabelSelect/Testing/CMakeLists.txt Diff File
rm - Modules/CLI/FiberBundleLabelSelect/Testing/CompareTensorMeasure.cxx Diff File
rm - Modules/CLI/FiberBundleLabelSelect/Testing/FiberBundleLabelSelectTest.cxx Diff File

master 68c6ef2b

2016-01-08 13:52:46

jcfr

Details Diff 		ENH: Remove FiberTractMeasurements CLI module.

It will be re-added as part of SlicerDMRI remote module.

See See http://slicerdmri.github.io/

From: Isaiah Norton <inorton@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24841 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/CMakeLists.txt Diff File
rm - Modules/CLI/FiberTractMeasurements/CMakeLists.txt Diff File
rm - Modules/CLI/FiberTractMeasurements/FiberTractMeasurements.cxx Diff File
rm - Modules/CLI/FiberTractMeasurements/FiberTractMeasurements.xml Diff File

master b12cc450

2016-01-08 10:36:25

fedorov

Details Diff 		ENH: update MultiVolumeImporting

This update should resolve the regression introduced by 0000440 and improves
robustness by not returning multivolumes that have single frames when parsed
based on ImagePositionPatient+AcquisitionTime.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24840 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master 95443f23

2016-01-08 08:14:29

jcfr

Details Diff 		ENH: Update CTKAppLauncher to support build with older version of CentOS 5

The launcher is build with an old version of CentOS 5, which has a very
old version of glibc, to ensure better binary executable compatibility.

Co-authored-by: Matt McCormick <matt.mccormick@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24839 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTKAPPLAUNCHER.cmake Diff File

master 311dc32a

2016-01-07 23:44:03

jcfr

Details Diff 		BUG: Update CTKAppLauncher to avoid startup warning reported on Window >= 7

This commit updates the version of the launcher windows binaries to a new
package built against Qt4.8.6 instead of Qt 4.7.4. It will avoid to get
the startup time error message like the one report below:

Untested Windows version 6.3 detected!

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24838 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTKAPPLAUNCHER.cmake Diff File

master f06d2800

2016-01-07 22:15:10

jcfr

Details Diff 		BUG: Update CTK to include DICOMDIR parsing fix

$ git shortlog 5f58132..caaf2c8 --no-merges

Andras Lasso (1):
ENH: Added error logging to DICOMDIR file parsing

Andreas Fetzer (1):
Fixed error when fetching files if resource has no name

Caspar Goch (1):
Extend the convenience run method to accept cl args

Daniel Knorr (3):
Added conditions for subject and experiment. If no ID is set, then the label is used now in the resource uri.
Creating of subjects works without ID now so setId is not neccessary anymore. The ID of a subject should be created by XNAT itself. This rule also is effective to the ID of an experiment.
If the identifierPattern.exactMatch-CASE is used, the map has 2 entries (ID, content). Now the ID is set to a lately created object. content is unused.

Julien Finet (1):
Support Qt 5.5 compilation

Nicole Aucoin (1):
BUG: Add pointfile element

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24837 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTK.cmake Diff File

master 767e824c

2016-01-07 22:15:08

jcfr

Details Diff 		ENH: Update ITKv4 to v4.9.0 release branch

$ git shortlog 0305504..51760b2 --no-merges

Adam Snyder (1):
PERF: Reworked MMI Threading using a per-thread buffer

Alexander Leinoff (6):
ENH: Adds IsInteger and IsSigned to NumericTraits.
COMP: Doxygen itkMath.h 'OneValue()' could not be resolved.
ENH: Adds ExactlyEquals and NotExactlyEquals functions to itkMath.h
COMP: Removes floating-point equality checks
ENH: COMP: Adds support for complex values to Math::AlmostEquals
ENH: Updates fftw dependency

Alexis Girault (1):
BUG: Implement SetAutoMinimumMaximum in itkScalarImageToHistogramGenerator

Arnaud Gelas (5):
COMP: fix warning (unused local typedef)
COMP: simplify ITKVideoBridgeOpenCV dependency
DOC: add doxgen documentation for BinaryImageToLevelSetImageAdaptor
ENH: add tests to exercise itk::ThreadedIteratorRangePartitioner
COMP: fix compilation error with OpenCV2 and OpenCV3

Betsy McPhail (1):
BUG: Improve buffer alignment in OctreeNode .

