Changesets: Slicer

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2145-support-for-installing-extension-from-file bbb85f2a

2013-09-10 11:51:47

naucoin

Details Diff 		STYLE: print out widget projections

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22421 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/MRMLDM/vtkMRMLMarkupsDisplayableManagerHelper.cxx Diff File

2145-support-for-installing-extension-from-file 73371061

2013-09-09 18:47:20

fedorov

Details Diff 		ENH: adding default method for initializing of the node-specific display node


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22420 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_MultiVolumeExplorer.cmake Diff File

2145-support-for-installing-extension-from-file 50fa25bb

2013-09-09 11:59:40

fedorov

Details Diff 		ENH: explicit selection of the secondary multivolume using the module GUI


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22416 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_MultiVolumeExplorer.cmake Diff File

2145-support-for-installing-extension-from-file 15b410f4

2013-09-08 20:58:28

fedorov

Details Diff 		ENH: adding the capability for interactive plotting of the multivolume selected in Fg; this feature is needed for debugging PkModeling and similar extensions that implement multivolume fitting


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22415 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_MultiVolumeExplorer.cmake Diff File

2145-support-for-installing-extension-from-file e0101cd1

2013-09-06 16:16:32

alexy

Details Diff 		ENH: 3379. Added a "Include Fibers" checkbox to the Models module to allow hierarchical grouping of Fiber Bundles

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22414 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Models/Resources/UI/qSlicerModelsModuleWidget.ui Diff File
mod - Modules/Loadable/Models/qSlicerModelsModuleWidget.cxx Diff File
mod - Modules/Loadable/Models/qSlicerModelsModuleWidget.h Diff File

2145-support-for-installing-extension-from-file 7b7aec09

2013-09-04 22:58:49

jcfr

Details Diff 		COMP: Do not build DWIConvert module if DICOM support is disabled

"DWIConvert.cxx" expects "itkDCMTKFileReader.h" header.
See https://github.com/BRAINSia/BRAINSTools/blob/ddf903b56fd6633945e1927b54393f7c65268dea/DWIConvert/DWIConvert.cxx#L47

Fixes 0003370

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22412 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Remote/CMakeLists.txt Diff File

2145-support-for-installing-extension-from-file cf30e1e5

2013-09-04 22:47:40

jcfr

Details Diff 		COMP: Ensure teem is properly link against png if CMake > 2.8.11.2 is used

See inlined comment for more details.

Associated discussion: http://massmail.spl.harvard.edu/public-archives/slicer-devel/2013/thread.html#13536

Fixes 0003369

Co-authored-by: Steve Pieper <pieper@bwh.harvard.edu>
Co-authored-by: James Cook <james.j.cook@duke.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22411 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_teem.cmake Diff File

2145-support-for-installing-extension-from-file 18f52c4b

2013-09-04 10:48:07

naucoin

Details Diff 		COMP: fix compiling in debug mode

A variable was removed to fix a release mode unused variable warning,
in svn 22402, remove it from the vtkDebugMacro.



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22410 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/Logic/vtkSlicerMarkupsLogic.cxx Diff File

2145-support-for-installing-extension-from-file 315c348c

2013-09-04 07:07:57

jcfr

Details Diff 		ENH: Begin post-4.3.0 development

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22409 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMakeLists.txt Diff File

2145-support-for-installing-extension-from-file a1f6594f

2013-09-04 06:48:37

jcfr

Details Diff 		ENH: Slicer 4.3.0

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22408 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMakeLists.txt Diff File

