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

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master c63cd9e9

2015-06-09 10:45:22

lassoan

Details Diff 		BUG: Fixed FOV reset during volume selection propagation

FOV of all slice views were reset during volume selection propagation. Even for views where volume selection propagation was disabled.

Fixes (at least partially) http://www.na-mic.org/Bug/view.php?id=4000

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24304 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Python/sitkUtils.py Diff File
mod - Libs/MRML/Logic/vtkMRMLApplicationLogic.cxx Diff File
mod - Libs/MRML/Logic/vtkMRMLApplicationLogic.h Diff File
mod - Modules/Loadable/Volumes/qSlicerVolumesReader.cxx Diff File

master 959b3718

2015-06-08 18:29:33

jcfr

Details Diff 		COMP: Fix packaging and upload for superbuild based extension

This commit fixes a regression introduced in r24289 (BUG: Update extension
build system to report packaging error on CDash.) ensuring the "packageupload"
target is built in the inner build directory.

Thanks to "Jinho Lee <jinho89@gmail.com>" for reporting the problem.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24303 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Extensions/CMake/SlicerBlockBuildPackageAndUploadExtension.cmake Diff File

master a239e780

2015-06-05 09:51:41

lassoan

Details Diff 		BUG: Attempt to fix py_nomainwindow_MRMLCreateNodeByClassWithSetReferenceCountToOne test

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24302 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Python/slicer/slicerqt.py Diff File

master 0341460a

2015-06-05 09:40:49

pieper

Details Diff 		ENH: update CompareVolumes to support label map nodes

https://github.com/pieper/CompareVolumes/pull/5

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24301 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master 96e0e244

2015-06-05 09:23:00

lassoan

Details Diff 		BUG: Fixed EMSegCL_Task_MRIHumanBrainFullParcellation_BRAINS_small test

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24300 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master bca90af7

2015-06-04 20:56:44

jcfr

Details Diff 		BUG: Update EMSegment to fix regression introduced in labelmap node support

This commit fixes a regression introduced in r24291 (ENH: Use vtkMRMLLabelMapVolumeNode
class for labelmap volumes).

The issue has been found thanks to the following unused variable warning:

/home/jcfr/Projects/Slicer-Debug/EMSegment/CommandLineApplication/EMSegmentCommandLineFct.cxx:44:1: warning: unused parameter ‘labelMap’ [-Wunused-parameter]
AddNewScalarArchetypeVolume(vtkMRMLScene* mrmlScene,

EMSegment commit:
------------------------------------------------------------------------
r17103 | jcfr | 2015-06-04 20:51:49 -0400 (Thu, 04 Jun 2015) | 4 lines

BUG: Fix unused variable warning fix regression introduced in previous commit.

Update AddNewScalarArchetypeVolume function to create either a scalar volume node
or a labelmap volume node.
------------------------------------------------------------------------

Reviewed-by: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24299 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master ed659852

2015-06-04 18:48:41

fedorov

Details Diff 		ENH: add echoscu DCMTK application

this is a useful tool for testing connection for DICOM communication

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24298 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerBlockInstallDCMTKApps.cmake Diff File

master edc82e7c

2015-06-04 18:30:59

jcfr

Details Diff 		STYLE: Fix unused variable warning in vtkMRMLSliceLayerLogic

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24297 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/vtkMRMLSliceLayerLogic.cxx Diff File

master 69e73cb3

2015-06-04 18:30:57

jcfr

Details Diff 		COMP: Fix missing "ctkcheckbox.h" compilation error on case-sensitive system

This commit fixes a regression introduced in r24290 (BUG: revert to not
showing tick labels on ruler by default) where the UI file
"qSlicerAnnotationModulePropertyDialog.ui" has been updated omitting the
customwidget specification. The header name associated with ctkCheckBox
was defaulting to "ctkcheckbox.h" which was causing problem on system
using case sensitive filesystem (Linux and MacOSX).

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24296 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Annotations/Resources/UI/qSlicerAnnotationModulePropertyDialog.ui Diff File

master 17ee4717

2015-06-04 18:22:36

fedorov

Details Diff 		ENH: update MultiVolumeExplorer hash

This fixes the issues related to the new label node, contributed by Andras Lasso

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24295 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master bccba77c

2015-06-04 17:45:36

pinter

Details Diff 		BUG: Fixed save data dialog cras in case of certain node names

Save data dialog crashed if node name started with a non-drive-letter character followed by a colon. A zero is prepended to node names if it is in the form "1: Something", which is "cleaned up" by Qt to "1:\Something" on Windows, and crashes because the first character is not a letter in the path.