Bill Hoffman (7):
ENH: Use new CMake Windows export symbol dll feature.
COMP: Put vnl_export.h in the list of sources so it gets installed.
COMP: Put vnl_export.h in the list of sources so it gets installed.
COMP: Put vnl_export.h in the list of sources so it gets installed.
COMP: fix 64 bit build warnings with windows auto-export on.
COMP: work around for VS 2015 optimizer bug causing test failures.
COMP: work around for VS 2015 optimizer bug causing test failures.

Bill Lorensen (6):
COMP: VTkGlue linker errors
BUG: Inappropriate use of AlmostEquals
ENH: Bump tag for wiki examples
ENH: Better layout strategy
BUG: Valgrind detected an invalid read
BUG: nifti_read_subregion_image was leaking file pointers

Brad King (10):
ENH: Remove use of include <itksys/ios/*> and itksys_ios::*
ENH: Remove use of include <itksys/stl/*> and itksys_stl::*
ENH: Update CMake Policy settings in Testing/TestExternal project
ENH: Teach ITK module macros to support independent header-only modules
ENH: Add script to import KWIML library source code
ENH: Add `ITKKWIML` module to provide external KWIML library
ENH: Port TIFF integer types from KWSys to KWIML
ENH: Port LSM integer types from KWSys to KWIML
ENH: Port itkIntTypes.h from KWSys to KWIML
ENH: Drop KWSys FundamentalType component

Bradley Lowekamp (29):
BUG: Avoid null deference in PrintSelf with default construction
ENH: Enable base classes for templates of landmark initializer
STYLE: Use "Swap" for ITK member name
BUG: Demonstrate Eigen analysis failure
BUG: Fix computation of Eigen analysis
ENH: Update DiscreteHessianGaussian Test baseline
ENH: Correctly demonstrate float point Eigen failure
ENH: compile vnl_math_hypot, and use at least double
ENH: Adding initial update script from used libpng version.
ENH: removing non-subtree files for itkpng
ENH: Ported ITK changes for building to subtree merged code
ENH: Update libpng update script for v1.6.9
BUG: Use ParameterValueType for computation of landmark affine
ENH: Wrap LandmarkBasedTransformInitializer
BUG: Avoid potential exception in itk::Object::UnRegister
ENH: Update itkpng zlib, configuration, and rename
ENH: Update itkpng name mangling
BUG: Use const pointer in Set method for constant ReferenceImage ivar
BUG: Increase tolerance for PhysicsBasedNonRigidRegistrationMethod
BUG: Demonstrate side effect on registration due to BSplineScatter change
ENH: Move MovingHistogramImageFilter base classes to ImageFilterBase
ENH: Optimize AdaptiveHistogramEqualization with MovingHistogram base
COMP: address sign unsigned comparison warning
COMP: Address signed unsigned comparison warning
COMP: Address unused member variable and methods in anonymous ns
BUG: Fix segfault when with empty IsolatedWatershed Threshold range
BUG: Adjust intensity tolerance for PhysicsBasedNonRigid test
BUG: Reduce number of targets with MSVC
ENH: Add option to choose scheme for git download

Davis Vigneault (7):
DOC: Minor improvements to segmentation examples.
DOC: Expanded Canny Edge Detection Example
COMP: Warnings in FFTW Classes when compiling with c++11
COMP: Update Git Tag for Subdivision Module
STYLE: Address some warnings when running cppcheck
STYLE: Use cstdlib return macros in ITK examples
COMP: Include itkMacro.h in itkTestingMacros.h

Dženan Zukić (4):
STYLE: better formatting of the "usage" message
BUG: do not pass 0,0,0 to Versor.Set()
STYLE: Removing the unused NeighborhoodRadius property
ENH: Write out transform in DeformableRegistration15

Eugene Prilepin (1):
BUG: Fix a template name formation in python wrappings

Floris Berendsen (1):
STYLE: Improve naming conventions in comments.

