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

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master 640e4581

2016-10-20 11:47:11

jcfr

Details Diff 		BUG: Fix JsonCpp packaging on Linux. Fixes 0004281

$ git shortlog 0.10.6..f4afa75 --no-merges
Jean-Christophe Fillion-Robin (1):
Revert "0001-multiarch-path-support.patch"

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25465 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_JsonCpp.cmake Diff File

master a5627753

2016-10-20 09:10:27

lassoan

Details Diff 		ENH: Added Edit button to Reload&test area

It is now simpler to open a scripted module's source code in an editor.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25464 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Python/slicer/ScriptedLoadableModule.py Diff File

master feda832c

2016-10-19 23:13:22

lassoan

Details Diff 		ENH: Improved auto-complete effect preview opacity options

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25463 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorAutoCompleteEffect.py Diff File

master 7b0a17f8

2016-10-19 23:01:59

lassoan

Details Diff 		ENH: Added auto-update to auto-complete segmentation tool

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25462 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorAutoCompleteEffect.py Diff File

master cec69f7c

2016-10-19 21:15:43

lassoan

Details Diff 		ENH: Updated CTK

SHA-1: afe8505a8286a701900fca1c97a4ad8876bbbe1a

* Merge pull request 0000674 from lassoan/checkable-combobox-python

ENH: Make ctkCheckableComboBox methods Python-wrapped

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25461 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTK.cmake Diff File

master 2ab3231f

2016-10-18 23:19:19

lassoan

Details Diff 		BUG: Revert accidentally committed change

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25460 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/vtkMRMLSliceLogic.cxx Diff File

master 55a08610

2016-10-18 22:55:44

lassoan

Details Diff 		BUG: Fixed vtkOrientedImageDataResample::TransformOrientedImageDataBounds

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25459 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkSegmentationCore/vtkOrientedImageDataResample.cxx Diff File

master 91cbcb28

2016-10-18 22:55:40

lassoan

Details Diff 		ENH: Added OBJ file save option for model nodes

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25458 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/vtkMRMLSliceLogic.cxx Diff File

master 1f8bbb3f

2016-10-18 12:49:42

lassoan

Details Diff 		ENH: Changed label values in vtkMRMLSegmentationNode::GenerateMergedLabelmap

For label values generation use order of provided segment IDs instead of all segment IDs in the segmentation.
This is easier to use (as there is no need to look up the segment order in the original segmentation node)
and more flexible (order of label values can be chosen freely).

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25457 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLSegmentationNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLSegmentationNode.h Diff File

master d9cb79c7

2016-10-18 10:51:41

lassoan

Details Diff 		ENH: Reduce memory usage of IdentifyIsland effect

Islands are now clipped to their effective extent to reduce memory usage.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25456 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Segmentations/Logic/vtkSlicerSegmentationsModuleLogic.cxx Diff File

master 73f78806

2016-10-18 10:51:37

lassoan

Details Diff 		ENH: Add easy access to node selector in qSlicerSimpleMarkupsWidget

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25455 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/Widgets/qSlicerSimpleMarkupsWidget.cxx Diff File
mod - Modules/Loadable/Markups/Widgets/qSlicerSimpleMarkupsWidget.h Diff File

master 19182dd6

2016-10-18 01:27:31

lassoan

Details Diff 		ENH: Made fast growcut in segmentations module more robust

Switching between inputs and closing scene does not cause problems anymore.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25454 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorAutoCompleteEffect.py Diff File
mod - Modules/Loadable/Segmentations/Logic/vtkImageGrowCutSegment.cxx Diff File

master ab7c71f3

2016-10-18 00:43:43

lassoan

Details Diff 		ENH: Cleaned up fast growcut algorithm implementation in segmentations logic

