Changesets: Slicer

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2145-support-for-installing-extension-from-file aea2be6a

2013-09-03 14:29:40

jcfr

Details Diff 		COMP: Fix unused variable warnings in vtkMRMLMarkupsStorageNode

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22392 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/MRML/vtkMRMLMarkupsStorageNode.cxx Diff File

2145-support-for-installing-extension-from-file 7149ad16

2013-09-03 14:29:38

jcfr

Details Diff 		COMP: Fix unused variable warnings in vtkSlicerCLIModuleLogic

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22391 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCLI/vtkSlicerCLIModuleLogic.cxx Diff File

2145-support-for-installing-extension-from-file cf361133

2013-09-03 07:44:06

fedorov

Details Diff 		BUG: fix the issue where warning field is editable

If non populated, warning is initialized to '', allowing to set item flags.
The solution was discussed with @pieper. Closes issue 3284.


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22390 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DICOM/DICOMLib/DICOMWidgets.py Diff File

2145-support-for-installing-extension-from-file 6fbd582a

2013-09-03 01:58:20

jcfr

Details Diff 		BUG: With "--launch" arg - Add symlink support / Do not show splashscreen

Fixes 0002356
Fixes 0003075

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22389 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTKAPPLAUNCHER.cmake Diff File

2145-support-for-installing-extension-from-file 57ea2a92

2013-09-03 00:04:53

jcfr

Details Diff 		BUG: Remove DTI tutorial until pipeline for glyphing is fixed.

See r22363 [1], issue 0003323 [2] and issue 0002808 [3]

[1] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22363
[2] http://www.na-mic.org/Bug/view.php?id=3323
[2] http://www.na-mic.org/Bug/view.php?id=2808

Co-authored-by: Chrystel Juan <chrystel.juan@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22388 3bd1e089-480b-0410-8dfb-8563597acbee
rm - Applications/SlicerApp/Data/Input/DiffusionTensorImagingTutorial.xml Diff File
mod - Applications/SlicerApp/Testing/Python/CMakeLists.txt Diff File

2145-support-for-installing-extension-from-file ddce69ba

2013-09-02 23:10:35

jcfr

Details Diff 		COMP: Fix unused variable warning in qSlicerViewControllersModuleWidget

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22387 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/ViewControllers/qSlicerViewControllersModuleWidget.cxx Diff File

2145-support-for-installing-extension-from-file 31a2ac7e

2013-09-02 23:10:31

jcfr

Details Diff 		ENH: Associate icon with the new Slice view layouts

This is a follow-up of previous commit r22385

See 0002384

From: Andrey Fedorov <fedorov@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22386 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Resources/UI/qSlicerAppMainWindow.ui Diff File
add - Libs/MRML/Widgets/Resources/Icons/LayoutFiveByTwoSliceView.png Diff File
add - Libs/MRML/Widgets/Resources/Icons/LayoutFourByThreeSliceView.png Diff File
add - Libs/MRML/Widgets/Resources/Icons/LayoutFourByTwoSliceView.png Diff File
mod - Libs/MRML/Widgets/Resources/qMRMLWidgets.qrc Diff File

2145-support-for-installing-extension-from-file 8f9a9c3a

2013-09-02 17:57:29

jcfr

Details Diff 		ENH: Adding three new layouts

Slice view only configurations added: 4x3, 4x2, 5x2.

See 0002384

From: Andrey Fedorov <fedorov@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22385 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Resources/UI/qSlicerAppMainWindow.ui Diff File
mod - Applications/SlicerApp/qSlicerAppMainWindow.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLLayoutNode.h Diff File
mod - Libs/MRML/Logic/vtkMRMLLayoutLogic.cxx Diff File

2145-support-for-installing-extension-from-file 85b98c19

2013-09-02 16:07:13

fedorov

Details Diff 		BUG: fix the issues related to incorrect coloring of the static chart and incorrect baseline used for percent change visualization


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22384 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_MultiVolumeExplorer.cmake Diff File

2145-support-for-installing-extension-from-file 269ef449

2013-09-02 15:36:46

jcfr

Details Diff 		COMP: Explicitly require CMake >= 2.8.11.2 on Mountain Lion

See comment in the code for details.