Gert Wollny (1):
BUG: Remove double-conversion from public interface, use system.

Hans Johnson (24):
STYLE: Instrument for FixedParameters typedef
BUG: Demonstrate DisplacementTransformFailure
BUG: FixedParameters should be double precision
STYLE: Minor code style issues for MGHIO
COMP: Update to version for WikiExamples
ENH: Update Sphinx for ITK 4.8.0
ENH: Update MGHIO to be shared lib
ENH: Provide consistent floating point comparisons
BUG: Fix MGHIO to fix write failures
PERF: Remove floating point as sentinal value
COMP: Const correctness needs to be maintained
BUG: Preserve backwards compatibility
DOC: Provide consistent naming in comments
ENH: Conversion between transform type tolerance
STYLE: Prefer initialization to assignment
ENH: Missing ITK_OVERRIDE
COMP: Need to propagate ITKGDCM
COMP: Need to propagate ITKGDCM
COMP: Add missing ITK_OVERRIDE
ENH: C++11 allows for rigorous =delete
COMP: Remove unnecessary failing assert test
ENH: Ignore internal files for the Clion editor
COMP: Fix VNL compilation for wider C++11 support
BUG: In configuration test need to mirror code

Hyun Jae Kang (49):
BUG: Remove std::cout calls from class
BUG: Avoid an unexpected output of static_cast
BUG: Update python example codes for ImageRegistration
BUG: Retrieve the missed wrap file
BUG: itkVTKImageIO class does not handle blank lines in VTK file header.
BUG: Fix a compilation issue on ITK4 with FFTW and shared libraries
BUG: Fixed older XCode linking error
ENH: Use CastXML binaries when building with x86_64 Mac OS X
BUG: Remove std::cout calls from class
BUG: itkVTKImageIO class does not handle blank lines in VTK file header.
BUG: Fixed older XCode linking error
ENH: Add automatic KWStyle build and configuration setup
COMP: KWStyle shadow, format-nonliteral and autological-compare warning.
COMP: Fixed the warning messages from itkGPU Module
COMP: Fixed a warning message of unused-private-field
COMP: Apply latest version of KWStyle
COMP: Update KWStyle to fix its additional warning messages
COMP: Update KWStyle to fix its additional warning messages
COMP: Fix data-conversion warning messages on Windows
ENH: Update itkResourceProbe to calculate statistical data
COMP: Fix data-conversion warning messages on VS14
COMP: Fixed 'std::sqrt' : ambiguous call to overloaded function
ENH: Update the Report() function of itkResourceProbesCollectorBase
COMP: Fix data-conversion warning message on itkResourceProbe
COMP: Fix additional warning messages of KWStyle
COMP: Fix data-conversion warning messages
COMP: Fixed a warning message of data-conversion on VS14
COMP: Update KWStyle to remove format-string warning message
ENH: Use a data struct to export the system information of a probe.
ENH: Create a test for the SpawnThread function ( ITK-3317)
STYLE: Remove an unnecessary file (-w) from source code
COMP: Revert itkResourceProbe to its previous version
BUG: Fixed the failed case of itkStdStreamStateSaveTest on OS X 10.8
BUG: Fixed the failed test case of itkThreadPoolTest on OS X 10.8
BUG: Fixed a failed test of ITKDistanceMapTestDriver
BUG: Fixed the failed test VideoSourceTest
PERF: Improve the performance of a test of ITKRegistrationMethodsv4TestDriver
COMP: Fixed the compiler error of itkDisplacementFieldToBSplineImageFilterTest
COMP: Fixed the compiler error of ITKCommon2TestDriver on OSX 10.6
BUG: Fixed the runtime crash of vnl_test_complex on OSX 10.6
BUG: Fixed the runtime crash of itkTimeProbeTest2
BUG: Fixed the runtime crash of VideoSourceTest on OSX 10.6
BUG: Fixed the runtime crash of ITKReviewTestDriver on OSX 10.6
BUG: Fixed the runtime crash of ITKFastMarchingTestDriver's tests on OSX 10.6
COMP: Fixed the data conversion warning messages of itkResourceProbe
BUG: Fixed the runtime crash of ITKStatisticsTestDriver tests on OSX 10.6
BUG: Fixed the runtime crash of itkBinaryShapeOpeningImageFilterTest1
BUG: Fixed the runtime crash of test_pow_log on OSX 10.6
BUG: Fixed the runtime crash of vnl_test_numeric_traits