2145-support-for-installing-extension-from-file c35fe88c

2013-09-04 06:48:34

jcfr

Details Diff 		ENH: Update Documentation to 4.3

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22407 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/CMakeLists.txt Diff File
mod - Applications/SlicerApp/Testing/Python/ScenePerformance.py Diff File
mod - CMake/SlicerDashboardScript.TEMPLATE.cmake Diff File
mod - CMakeLists.txt Diff File
mod - Extensions/CMake/CMakeLists.txt Diff File
mod - Extensions/CMake/SlicerEnableExtensionTesting.cmake Diff File
mod - Extensions/CMake/SlicerExtensionsDashboardScript.TEMPLATE.cmake Diff File
mod - Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplate/CLIModuleTemplate.xml Diff File
mod - Extensions/Testing/CLIExtensionTemplate/CMakeLists.txt Diff File
mod - Extensions/Testing/EditorExtensionTemplate/CMakeLists.txt Diff File
mod - Extensions/Testing/LoadableExtensionTemplate/CMakeLists.txt Diff File
mod - Extensions/Testing/ScriptedLoadableExtensionTemplate/CMakeLists.txt Diff File
mod - Extensions/Testing/SuperBuildExtensionTemplate/CMakeLists.txt Diff File
mod - Extensions/Testing/SuperBuildExtensionTemplate/SuperCLIModuleTemplate/SuperCLIModuleTemplate.xml Diff File
mod - Modules/CLI/ACPCTransform/ACPCTransform.xml Diff File
mod - Modules/CLI/AddScalarVolumes/AddScalarVolumes.xml Diff File
mod - Modules/CLI/AffineRegistration/AffineRegistration.xml Diff File
mod - Modules/CLI/BSplineDeformableRegistration/BSplineDeformableRegistration.xml Diff File
mod - Modules/CLI/BSplineToDeformationField/BSplineToDeformationField.xml Diff File
mod - Modules/CLI/BlobDetection/BlobDetection.xml Diff File
mod - Modules/CLI/CastScalarVolume/CastScalarVolume.xml Diff File
mod - Modules/CLI/CheckerBoardFilter/CheckerBoardFilter.xml Diff File
mod - Modules/CLI/ConnectedComponent/ConnectedComponent.xml Diff File
mod - Modules/CLI/CreateDICOMSeries/CreateDICOMSeries.xml Diff File
mod - Modules/CLI/CurvatureAnisotropicDiffusion/CurvatureAnisotropicDiffusion.xml Diff File
mod - Modules/CLI/DTIImportExport/DTIexport.xml Diff File
mod - Modules/CLI/DTIImportExport/DTIimport.xml Diff File
mod - Modules/CLI/DWIJointRicianLMMSEFilter/DWIJointRicianLMMSEFilter.xml Diff File
mod - Modules/CLI/DWIRicianLMMSEFilter/DWIRicianLMMSEFilter.xml Diff File
mod - Modules/CLI/DWIToDTIEstimation/DWIToDTIEstimation.xml Diff File
mod - Modules/CLI/DWIUnbiasedNonLocalMeansFilter/DWIUnbiasedNonLocalMeansFilter.xml Diff File
mod - Modules/CLI/DicomToNrrdConverter/DicomToNrrdConverter.xml Diff File
mod - Modules/CLI/DicomToNrrdConverter/ExtendedTesting/DWICompare.xml Diff File
mod - Modules/CLI/DiffusionTensorScalarMeasurements/DiffusionTensorScalarMeasurements.xml Diff File
mod - Modules/CLI/DiffusionWeightedVolumeMasking/DiffusionWeightedVolumeMasking.xml Diff File
mod - Modules/CLI/ExecutionModelTour/ExecutionModelTour.xml Diff File
mod - Modules/CLI/ExpertAutomatedRegistration/ExpertAutomatedRegistration.xml Diff File
mod - Modules/CLI/ExtractSkeleton/ExtractSkeleton.xml Diff File
mod - Modules/CLI/FiducialRegistration/FiducialRegistration.xml Diff File
mod - Modules/CLI/GaussianBlurImageFilter/GaussianBlurImageFilter.xml Diff File
mod - Modules/CLI/GradientAnisotropicDiffusion/GradientAnisotropicDiffusion.xml Diff File
mod - Modules/CLI/GrayscaleFillHoleImageFilter/GrayscaleFillHoleImageFilter.xml Diff File