Fixes 0002025
Fixes 0002022
See also 0002957

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22383 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerBlockPlatformCheck.cmake Diff File

2145-support-for-installing-extension-from-file 3d677f31

2013-09-02 15:36:44

jcfr

Details Diff 		COMP: Change minimum supported MacOSX version from 10.4 to 10.5

The build system is now consistent with what is reported on
http://download.slicer.org

See 0002025

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22382 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerBlockPlatformCheck.cmake Diff File

2145-support-for-installing-extension-from-file 072bbef3

2013-09-02 13:14:16

jcfr

Details Diff 		COMP: Remove obsolete comment in module CMakeLists.txt

Following r22038, the comment "# Do not use 'project()'" doesn't make
sense anymore.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22381 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/CLI/ACPCTransform/CMakeLists.txt Diff File
mod - Modules/CLI/AddScalarVolumes/CMakeLists.txt Diff File
mod - Modules/CLI/AffineRegistration/CMakeLists.txt Diff File
mod - Modules/CLI/BSplineDeformableRegistration/CMakeLists.txt Diff File
mod - Modules/CLI/BSplineToDeformationField/CMakeLists.txt Diff File
mod - Modules/CLI/BlobDetection/CMakeLists.txt Diff File
mod - Modules/CLI/CastScalarVolume/CMakeLists.txt Diff File
mod - Modules/CLI/CheckerBoardFilter/CMakeLists.txt Diff File
mod - Modules/CLI/ConnectedComponent/CMakeLists.txt Diff File
mod - Modules/CLI/CreateDICOMSeries/CMakeLists.txt Diff File
mod - Modules/CLI/CurvatureAnisotropicDiffusion/CMakeLists.txt Diff File
mod - Modules/CLI/DTIImportExport/CMakeLists.txt Diff File
mod - Modules/CLI/DWIJointRicianLMMSEFilter/CMakeLists.txt Diff File
mod - Modules/CLI/DWIRicianLMMSEFilter/CMakeLists.txt Diff File
mod - Modules/CLI/DWIToDTIEstimation/CMakeLists.txt Diff File
mod - Modules/CLI/DWIUnbiasedNonLocalMeansFilter/CMakeLists.txt Diff File
mod - Modules/CLI/DicomToNrrdConverter/CMakeLists.txt Diff File
mod - Modules/CLI/DiffusionTensorScalarMeasurements/CMakeLists.txt Diff File
mod - Modules/CLI/DiffusionTensorTest/CMakeLists.txt Diff File
mod - Modules/CLI/DiffusionWeightedVolumeMasking/CMakeLists.txt Diff File
mod - Modules/CLI/ExecutionModelTour/CMakeLists.txt Diff File
mod - Modules/CLI/ExpertAutomatedRegistration/CMakeLists.txt Diff File
mod - Modules/CLI/ExtractSkeleton/CMakeLists.txt Diff File
mod - Modules/CLI/FiberBundleLabelSelect/CMakeLists.txt Diff File
mod - Modules/CLI/FiducialRegistration/CMakeLists.txt Diff File
mod - Modules/CLI/FreesurferSurfaceSectionExtraction/CMakeLists.txt Diff File
mod - Modules/CLI/GaussianBlurImageFilter/CMakeLists.txt Diff File
mod - Modules/CLI/GradientAnisotropicDiffusion/CMakeLists.txt Diff File
mod - Modules/CLI/GrayscaleFillHoleImageFilter/CMakeLists.txt Diff File
mod - Modules/CLI/GrayscaleGrindPeakImageFilter/CMakeLists.txt Diff File
mod - Modules/CLI/GrayscaleModelMaker/CMakeLists.txt Diff File
mod - Modules/CLI/HistogramMatching/CMakeLists.txt Diff File
mod - Modules/CLI/ImageLabelCombine/CMakeLists.txt Diff File
mod - Modules/CLI/LabelMapSmoothing/CMakeLists.txt Diff File
mod - Modules/CLI/LinearRegistration/CMakeLists.txt Diff File
mod - Modules/CLI/MRIBiasFieldCorrection/CMakeLists.txt Diff File
mod - Modules/CLI/MaskScalarVolume/CMakeLists.txt Diff File
mod - Modules/CLI/MedianImageFilter/CMakeLists.txt Diff File
mod - Modules/CLI/MergeModels/CMakeLists.txt Diff File
mod - Modules/CLI/ModelMaker/CMakeLists.txt Diff File
mod - Modules/CLI/ModelToLabelMap/CMakeLists.txt Diff File
mod - Modules/CLI/MultiResolutionAffineRegistration/CMakeLists.txt Diff File
mod - Modules/CLI/MultiplyScalarVolumes/CMakeLists.txt Diff File
mod - Modules/CLI/N4ITKBiasFieldCorrection/CMakeLists.txt Diff File
mod - Modules/CLI/OrientScalarVolume/CMakeLists.txt Diff File
mod - Modules/CLI/OtsuThresholdImageFilter/CMakeLists.txt Diff File
mod - Modules/CLI/OtsuThresholdSegmentation/CMakeLists.txt Diff File
mod - Modules/CLI/PETStandardUptakeValueComputation/CMakeLists.txt Diff File
mod - Modules/CLI/ProbeVolumeWithModel/CMakeLists.txt Diff File
mod - Modules/CLI/ROITest/CMakeLists.txt Diff File
mod - Modules/CLI/ResampleDTIVolume/CMakeLists.txt Diff File
mod - Modules/CLI/ResampleScalarVectorDWIVolume/CMakeLists.txt Diff File
mod - Modules/CLI/ResampleScalarVolume/CMakeLists.txt Diff File
mod - Modules/CLI/RigidRegistration/CMakeLists.txt Diff File
mod - Modules/CLI/RobustStatisticsSegmenter/CMakeLists.txt Diff File
mod - Modules/CLI/SimpleRegionGrowingSegmentation/CMakeLists.txt Diff File
mod - Modules/CLI/SubtractScalarVolumes/CMakeLists.txt Diff File
mod - Modules/CLI/TestGridTransformRegistration/CMakeLists.txt Diff File
mod - Modules/CLI/ThresholdScalarVolume/CMakeLists.txt Diff File
mod - Modules/CLI/TractographyLabelMapSeeding/CMakeLists.txt Diff File
mod - Modules/CLI/VotingBinaryHoleFillingImageFilter/CMakeLists.txt Diff File
mod - Modules/Loadable/Annotations/CMakeLists.txt Diff File