Jean-Christophe Fillion-Robin (26):
BUG: Build ITKIOTransformHDF5 as shared library. See 0003393
BUG: Build ITKIOTransformMINC as shared library. See 0003393
BUG: Build ITKIOTransformMatlab as shared library. See 0003393
BUG: Build ITKIOTransformInsightLegacy as shared library. See 0003393
STYLE: TransformIOFactory: Remove obsolete declaration. See 0003393
COMP: TransformIOFactory: Add missing ctor/dtor from hxx file. See 0003393
COMP: TransformFileWriter: Remove method "OpenStream()" without definition
COMP: TransformFileReaderTemplate: Remove undefined method "CreateTransform()"
ENH: Update ITKIOPhilipsREC to allow static initialization. See 0003393
ENH: Update ITKIOTransformMINC to allow static initialization. See 0003393
COMP: MINC: Fix VS2008 "unknown round" build error. See 0003393
COMP: MINC: Fix VS2008 "unknown arpa/inet.h" build error. See 0003393
COMP: Configure ENABLE_SHARED into <ModuleName>.cmake file. See 0003393
COMP: Fix configuration of IOFactory header. See 0003393
STYLE: UseITK: Removed redundant code setting ImageIO factory name. See 0003393
STYLE: UseITK: Re-factor introducing _configure_IOFactoryRegisterManager
STYLE: UseITK: Set TransformIO factory and module name using convention.
BUG: Ensure Image IO factories are registered once. See 0003393
BUG: Ensure Transform IO factories are registered once.
COMP: ITKIOXML: Fix VS11 "already defined std::string" link error. See 0003393
BUG: TransformIO: Implement explicit template instantiation using "extern".
COMP: TransformIO: Fix VS build errors removing extra EXPORT
COMP: TransformIO: Handle compiler not supporting "pragma diagnostic".
COMP: TransformIO: TransformFile(Reader|Writer) still need to be exported.
COMP: TransformIO: Fix explicit instantiation approach
COMP: Fix Slicer MacOSX extension packaging setting CMP0042 policy to OLD

Johan Andruejol (1):
ENH: Add ITK_RUNTIME_LIBRARY_DIRS for external projects

Jon Haitz Legarreta (6):
ENH: Add test for itkStatisticsUniqueLabelMapFilter
BUG: Fix compilation issues for StatisticsUniqueLabelMapFilterTest
BUG: Fix comparison issues for itkStatisticsUniqueLabelMapFilter
BUG: Test for StatisticsUniqueLabelMapFilter stability
ENH: Add test for itkParametricStpaceToImageSpaceFilter
ENH: Improve code coverage for itkParametricSpaceToImageSpaceMeshFilter

Julien Michel (1):
ENH: Support of VectorImage as template parameters for WarpImageFilter

Junjie Bai (2):
BUG: ConvertLabelMap with different LabelMapTypes
BUG: LabelObject CopyAttribute support different LabelObject type

KWIML Upstream (1):
KWIML 2015-12-09 (43f9f8d0)