mod - Modules/CLI/GrayscaleGrindPeakImageFilter/GrayscaleGrindPeakImageFilter.xml Diff File
mod - Modules/CLI/GrayscaleModelMaker/GrayscaleModelMaker.xml Diff File
mod - Modules/CLI/HistogramMatching/HistogramMatching.xml Diff File
mod - Modules/CLI/ImageLabelCombine/ImageLabelCombine.xml Diff File
mod - Modules/CLI/LabelMapSmoothing/LabelMapSmoothing.xml Diff File
mod - Modules/CLI/LinearRegistration/LinearRegistration.xml Diff File
mod - Modules/CLI/MRIBiasFieldCorrection/MRIBiasFieldCorrection.xml Diff File
mod - Modules/CLI/MaskScalarVolume/MaskScalarVolume.xml Diff File
mod - Modules/CLI/MedianImageFilter/MedianImageFilter.xml Diff File
mod - Modules/CLI/MergeModels/MergeModels.xml Diff File
mod - Modules/CLI/ModelMaker/ModelMaker.xml Diff File
mod - Modules/CLI/ModelToLabelMap/ModelToLabelMap.xml Diff File
mod - Modules/CLI/MultiResolutionAffineRegistration/MultiResolutionAffineRegistration.xml Diff File
mod - Modules/CLI/MultiplyScalarVolumes/MultiplyScalarVolumes.xml Diff File
mod - Modules/CLI/N4ITKBiasFieldCorrection/N4ITKBiasFieldCorrection.xml Diff File
mod - Modules/CLI/OrientScalarVolume/OrientScalarVolume.xml Diff File
mod - Modules/CLI/OtsuThresholdImageFilter/OtsuThresholdImageFilter.xml Diff File
mod - Modules/CLI/OtsuThresholdSegmentation/OtsuThresholdSegmentation.xml Diff File
mod - Modules/CLI/PETStandardUptakeValueComputation/PETStandardUptakeValueComputation.xml Diff File
mod - Modules/CLI/ProbeVolumeWithModel/ProbeVolumeWithModel.xml Diff File
mod - Modules/CLI/ResampleDTIVolume/ResampleDTIVolume.xml Diff File
mod - Modules/CLI/ResampleScalarVectorDWIVolume/ResampleScalarVectorDWIVolume.xml Diff File
mod - Modules/CLI/ResampleScalarVolume/ResampleScalarVolume.xml Diff File
mod - Modules/CLI/RigidRegistration/RigidRegistration.xml Diff File
mod - Modules/CLI/RobustStatisticsSegmenter/RobustStatisticsSegmenter.xml Diff File
mod - Modules/CLI/SimpleRegionGrowingSegmentation/SimpleRegionGrowingSegmentation.xml Diff File
mod - Modules/CLI/SubtractScalarVolumes/SubtractScalarVolumes.xml Diff File
mod - Modules/CLI/TestGridTransformRegistration/TestGridTransformRegistration.xml Diff File
mod - Modules/CLI/ThresholdScalarVolume/ThresholdScalarVolume.xml Diff File
mod - Modules/CLI/TractographyLabelMapSeeding/TractographyLabelMapSeeding.xml Diff File
mod - Modules/CLI/VotingBinaryHoleFillingImageFilter/VotingBinaryHoleFillingImageFilter.xml Diff File
mod - Modules/Core/EventBroker/Documentation/EventBroker.xml Diff File
mod - Modules/Loadable/Annotations/Documentation/Annotations.xml Diff File
mod - Modules/Loadable/Cameras/Documentation/Cameras.xml Diff File
mod - Modules/Loadable/Data/Documentation/Data.xml Diff File
mod - Modules/Loadable/Models/Documentation/Models.xml Diff File
mod - Modules/Loadable/Reformat/Documentation/Reformat.xml Diff File
mod - Modules/Loadable/SceneViews/Documentation/SceneViews.xml Diff File
mod - Modules/Loadable/SlicerWelcome/Resources/HTML/Acknowledgment.html Diff File
mod - Modules/Loadable/SlicerWelcome/Resources/HTML/OtherUsefulHints.html Diff File
mod - Modules/Loadable/Transforms/Documentation/Transforms.xml Diff File
mod - Modules/Loadable/ViewControllers/Documentation/ViewControllers.xml Diff File
mod - Modules/Loadable/VolumeRendering/Documentation/VolumeRendering.xml Diff File
mod - Modules/Loadable/Volumes/Documentation/Volumes.xml Diff File