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25453 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkSegmentationCore/vtkSegmentationConverter.cxx Diff File
mod - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorAutoCompleteEffect.py Diff File
mod - Modules/Loadable/Segmentations/EditorEffects/qSlicerSegmentEditorPaintEffect.cxx Diff File
mod - Modules/Loadable/Segmentations/Logic/CMakeLists.txt Diff File
mod - Modules/Loadable/Segmentations/Logic/FibHeap.h Diff File
rm - Modules/Loadable/Segmentations/Logic/vtkFastGrowCutSeg.cxx Diff File
rm - Modules/Loadable/Segmentations/Logic/vtkFastGrowCutSeg.h Diff File
add - Modules/Loadable/Segmentations/Logic/vtkImageGrowCutSegment.cxx Diff File
add - Modules/Loadable/Segmentations/Logic/vtkImageGrowCutSegment.h Diff File
mod - Modules/Loadable/Segmentations/Widgets/qMRMLSegmentEditorWidget.cxx Diff File

master 5d0bdf5a

2016-10-15 12:36:30

pinter

Details Diff 		BUG: Fixed py_nomainwindow_SegmentationsModuleTest1

The test failed because the merged labelmap used to use the segments' color index tag to set the labels of the binary labelmaps written in the merged labelmap. With the recent removal of this tag, the merged labelmap simply writes the segments in the order of the containing segment map

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25452 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Segmentations/Testing/Python/SegmentationsModuleTest1.py Diff File

master 82534ed9

2016-10-15 11:08:29

lassoan

Details Diff 		ENH: Quick update of growcut preview

Now growcut is just updated, not recomputed from scratch when making adjustments to the seeds.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25451 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorAutoCompleteEffect.py Diff File
mod - Modules/Loadable/Segmentations/Logic/FibHeap.cxx Diff File
mod - Modules/Loadable/Segmentations/Logic/vtkFastGrowCutSeg.cxx Diff File
mod - Modules/Loadable/Segmentations/Logic/vtkFastGrowCutSeg.h Diff File

master d10dc5f4

2016-10-15 11:08:25

lassoan

Details Diff 		ENH: Made segment display node update more robust

Don't emit modified event when just updating internal cache to avoid reentrant updates in displayable managers.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25450 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLSegmentationDisplayNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLSegmentationDisplayNode.h Diff File
mod - Modules/Loadable/Segmentations/Widgets/qMRMLSegmentsTableView.cxx Diff File

master 7adbafb6

2016-10-15 11:08:21

lassoan

Details Diff 		PERF: Improved segment editor initialization speed

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25449 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkSegmentationCore/vtkOrientedImageDataResample.cxx Diff File

master b53695a1

2016-10-14 21:59:43

lassoan

Details Diff 		ENH: Create auto-complete effect from growcut and slice interpolation

The effect also has preview feature, so seeds or single-slice segmentation can be edited before result is finalized.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25448 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMakeLists.txt Diff File
mod - Libs/MRML/Core/vtkMRMLSegmentationDisplayNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLSegmentationNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLSegmentationNode.h Diff File
mod - Libs/vtkSegmentationCore/vtkOrientedImageDataResample.cxx Diff File
mod - Libs/vtkSegmentationCore/vtkOrientedImageDataResample.h Diff File
mod - Libs/vtkSegmentationCore/vtkSegmentation.cxx Diff File
mod - Libs/vtkSegmentationCore/vtkSegmentation.h Diff File
mod - Modules/Loadable/Segmentations/EditorEffects/Python/CMakeLists.txt Diff File
add - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorAutoCompleteEffect.py Diff File
mod - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorEffects.__init__.py.in Diff File
rm - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorGrowCutEffect.py Diff File
mod - Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorSmoothingEffect.py Diff File
mod - Modules/Loadable/Segmentations/EditorEffects/qSlicerSegmentEditorAbstractEffect.cxx Diff File
mod - Modules/Loadable/Segmentations/EditorEffects/qSlicerSegmentEditorAbstractEffect.h Diff File
mod - Modules/Loadable/Segmentations/Logic/CMakeLists.txt Diff File
add - Modules/Loadable/Segmentations/Logic/FibHeap.cxx Diff File
add - Modules/Loadable/Segmentations/Logic/FibHeap.h Diff File
add - Modules/Loadable/Segmentations/Logic/vtkFastGrowCutSeg.cxx Diff File
add - Modules/Loadable/Segmentations/Logic/vtkFastGrowCutSeg.h Diff File
mod - Modules/Loadable/Segmentations/MRMLDM/vtkMRMLSegmentationsDisplayableManager2D.cxx Diff File
mod - Modules/Loadable/Segmentations/Widgets/qMRMLSegmentEditorWidget.cxx Diff File
mod - Modules/Loadable/Terminologies/Logic/vtkSlicerTerminologiesModuleLogic.cxx Diff File

master 4bac13a6

2016-10-14 15:24:11

pinter

Details Diff 		ENH: Added Terminologies module for handling standard terminologies