KWSys Robot (4):
KWSys 2015-07-10 (c9336bcf)
KWSys 2015-07-30 (f63febb7)
KWSys 2015-08-24 (cdaf522c)
KWSys 2015-08-28 (dc3fdd7f)

LIBPNG Upstream (2):
PNG 2009-04-06 (e68f5a36)
PNG 2014-02-05 (3e753eb8)

Laurentiu Nicola (2):
PERF: Avoid temporary smartptr in ProcessObject::GetInput
PERF: Optimize WarpImageFilter by avoiding refcount bouncing

Luc Hermitte (8):
PERF: itk::Image::GetPixel() performance improvment.
PERF: Performance enhancements on VariableLengthVectors 1/...
ENH: Dependencies on itkVariableLengthVector.h reduced
BUG: Error in VariableLengthVector Unit Tests
PERF: Performance enhancements on VLV 2/...
PERF: Performances enhancements on VLV 3/...
COMP: Fix signed/unsigned warnings
BUG: std::copy/fill on empty VLV

Lucas Gandel (5):
ENH: Move ImageToPathFilter from ITKReview to ITKPath module.
BUG: Fixing ImageToPathFilter wrapping call from Review Module
STYLE: Fix KWStyle dashboard errors
BUG: Fix external module BUILD_SHARED_LIBS status
BUG: PhysicsBasedNonRigidRegistrationMethod test failure on Debian 32bit

Mathieu Malaterre (1):
BUG: Name mangle the included expat third party library.