2145-support-for-installing-extension-from-file 91c19a75

2013-09-04 06:47:55

jcfr

Details Diff 		COMP: Exclude html extension from git hook line lengths check

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22406 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Utilities/SetupForDevelopment.sh Diff File

2145-support-for-installing-extension-from-file 522bb5d1

2013-09-04 05:28:02

jcfr

Details Diff 		BUG: Add ".mgh.gz" to the list of FreeSurferModelOverlay read file types.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22405 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLFreeSurferModelOverlayStorageNode.cxx Diff File

2145-support-for-installing-extension-from-file 8a45c3d9

2013-09-04 05:27:59

jcfr

Details Diff 		BUG: Fix "py_nomainwindow_test_slicer_mgh" allowing "mgh" to be saved

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22404 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkDataFileFormatHelper.cxx Diff File

2145-support-for-installing-extension-from-file 63533ede

2013-09-04 05:27:56

jcfr

Details Diff 		BUG: Fix loading of ".mgh.gz" file in py_nomainwindow_test_slicer_mgh

Method "IsCompressedFilename" has been copied from the improved fork
of MGHImageIO maintained by ITK folks (Hans).
See https://github.com/Slicer/itkMGHImageIO

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22403 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MGHImageIO/itkMGHImageIO.cxx Diff File
mod - Libs/MGHImageIO/itkMGHImageIO.h Diff File

2145-support-for-installing-extension-from-file 57eb2724

2013-09-04 05:27:53

jcfr

Details Diff 		COMP: Fix unused variable warnings

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22402 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkITK/vtkITKArchetypeImageSeriesReader.cxx Diff File
mod - Modules/Loadable/Markups/Logic/vtkSlicerMarkupsLogic.cxx Diff File

2145-support-for-installing-extension-from-file 90b5bbb4

2013-09-04 01:26:37

jcfr

Details Diff 		BUG: Fix logic checking for readonly folder in writeToMRB method

Following r22395 "qSlicerSceneWriter::writeToMRB" has been updated to
check is the MRB file to be written was writable or not, the test was
always failing since the file itself wasn't existing.

This commit implement the appropriate logic by checking if the destination
folder where the MRB should be saved is writable.

This commit also fix the test "test_slicer_util_save.test_saveSceneAsMRB"

See 0003242

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22401 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Data/qSlicerSceneWriter.cxx Diff File

2145-support-for-installing-extension-from-file c22c0514

2013-09-03 19:22:49

jcfr

Details Diff 		BUG: Disable AutoRestart to workaround issue 0002535

Instead of asking the user if he would like to restart, he is asked
if he would like to exit Slicer and manually restart.

The restart confirm dialog is associated with the
settings key "MainWindow/DontConfirmExit"

See 0002535

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22400 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerApplication.cxx Diff File
mod - Base/QTGUI/qSlicerSettingsGeneralPanel.cxx Diff File

2145-support-for-installing-extension-from-file b4c3236c

2013-09-03 18:52:59

naucoin

Details Diff 		BUG: fix failing test

Fix the write CLI test for the markpus node by adjusting the expected number
of arguments to be 2 times the number of points, as the flag is written
separately now.

Related to fixes for issue 0001910


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22399 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/Testing/Cxx/vtkMRMLMarkupsNodeTest1.cxx Diff File

2145-support-for-installing-extension-from-file f28dcf5e

2013-09-03 18:24:33

fedorov

Details Diff 		BUG: fix issues causing inability to import multi-frame data from individual non-DICOM files, attempt to fix 3299


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22398 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_MultiVolumeImporter.cmake Diff File

2145-support-for-installing-extension-from-file 8113bdc9

2013-09-03 18:24:08

jcfr

Details Diff 		BUG: Fixes py_NeurosurgicalPlanningTutorial test

Beside of memory leak and error related to the glyphing pipeline (captured
by issue 0003349).
The script can be successfully replayed within Slicer or if executed
using CTest with a Slicer build without leak detection.