Fixed indentation issue in vtkSlicerApplicationLogic.cxx

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24294 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Logic/vtkSlicerApplicationLogic.cxx Diff File
mod - Base/QTGUI/qSlicerSaveDataDialog.cxx Diff File

master d015ac9f

2015-06-04 17:28:22

pinter

Details Diff 		ENH: Added labelmap node support to subject hierarchy

Subject hierarchy knew about the single vtkMRMLScalarVolumeNode class, but now that the vtkMRMLLabelMapVolumeNode has been introduced, a separate subject hierarchy plugin was created for labelmaps. This way it is cleaner that one role plugin assigns one icon and the same set of functionality to its owned nodes.

Fixed issue in sitkUtils: it created a scalar volume node regardless whether a labelmap was already created

Removed temporary contour references from model slice displayable manager (segmentations has its own displayable manager)

Added concept of virtual subject hierarchy branches, which is a branch for which its parent is solely reaponsible, i.e. the child nodes do not correspond to actual MRML nodes, but to items contained in the parent node to enable per-item handling from subject hierarchy (e.g. segments in segmentations and fiducials in markups)

Create and expose cloneSubjectHierarchyNode method in qSlicerSubjectHierarchyCloneNodePlugin to enable easy cloning of any node (clone SH node, data node, display and storage nodes)

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24293 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/SubjectHierarchyGenericSelfTest.py Diff File
mod - Base/Python/sitkUtils.py Diff File
mod - Libs/MRML/DisplayableManager/vtkMRMLModelSliceDisplayableManager.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/MRML/vtkMRMLSubjectHierarchyConstants.h Diff File
mod - Modules/Loadable/SubjectHierarchy/MRML/vtkMRMLSubjectHierarchyNode.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/MRML/vtkMRMLSubjectHierarchyNode.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSceneSubjectHierarchyModel.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyAbstractPlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyCloneNodePlugin.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyCloneNodePlugin.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchyPluginLogic.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchySegmentPlugin.cxx Diff File
mod - Modules/Loadable/Volumes/SubjectHierarchyPlugins/CMakeLists.txt Diff File
add - Modules/Loadable/Volumes/SubjectHierarchyPlugins/qSlicerSubjectHierarchyLabelMapsPlugin.cxx Diff File
add - Modules/Loadable/Volumes/SubjectHierarchyPlugins/qSlicerSubjectHierarchyLabelMapsPlugin.h Diff File
mod - Modules/Loadable/Volumes/SubjectHierarchyPlugins/qSlicerSubjectHierarchyVolumesPlugin.cxx Diff File
mod - Modules/Loadable/Volumes/SubjectHierarchyPlugins/qSlicerSubjectHierarchyVolumesPlugin.h Diff File
mod - Modules/Loadable/Volumes/qSlicerVolumesModule.cxx Diff File

master d41a67d0

2015-06-04 17:10:56

pinter

Details Diff 		STYLE: Indentation fixes

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24292 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/vtkMRMLSliceLayerLogic.cxx Diff File
mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx Diff File
mod - Modules/Loadable/Volumes/Testing/Cxx/vtkSlicerVolumesLogicTest1.cxx Diff File

master e4ffa1f6

2015-06-04 16:12:02

lassoan

Details Diff 		ENH: Use vtkMRMLLabelMapVolumeNode class for labelmap volumes

Before vtkMRMLScalarVolumeNode was used for both scalar and label map
volumes and the LabelMap custom MRML node attribute was used for
distinguishing between them (0=scalar; 1=label map volume).
This made conversion between labelmap/scalar volumes very easy but made
it difficult to customize behavior, display, processing of segmentation
information.

Now a new vtkMRMLLabelMapVolumeNode class is used for storing segmentation
information (still using vtkMRMLScalarVolume used as base class for backward
compatibility; but in the future the base class may be changed to reflect
that segmentation can be represented in various ways, not just as volumes).

Notes:

A new "segmentation" node has been developed that is based on vtkMRMLLabelMapVolumeNode,
which can store segmentation information in various ways (not just labelmaps but planar
contours, closed surfaces, etc). To allow using of this new segmentation node,
first the vtkMRMLLabelMapVolumeNode has to be integrated into the Slicer core.