Matthew McCormick (100):
ENH: Change itkSystemInformationTest to itkCMakeConfigurationTest.
ENH: Add AnisotropicDiffusionLBR Remote Module.
ENH: Bump ITK version to 4.9.0.
BUG: Remove std::cout calls from classes.
COMP: Remove unused argument in ConditionVariableNoThreads.
COMP: Add link interface specification for wrapping target_link_libraries.
STYLE: Fix indentation in itkMINCTransformIOFactory.cxx.
COMP: Fix MINCTransformIO factory registration.
COMP: Add -D_LARGEFILE64_SOURCE for HDF5 with Emscripten-1.
COMP: Remove unknown doxygen command in AnisotropicDiffusionLBR.
ENH: Use CastXML binaries when building with x86_64 Linux.
STYLE: Rename gccxml -> castxml in {idx,igenerator}.py.
ENH: Use Windows binaries for CastXML.
ENH: Add better scoping in igenerator.py.
BUG: Fix CMAKE_BUILD_TYPE initialization with Ninja + MSVC.
BUG: LevelSetsv4 used signed char instead of char.
ENH: Add better scoping to idx.py.
COMP: Define newSize and oldSize in VariableLengthVector.
STYLE: Use prefix increment operator in ImageBase.
DOC: Correct spelling of Continuous.
ENH: Add more progress information to IterativeClosestPoint2.
ENH: Add ITKModuleExternal.cmake
COMP: Wrap Image< bool, D > for FlatStructuringElement.
BUG: Use CastXML binary built in Release.
BUG: ContinuousIndex should not be templated over TCoordRep.
COMP: Set CMP0054 to new.
COMP: Address line length too long for Software Guide.
COMP: Fix CannyEdgeDetectionImageFilter.cxx types.
BUG: Replace __GCCXML__ with CABLE_CONFIGURATION.
ENH: Allow projects to build against an external module.
ENH: Replace CABLE_CONFIGURATION with ITK_WRAPPING_PARSER.
ENH: Rename _cable_ to _wrappers_.
BUG: Define ITK_WRAPPING_PARSER when wrapping.
BUG: Pass the CMAKE_CXX_FLAGS to castxml.
ENH: Bump CastXML version to 2015-30-29.
ENH: Bump LLVM / Clang to 3.7.0.
COMP: Avoid itklibminc linking with ITK_USE_SYSTEM_HDF5.
COMP: Add missing ITKIOImageBase dependency for ITKTransformMINC.
COMP: Use itkSimpleNewMacro in ThreadedIteratorRangePartitionerTest.
ENH: Add wrapping support for building modules externally.
BUG: Fix KWStyle test paths when building a module externally.
ENH: Add Cuberille Remote module.
COMP: Remove carriage returns from Cuberille remote.
ENH: Bump the MinimalPathExtraction Remote to 2015-10-20.
COMP: Fix KernelTransform SetFixedParameters argument type.
COMP: Use ITK's pygccxml by correctly setting up the sys.path
Revert "COMP: Put vnl_export.h in the list of sources so it gets installed."
BUG: Revert "BUG: ConvertLabelMap with different LabelMapTypes"
ENH: Marking wrapping CMake configuration variables as advanced.
STYLE: Rename CASTXML to CASTXML_EXECUTABLE.
COMP: Non-virtual copy attribute members in LabelMap cannot have override.
COMP: Add wrapping for AdaptiveHistogramEqualizationImageFilter.
COMP: Add itkMacro.h to itkPromoteType.h for ITK_EXCEPT.
ENH: Remove CMake version check in ITKModuleHeaderTest.cmake
BUG: Improve KWStyle ExternalProject utilization.
ENH: Remove old KWStyle build script.
COMP: Address VariableLengthVector Doxygen rhs @param not found.
ENH: Rename WRAPPING_LIBRARY_GROUPS to WRAPPING_SUBMODULE_ORDER.
ENH: Install Python bindings into site-packages.
ENH: Improve readability of Python site-packages path detection.
COMP: DiscreteGaussianDerivativeImageFilter unsigned expression warning.
BUG: ITKCommon publically depends on ITKDoubleConversion.
COMP: Improve scoping in CovariantVectorGeometryTest.
ENH: Improves names and export of module dependencies.
STYLE: Improve namespace bracket style in itkIsConvertible.
COMP: Set CMP0054 to new.
BUG: Remove unused wrapping files.
BUG: Do install install wrapping development files.
ENH: Add WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER.
BUG: Remove duplicate inclusion of wrapping submodules.
COMP: Do not use C++ style comments for Doxygen cond.
BUG: Fix detection of the gold linker.
BUG: Update Python package installation locations.
ENH: Bump CMakeLists.txt version to 4.8.2.
ENH: Change BUILD_EXAMPLES default to OFF.
BUG: Use 'from itk import ITKCommon' in module2module test.
COMP: Link to VTK Python when built with Kits support.
BUG: Install itk_minc2.h header.
COMP: ITKIOMINC has a public dependency on ITKIOImageBase.
DOC: Remove invalid wrapping example.
BUG: Wrap AdaptiveEqualizationHistogram.
COMP: Ignore Doxygen endcond warning in itkIsConvertible.h.
COMP: Fix PointDimension reference in AzimuthElevationToCartesian test.
STYLE: Improve scoping in AzimuthElevationToCartesian test.
STYLE: Explicitly mark the ProcessObject methods virtual in SignedMaurer.
BUG: Do not try to install targets that do not exist when building externally.
BUG: ITKIOMeta needs a public dependency on ITKMetaIO.
COMP: Update LesionSizingToolkit for external build and style test failures.
BUG: Add CMake OpenCV export code to ITKVideoBridgeOpenCV.
COMP: Improve compatibility with OpenCV 3.
DOC: Fix class references in StatisticsLabelMapFilter.
STYLE: Improved readability of itkStatisticsUniqueLabelMapFilterTest1.
DOC: Correct ReverseOrdering description in ShapeUniqueLabelMapFilter.
STYLE: Add own copy of GenerateExportHeader
COMP: Create _TEMPLATE_EXPORT macros.
COMP: TransformIOBaseTemplate must be explicitly instantiated.
BUG: Do not use dynamic_cast for DisplacementFieldType in HDF5 test.
COMP: Do not use string(MAKE_C_IDENTIFIER with CMake < 2.8.12
BUG: Do not perform dynamic_cast in CompositeIOTransformIOHelper.
COMP: Do not set property on itkhdf5 with ITK_USE_SYSTEM_HDF5.