// ---------------------------
Errors:

565: ERROR: In /home/jchris/Projects/Slicer-AHM-Superbuild-Release/VTK/Filtering/vtkDemandDrivenPipeline.cxx, line 727
565: vtkStreamingDemandDrivenPipeline (0x957b600): Input port 0 of algorithm vtkExtractSelectedPolyDataIds(0x957b370) has 0 connections but is not optional.
565:
565:
565: ERROR: In /home/jchris/Projects/Slicer-AHM/Libs/vtkTeem/vtkDiffusionTensorGlyph.cxx, line 222
565: vtkDiffusionTensorGlyph (0xcd1db10): No data to glyph!
// ---------------------------

// ---------------------------
Leaks:

565: vtkDebugLeaks has detected LEAKS!
565: Class "vtkSynchronizedTemplatesCutter3D" has 21 instances still around.
565: Class "vtkTransformPolyDataFilter" has 21 instances still around.
565: Class "vtkInformationVector" has 441 instances still around.
565: Class "vtkMatrix4x4" has 42 instances still around.
565: Class "vtkCoordinate" has 42 instances still around.
565: Class "vtkPlane" has 21 instances still around.
565: Class "vtkInformation" has 525 instances still around.
565: Class "vtkSynchronizedTemplates3D" has 21 instances still around.
565: Class "vtkActor2D" has 21 instances still around.
565: Class "vtkRectilinearSynchronizedTemplates" has 21 instances still around.
565: Class "vtkDoubleArray" has 105 instances still around.
565: Class "vtkAlgorithmOutput" has 21 instances still around.
565: Class "vtkInformationIntegerValue" has 378 instances still around.
565: Class "vtkOpenGLPolyDataMapper2D" has 21 instances still around.
565: Class "vtkGridSynchronizedTemplates3D" has 21 instances still around.
565: Class "vtkCutter" has 21 instances still around.
565: Class "vtkInformationExecutivePortVectorValue" has 21 instances still around.
565: Class "vtkContourValues" has 105 instances still around.
565: Class "vtkTransform" has 21 instances still around.
565: Class "vtkStreamingDemandDrivenPipeline" has 42 instances still around.
565: Class "vtkTimerLog" has 21 instances still around.
565: Class "vtkInformationExecutivePortValue" has 21 instances still around.

// ---------------------------

Fixes 0002808

Co-authored-by: Jean-Christophe Fillion-Robin <JChris.FillionR@kitware.com>

From: Chrystel Juan <chrystel.juan@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22397 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Data/Input/NeurosurgicalPlanningTutorial.xml Diff File

2145-support-for-installing-extension-from-file 93d3f5d4

2013-09-03 17:47:50

naucoin

Details Diff 		BUG: fix loading of double array files

The file extension didn't match that in the double array storage node.

Fixes issue 0003289



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22396 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/DoubleArrays/qSlicerDoubleArraysIO.cxx Diff File

2145-support-for-installing-extension-from-file b75926b2

2013-09-03 16:00:23

jcfr

Details Diff 		BUG: Prevent crash when attempting to save a *.mrb in a readonly folder.

Fixes 0003242

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22395 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Data/qSlicerSceneWriter.cxx Diff File

2145-support-for-installing-extension-from-file b985899f

2013-09-03 14:29:44

jcfr

Details Diff 		BUG: Fix crash preventing the same color file to be loaded more than once

As the documentation associated "AddNode" method explains, in the case
of singleton node, the return node should be considered instead of the
one passed to the method.

AddNode documentation:

/// [...]
/// If node is a singleton, and a node of the same class with the
/// same singleton tag already exists in the scene, \a nodeToAdd is NOT
/// added but its properties are copied (c.f. vtkMRMLNode::CopyWithScene())
/// into the already existing singleton node. That node is then returned.

Fixes 0002989

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22394 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/vtkMRMLColorLogic.cxx Diff File

2145-support-for-installing-extension-from-file c73e9b50

2013-09-03 14:29:42

jcfr

Details Diff 		COMP: Fix "sign-compare" warning in vtkSlicerMarkupsLogic

vtkSlicerMarkupsLogic.cxx: In member function ‘void vtkSlicerMarkupsLogic::ConvertAnnotationFiducialsToMarkups()’:
vtkSlicerMarkupsLogic.cxx:882: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
vtkSlicerMarkupsLogic.cxx:954: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22393 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/Logic/vtkSlicerMarkupsLogic.cxx Diff File
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