When reading a scene that was saved with an old version of Slicer, label maps are stored
in vtkMRMLScalarVolumeNode with label map attribute set to 1. Added a check for this case
and handle it by converting the vtkMRMLScalarVolumeNode to a vtkMRMLLabelMapVolumeNode during import.


git-svn-id: http://svn.slicer.org/Slicer4/trunk@24291 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/CMakeLists.txt Diff File
mod - Applications/SlicerApp/Testing/Python/SubjectHierarchyGenericSelfTest.py Diff File
rm - Applications/SlicerApp/Testing/Python/labelToggleBug2049.py Diff File
mod - Base/Logic/vtkSlicerApplicationLogic.cxx Diff File
mod - Base/Python/sitkUtils.py Diff File
mod - Base/Python/slicer/util.py Diff File
mod - Base/QTCLI/qSlicerCLIModuleUIHelper.cxx Diff File
mod - Base/QTCLI/vtkSlicerCLIModuleLogic.cxx Diff File
mod - Base/QTCore/qSlicerSlicer2SceneReader.cxx Diff File
mod - Extensions/Testing/ScriptedLoadableExtensionTemplate/ScriptedLoadableModuleTemplate/ScriptedLoadableModuleTemplate.py Diff File
mod - Libs/MRML/Core/CMakeLists.txt Diff File
add - Libs/MRML/Core/vtkMRMLLabelMapVolumeNode.cxx Diff File
add - Libs/MRML/Core/vtkMRMLLabelMapVolumeNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLParser.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLScalarVolumeNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLScalarVolumeNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLScene.cxx Diff File
mod - Libs/MRML/Logic/vtkMRMLSliceLayerLogic.cxx Diff File
mod - Libs/MRML/Widgets/Resources/UI/qMRMLSliceControllerWidget.ui Diff File
mod - Libs/MRML/Widgets/Resources/UI/qMRMLVolumeInfoWidget.ui Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLNodeComboBoxTest4.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLSliceControllerWidgetTest.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLVolumeInfoWidgetEventTranslatorPlayerTest1.xml Diff File
mod - Libs/MRML/Widgets/qMRMLNodeComboBox.h Diff File
mod - Libs/MRML/Widgets/qMRMLSliceControllerWidget.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLVolumeInfoWidget.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLVolumeInfoWidget.h Diff File
mod - Modules/Loadable/CropVolume/Logic/vtkSlicerCropVolumeLogic.cxx Diff File
mod - Modules/Loadable/MultiVolumeRendering/Resources/UI/qSlicerMultiVolumeRenderingModuleWidget.ui Diff File
mod - Modules/Loadable/MultiVolumeRendering/qSlicerMultiVolumeRenderingModuleWidget.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qSlicerSubjectHierarchySegmentPlugin.cxx Diff File
mod - Modules/Loadable/TractographyInteractiveSeeding/Resources/UI/qSlicerTractographyInteractiveSeedingModuleWidget.ui Diff File
mod - Modules/Loadable/TractographyInteractiveSeeding/qSlicerTractographyInteractiveSeedingModuleWidget.cxx Diff File
mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.cxx Diff File
mod - Modules/Loadable/Volumes/Logic/vtkSlicerVolumesLogic.h Diff File
mod - Modules/Loadable/Volumes/SubjectHierarchyPlugins/qSlicerSubjectHierarchyVolumesPlugin.cxx Diff File
mod - Modules/Loadable/Volumes/Testing/Cxx/vtkSlicerVolumesLogicTest1.cxx Diff File
mod - Modules/Loadable/Volumes/Widgets/qSlicerVolumeDisplayWidget.cxx Diff File
mod - Modules/Loadable/Volumes/Widgets/qSlicerVolumeDisplayWidget.h Diff File
mod - Modules/Loadable/Volumes/qSlicerVolumesReader.cxx Diff File
mod - Modules/Scripted/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/full_tractography_workflow.py Diff File
mod - Modules/Scripted/DataProbe/DataProbe.py Diff File
mod - Modules/Scripted/EditorLib/HelperBox.py Diff File
mod - Modules/Scripted/EditorLib/WatershedFromMarkerEffect.py Diff File
mod - Modules/Scripted/FiberBundleToLabelMap/FiberBundleToLabelMap.py Diff File
mod - Modules/Scripted/LabelStatistics/LabelStatistics.py Diff File
mod - SuperBuild.cmake Diff File
mod - Utilities/Templates/Modules/Scripted/TemplateKey.py Diff File

master 55215ab9

2015-06-04 15:39:10

naucoin

Details Diff 		BUG: revert to not showing tick labels on ruler by default

After svn 24288 tick labels started showing, this change turns
them off by default to preserve prior behaviour. When they're
on, can now use the text display node to over ride showing
both the measurement text and the label text.

Issue 0003196


git-svn-id: http://svn.slicer.org/Slicer4/trunk@24290 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Annotations/GUI/qSlicerAnnotationModulePropertyDialog.cxx Diff File
mod - Modules/Loadable/Annotations/GUI/qSlicerAnnotationModulePropertyDialog.h Diff File
mod - Modules/Loadable/Annotations/MRML/vtkMRMLAnnotationLineDisplayNode.cxx Diff File
mod - Modules/Loadable/Annotations/MRMLDM/vtkMRMLAnnotationRulerDisplayableManager.cxx Diff File
mod - Modules/Loadable/Annotations/Resources/UI/qSlicerAnnotationModulePropertyDialog.ui Diff File

master cc1182d3

2015-06-04 09:41:35

jcfr

Details Diff 		BUG: Update extension build system to report packaging error on CDash.