Max Smolens (1):
BUG: VoronoiSegmentationRGBImageFilter: add pixel dimension check

Michka Popoff (10):
ENH: Update to swig 3.0.7
ENH: Do not link against specific Python library on OS X
COMP: Fix wrapping warnings when building with ITK_WRAP_IMAGE_DIMS=2
COMP: Add missing wrapping for TransformBase
COMP: Use ITK's pygccxml by correctly setting up the sys.path
COMP: Disable incompatible modules when using Python 3 wrapping
COMP: Move MovingHistogramImageFilterBase wrapping to ImageFilterBase module
COMP: Disable incompatible modules when using Python 3 wrapping
ENH: Allow operations on Indexes and Offsets in Python
ENH: Allow Python 3 wrapping for Glue and Review Modules with VTK 7

Mikhail Isakov (2):
BUG: DiffusionTensor3DReconstruction segfault if no baseline image
DOC: correction in DiffusionTensor3D Reconstruction

Nick Tustison (5):
BUG: Set a default b-spline epsilon.
ENH: Adding testing for closed loop.
BUG: Updating B-spline classes with the same epsilon strategy.
PERF: Switch vnl_vectors for fixed arrays.
ENH: Point-set registration with time-varying B-spline.

Olivier Commowick (3):
BUG: Correct discrepancy in tridiagonal reduction wrt VNL eigen system
BUG: Correct under/overflows in vnl_math_hypot (taken from pythag from V3P)
BUG: Switch eigenvalues computation to double

Pablo Hernandez-Cerdan (2):
ENH: Help class for itkFlatStructuringElement with constructor from images.
COMP: Fix test errors and warnings in FlatStructuringElement.

Ricardo Ortiz (1):
BUG: Set itkBinaryImageTo*LabelMapFilter foreground/background values

Seun Odutola (3):
COMP: Fixed name clash with Apple header (check Macro), renamed check to Check
COMP: Corrected minc2.h path installation from libsrc2/minc2.h to minc2.h
BUG: absolute value of tolerance taken to cater for negative spacing

Shawn Waldon (1):
COMP: OSX set deployment target when building fftw

Simon Alexander (5):
BUG: incorrect closest point computation
STYLE: Change to make git bash on windows happy with the function name
COMP: fixes for visual studio 2015update1 x86 in release mode
COMP: fixes for visual studio 2015update1 x86 in release mode
COMP: fixes for visual studio 2015update1 x86 in release mode

Sreekanth Arikatla (2):
BUG: Resolved const correctness in itkMatrix.h
ENH: Fixes the symmetry of AzimuthElevationToCartesianTransform and adds tests

Vladimir S. FONOV (8):
BUG: Missing ITKIOMINC_EXPORT on __Private()
COMP: Splitting up IOMINC module into two parts: MINC and Transform
STYLE: updated comments to properly reference LIBMINC
ENH: Add script to merge upstream MINC as a subtree
MINC 2015-07-23 (c033d431)
COMP: Update MINC CMake code
MINC 2015-08-18 (6d7e3ba8)
MINC 2015-09-13 (95cd5374)

Xiaoxiao Liu (1):
DOC: update email address for xiaoxiao.

Zach Williamson (10):
BUG: Use correct libraries for ImageFusion tests
ENH: Consolidate Library Dependencies
COMP: Add a missing link to Review module
COMP: Use correct linking macro in DCMTK
BUG: Use correct libraries for TestKernel tests
COMP: Fix inconsistant naming of GPUPDEDeformableRegistration
ENH: Use new linking system macros
PERF: Avoid searching private dependencies for include directories
COMP: Recover missing dependencies
ENH: use new linking macros in Filtering module

Ziv Yaniv (2):
BUG: Affine transformation was estimated without sufficient number of points.
BUG: fixed BSpline initializer crash when reference image not set.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24836 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_ITKv4.cmake Diff File

master 210037a6

2016-01-07 11:42:38

fedorov

Details Diff 		ENH: update MultiVolumeImporter

This update adds support for parsing multivolumes from Siemens DSC MRI. The
functionality was tested on the examples provided by the QIICR MGH team.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24835 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master 3d5f63fc

2016-01-06 17:29:27

jcfr

Details Diff 		BUG: Fix CLI running issues and add tests to prevent future regression.