Default terminology dictionaries are loaded on Slicer startup and can be used from Segmentations and Segment Editor to assign terminology entries to segments that appear in tooltips (later will take part in DICOMSeg export). Terminologies module also contains a qSlicerTerminologyNavigatorWidget that allows exploring terminologies.

-------------------------------------------------
ENH: Use CTK color picker in terminology selector

BUG: Fixed known bugs in terminology selector

BUG: Fixed minor bugs; Added custom color selection

ENH: Terminology selector dialog is used for segment color in segments table

Opacity delegate reverted back to qMRMLItemDelegate, as the slider shows up properly now (need to check on standard resolution screens)

ENH: Added terminology dialog, selector button, and delegate

The delegate needs to be set to the segment table (and other widgets that will use terminology) to be able to show and change terminology information. The delegate's editor is the new selector button that only shows the recommended color, but when clicked, shows the new selector dialog. The dialog is a simple wrapper dialog class for the navigator widget with select and cancel buttons.

ENH: Added anatomic region handling to terminology logic and navigator widget

ENH: Added terminology navigator widget and Json parsing logic

ENH: Load default terminology into Terminologies logic

Added two json files for the full SnoMed and its subset for the SlicerGeneralAnatomy entries. The SlicerGeneralAnatomy dictionary is loaded by default when calling the LoadDefaultTerminology function