See 0003032

This commit adds a new target named "uploadpackage" that will
(1) build the standard 'package' target,
(2) extract the list of generated packages from its standard output and
(3) append the list of generated package filepaths to a file named PACKAGES.txt,
(4) upload the extension packages on midas.

Using this target an extension can be uploaded to midas without
relying on CTest.

Within the ctest script, the target "uploadpackage" is built and then
the URL to download packages from midas are uploaded to CDash based on the
content of the file PACKAGES.txt

This commit removes the now obsolete ExperimentalUploadOnly target.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24289 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerExtensionCPack.cmake Diff File
mod - Extensions/CMake/SlicerBlockBuildPackageAndUploadExtension.cmake Diff File
add - Extensions/CMake/SlicerExtensionPackageAndUploadTarget.cmake Diff File

master 38dbd5b6

2015-06-03 19:09:29

naucoin

Details Diff 		BUG: fix translucency rendering of ruler

The subclass vtkAnnotationRulerRepresentation3D needed to implement
HasTranslucentPolygonalGeometry in order to have rendering triggered when setting
the opacity on the ruler label -this fixes the problem where when the opacity was
set to anything other than 1, it was not rendered at all.
Fixed other opacity and color issues on the 2d and 3d rulers to make them behave
similarly.
Note: the label visibility being on now shows tick labels in 2D, turning it off
will hide both the tick labels and the measurement label. Setting text opacity
to 0 will do the same thing.
TODO: 2D font size is not changing when change the text scale.

Issue 0003196


git-svn-id: http://svn.slicer.org/Slicer4/trunk@24288 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Annotations/MRMLDM/vtkMRMLAnnotationRulerDisplayableManager.cxx Diff File
mod - Modules/Loadable/Annotations/VTKWidgets/vtkAnnotationRulerRepresentation.cxx Diff File
mod - Modules/Loadable/Annotations/VTKWidgets/vtkAnnotationRulerRepresentation3D.cxx Diff File
mod - Modules/Loadable/Annotations/VTKWidgets/vtkAnnotationRulerRepresentation3D.h Diff File

master fde226c9

2015-06-03 17:35:23

fedorov

Details Diff 		ENH: update MultiVolumeImporter tag

* added parsing of DWI by (0018,9087) DiffusionBValue
* corrected b-value units

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24287 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master a88da5dc

2015-06-03 07:27:01

pinter

Details Diff 		COMP: Reverting faulty fix

I accidentally committed a fix that was only applicable in the branch that we were going to integrate just now. Reverting.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24286 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSceneSubjectHierarchyModel.cxx Diff File

master 1948c23f

2015-06-02 18:10:07

pinter

Details Diff 		BUG: Fixed crash when SH node dropped onto scene

Parent node is NULL but there was no check.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24285 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSceneSubjectHierarchyModel.cxx Diff File

master f2bccaf9

2015-06-02 09:51:39

alexy

Details Diff 		ENH: added magnified slice view into DataProbe panel.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24284 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DataProbe/DataProbe.py Diff File

master 8406b410

2015-06-01 17:15:08

jcfr

Details Diff 		BUG: Address SimpleFilters FlipImageFilter

$ git shortlog 73add6..ceb133
Bradley Lowekamp (1):
BUG: Add method for vector of bool changed

From: Bradley Lowekamp <blowekamp@mail.nih.gov>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24283 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master 6537c3dd

2015-05-31 00:20:04

lassoan

Details Diff 		BUG: Fixed failure of disabling slice view annotations from another module

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24282 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DataProbe/DataProbeLib/SliceViewAnnotations.py Diff File

master d23bdcc1

2015-05-29 09:50:33

lassoan

Details Diff 		BUG: Fixed qMRMLVolumeWidget crash on scene close

Weak pointers should be used in all widgets for referencing MRML nodes because MRML nodes may be deleted without notifying widgets when closing the scene.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24281 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Widgets/qMRMLVolumeWidget_p.h Diff File

master 6750a615

2015-05-29 09:48:18

lassoan

Details Diff 		BUG: Fixed MRHead sample data download in CropVolumeSelfTest

On some computers the download failed. Using the SampleData module is simpler and seems to be more robust.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@24280 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/CropVolume/Testing/Python/CropVolumeSelfTest.py Diff File
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