Before, the CLI module logic would add the observer before running the CLI
and remove it once the CLI is modified. This proved to be error prone, for
example if two CLIs are ran at the same time. One CLI would finish and
remove the observation, preventing the other one from ever finishing.
Instead, we propose to always listen to the event. This make the code
simpler and more robust.

Thanks to Alexis and Dzenan for their help creating a simple test case.

Reported-by: Dzenan Zukic <dzenan.zukic@kitware.com>
Co-authored-by: Alexis Girault <alexis.girault@kitware.com>
Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

From: Johan Andruejol <johan.andruejol@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24834 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/CMakeLists.txt Diff File
add - Applications/SlicerApp/Testing/Python/TwoCLIsInARowTest.py Diff File
add - Applications/SlicerApp/Testing/Python/TwoCLIsInParallelTest.py Diff File
mod - Base/QTCLI/vtkSlicerCLIModuleLogic.cxx Diff File
mod - Base/QTCLI/vtkSlicerCLIModuleLogic.h Diff File

master 0ac807fb

2016-01-06 13:10:17

jcfr

Details Diff 		BUG: Fixed crash when calling widgetRepresentation().self()

How to reproduce:

1. Go to endoscopy module (just an example, the behavior is the same for every scripted modules)

2. Copy-paste this into the Python console:

import sys
for i in range(30):
w = slicer.modules.endoscopy.widgetRepresentation().self()
print("Reference count of widget object: "+str(sys.getrefcount(w)))

=> memory is corrupted now and Slicer will crash very soon (e.g., if the above code copy-pasted again or any other operation is performed)

Problem:
Each time pythonSelf() is used to return an reference to Python, the reference count is decreased by one (when the temporary Python object is deleted).

Solution:
When returning a reference to Python, the reference count has to be increased by one.
(for example, the same is done in CTK-build\PythonQt\tests\PythonQtTests.h)

This might (hopefully) also solve the frequent crash of Slicer on application exit due to double-delete of PythonQt widgets.

Reviewed-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Reviewed-by: Max Smolens <max.smolens@kitware.com>

From: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24833 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCore/qSlicerScriptedUtils.cxx Diff File

master ab337489

2016-01-06 10:50:17

jcfr

Details Diff 		STYLE: Fix unused variable warning in vtkMRMLStorageNodeTest1.cxx

This commit fixes the following warning:

vtkMRMLStorageNodeTest1.cxx:110:8: warning: unused variable ‘res’ [-Wunused-variable]
bool res = true;
^

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24832 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/Testing/vtkMRMLStorageNodeTest1.cxx Diff File

master c71b7a44

2016-01-06 10:33:45

jcfr

Details Diff 		ENH: Removed unused vtkMRMLGlyphableVolumeDisplayPropertiesNode

The node was not used anywhere and the class was inadvertently
introduced in r7369 (ENH: merged demianVolumeGlyph-Simple branch
as vtkMRMLGlyphVolumeDisplayPropertiesNode)

Isaiah Norton also confirmed that the node is not needed.

From: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24831 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/CMakeLists.txt Diff File
mod - Libs/MRML/Core/Testing/CMakeLists.txt Diff File
rm - Libs/MRML/Core/Testing/vtkMRMLGlyphVolumeDisplayPropertiesNodeTest1.cxx Diff File
rm - Libs/MRML/Core/vtkMRMLGlyphableVolumeDisplayPropertiesNode.cxx Diff File
rm - Libs/MRML/Core/vtkMRMLGlyphableVolumeDisplayPropertiesNode.h Diff File
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