ENH: Added Terminology module skeleton


git-svn-id: http://svn.slicer.org/Slicer4/trunk@25447 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkSegmentationCore/vtkSegment.cxx Diff File
mod - Libs/vtkSegmentationCore/vtkSegment.h Diff File
mod - Modules/Loadable/CMakeLists.txt Diff File
mod - Modules/Loadable/Segmentations/Widgets/CMakeLists.txt Diff File
mod - Modules/Loadable/Segmentations/Widgets/qMRMLSegmentsTableView.cxx Diff File
mod - Modules/Loadable/Segmentations/Widgets/qMRMLSegmentsTableView.h Diff File
add - Modules/Loadable/Terminologies/CMakeLists.txt Diff File
add - Modules/Loadable/Terminologies/Logic/CMakeLists.txt Diff File
add - Modules/Loadable/Terminologies/Logic/vtkSlicerTerminologiesModuleLogic.cxx Diff File
add - Modules/Loadable/Terminologies/Logic/vtkSlicerTerminologiesModuleLogic.h Diff File
add - Modules/Loadable/Terminologies/Logic/vtkSlicerTerminologyCategory.cxx Diff File
add - Modules/Loadable/Terminologies/Logic/vtkSlicerTerminologyCategory.h Diff File
add - Modules/Loadable/Terminologies/Logic/vtkSlicerTerminologyEntry.cxx Diff File
add - Modules/Loadable/Terminologies/Logic/vtkSlicerTerminologyEntry.h Diff File
add - Modules/Loadable/Terminologies/Logic/vtkSlicerTerminologyType.cxx Diff File
add - Modules/Loadable/Terminologies/Logic/vtkSlicerTerminologyType.h Diff File
add - Modules/Loadable/Terminologies/Resources/AnatomicRegionModifier-Master.json Diff File
add - Modules/Loadable/Terminologies/Resources/SegmentationCategoryTypeModifier-DICOM-Master.json Diff File
add - Modules/Loadable/Terminologies/Resources/SegmentationCategoryTypeModifier-SlicerGeneralAnatomy.json Diff File
add - Modules/Loadable/Terminologies/Resources/UI/qSlicerTerminologiesModule.ui Diff File
add - Modules/Loadable/Terminologies/Widgets/CMakeLists.txt Diff File
add - Modules/Loadable/Terminologies/Widgets/DesignerPlugins/CMakeLists.txt Diff File
add - Modules/Loadable/Terminologies/Widgets/DesignerPlugins/qSlicerTerminologiesModuleWidgetsAbstractPlugin.cxx Diff File
add - Modules/Loadable/Terminologies/Widgets/DesignerPlugins/qSlicerTerminologiesModuleWidgetsAbstractPlugin.h Diff File
add - Modules/Loadable/Terminologies/Widgets/DesignerPlugins/qSlicerTerminologiesModuleWidgetsPlugin.cxx Diff File
add - Modules/Loadable/Terminologies/Widgets/DesignerPlugins/qSlicerTerminologiesModuleWidgetsPlugin.h Diff File
add - Modules/Loadable/Terminologies/Widgets/DesignerPlugins/qSlicerTerminologyNavigatorWidgetPlugin.cxx Diff File
add - Modules/Loadable/Terminologies/Widgets/DesignerPlugins/qSlicerTerminologyNavigatorWidgetPlugin.h Diff File
add - Modules/Loadable/Terminologies/Widgets/Resources/UI/qSlicerTerminologyNavigatorWidget.ui Diff File
add - Modules/Loadable/Terminologies/Widgets/qSlicerTerminologyItemDelegate.cxx Diff File
add - Modules/Loadable/Terminologies/Widgets/qSlicerTerminologyItemDelegate.h Diff File
add - Modules/Loadable/Terminologies/Widgets/qSlicerTerminologyNavigatorWidget.cxx Diff File
add - Modules/Loadable/Terminologies/Widgets/qSlicerTerminologyNavigatorWidget.h Diff File
add - Modules/Loadable/Terminologies/Widgets/qSlicerTerminologySelectorButton.cxx Diff File
add - Modules/Loadable/Terminologies/Widgets/qSlicerTerminologySelectorButton.h Diff File
add - Modules/Loadable/Terminologies/Widgets/qSlicerTerminologySelectorDialog.cxx Diff File
add - Modules/Loadable/Terminologies/Widgets/qSlicerTerminologySelectorDialog.h Diff File
add - Modules/Loadable/Terminologies/qSlicerTerminologiesModule.cxx Diff File
add - Modules/Loadable/Terminologies/qSlicerTerminologiesModule.h Diff File
add - Modules/Loadable/Terminologies/qSlicerTerminologiesModuleWidget.cxx Diff File
add - Modules/Loadable/Terminologies/qSlicerTerminologiesModuleWidget.h Diff File

master 96681abe

2016-10-14 12:48:19

pinter

Details Diff 		BUG: Removed color index tag from segments WIP

Using color indices was a heritage from when segmentations had a color table associated to them, and caused instability in labelmap export. It is needed to remove usage of color index tags from joint smoothing and grow cut, which will be done by @lassoan soon

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25446 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLSegmentationDisplayNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLSegmentationDisplayNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLSegmentationNode.cxx Diff File

master fbde60de

2016-10-13 13:52:55

lassoan

Details Diff 		BUG: Fixed IdentifyIslandEffect on transformed segments

When IdentifyIslandEffect was applied on a transformed segment, the result was incorrectly transformed.
The reason was that vtkMRMLSlicerSegmentationsModuleLogic::ImportLabelmapToSegmentationNode(vtkOrientedImageData*, ...)
assumed the labelmap was in the world coordinate system.
A better assumption is that the labelmap to be imported is in the same coordinate system as the segmentation node.
Described the current behavior in the method's documentation.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25445 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Segmentations/Logic/vtkSlicerSegmentationsModuleLogic.cxx Diff File
mod - Modules/Loadable/Segmentations/Logic/vtkSlicerSegmentationsModuleLogic.h Diff File

master fdc102e9

2016-10-13 01:00:52

jcfr

Details Diff 		ENH: Begin 4.7.0 development

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25442 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMakeLists.txt Diff File
mod - Utilities/Scripts/SlicerWizard/__version__.py Diff File

master a4f5de2a

2016-10-13 00:29:11

jcfr

Details Diff 		ENH: Slicer 4.6.0

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25441 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMakeLists.txt Diff File
mod - Utilities/Scripts/SlicerWizard/__version__.py Diff File

master 41df9c1a

2016-10-12 23:50:40

jcfr

Details Diff 		BUG: Extension build system: Fix use of wrapper script on windows. Fixes 0004247

This commit ensures the build configuration is passed to the wrapped
command.

It fixes error like this one:


8: SetMakeCommand:C:\D\Support\CMake-3.5.0-rc3\bin\cmake.exe --build . --config "$(Configuration)"
8:
8: SetCTestConfiguration:MakeCommand:C:\D\Support\CMake-3.5.0-rc3\bin\cmake.exe --build . --config "$(Configuration)"
8:
8: Build project
8:
8: MakeCommand:C:\D\Support\CMake-3.5.0-rc3\bin\cmake.exe --build . --config "$(Configuration)"
8: Run command: "C:\D\Support\CMake-3.5.0-rc3\bin\cmake.exe" "--build" "." "--config" "$(Configuration)"
8:
8: Microsoft (R) Build Engine version 12.0.40629.0
8: [Microsoft .NET Framework, version 4.0.30319.34209]
8: Copyright (C) Microsoft Corporation. All rights reserved.
8: Build started 10/12/2016 10:57:46 PM.
8:
8: Project "C:\D\N\Slicer-1-build\Slicer-build\Extensions\CMake\Testing\build_with_upload-build\TestExtA-build\ALL_BUILD.vcxproj" on node 1 (default targets).
8: Project "C:\D\N\Slicer-1-build\Slicer-build\Extensions\CMake\Testing\build_with_upload-build\TestExtA-build\ALL_BUILD.vcxproj" (1) is building "C:\D\N\Slic
er-1-build\Slicer-build\Extensions\CMake\Testing\build_with_upload-build\TestExtA-build\ZERO_CHECK.vcxproj" (2) on node 1 (default targets).
8:
8:
8: C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.Cpp.Platform.targets(61,5): error MSB8013: This project doesn't contain the Configuration an
d Platform combination of $(Configuration)|x64. [C:\D\N\Slicer-1-build\Slicer-build\Extensions\CMake\Testing\build_with_upload-build\TestExtA-build\ZERO_CHECK.v
cxproj] [C:\D\N\Slicer-1-build\Slicer-build\Extensions\CMake\Testing\build_with_upload-build\TestExtA.vcxproj]
8:

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25440 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Extensions/CMake/SlicerBlockBuildPackageAndUploadExtensions.cmake Diff File
mod - Extensions/CMake/SlicerBlockUploadExtension.cmake Diff File

master c226f731

2016-10-12 23:50:38

jcfr

Details Diff 		BUG: Extension build system: Ignore extension CTest return code. Fixes 0004247

This commit ensures each "EXTENSION_UPLOAD_COMMAND" responsible to configure,
build, test and package any given extension is completely "sandboxed" by
using a wrapper script.

This is required because simply setting the RETURN_VALUE parameter
to the ctest_test() command is not enough to avoid the script from
exiting with error code.

#
# The following wrapper script is required to workaround issue 0004247
# and avoid the all extension build from failing if a test of
# extension fail.
#
# Note that as soon as CMake >= 3.6.7 is released, it should be possible
# to remove the wrapper script and simply specify CAPTURE_CMAKE_ERROR
# ctest_test option.
#
# See https://cmake.org/cmake/help/v3.7/command/ctest_test.html
#

Tested-by: Isaiah Norton <inorton@bwh.harvard.edu>
Tested-by: Johan Andruejol <johan.andruejol@kitware.com>
Tested-by: Nicole Aucoin <nicole@bwh.harvard.edu>
Tested-by: Steve Pieper <pieper@isomics.com>

Reported-by: Csaba Pinter <csaba.pinter@queensu.ca>
Reported-by: Andras Lasso <lasso@cs.queensu.ca>

Thanks: All of the above

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25439 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Extensions/CMake/SlicerBlockBuildPackageAndUploadExtensions.cmake Diff File
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