2145-support-for-installing-extension-from-file 3a11b357

2013-09-01 20:17:21

fedorov

Details Diff 		ENH: update MultiVolumeExplorer module

* BUG: fix 3058 - support relative change plotting
* BUG: fix static plotting
* STYLE: clean up the code a bit


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22380 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_MultiVolumeExplorer.cmake Diff File

2145-support-for-installing-extension-from-file 8adb97b0

2013-08-31 08:39:35

alexy

Details Diff 		BUG: 3290. Fixed handling of ROIs and Annotation nodes in CLI modules. Added CLI_ROI_Test module.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22379 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCLI/qSlicerCLIModuleUIHelper.cxx Diff File
mod - Base/QTCLI/vtkSlicerCLIModuleLogic.cxx Diff File
mod - Modules/CLI/CMakeLists.txt Diff File
add - Modules/CLI/ROITest/CLIROITest.cxx Diff File
add - Modules/CLI/ROITest/CLIROITest.xml Diff File
add - Modules/CLI/ROITest/CMakeLists.txt Diff File
mod - Modules/Loadable/Annotations/MRML/vtkMRMLAnnotationControlPointsNode.cxx Diff File

2145-support-for-installing-extension-from-file 4f68eb0f

2013-08-31 01:46:46

jcfr

Details Diff 		ENH: Increase maximum size for Recently loaded menu

See 0001669

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22378 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/Resources/UI/qSlicerSettingsGeneralPanel.ui Diff File

2145-support-for-installing-extension-from-file 14164b23

2013-08-31 01:25:08

jcfr

Details Diff 		ENH: In Recently loaded menu, rename "Clear Menu" into "Clear History"

See 0001669

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22377 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/qSlicerAppMainWindow.cxx Diff File

2145-support-for-installing-extension-from-file c4fd32d5

2013-08-30 23:19:57

jcfr

Details Diff 		COMP: Remove redundant option MRML_USE_Teem and only use MRML_USE_vtkTeem

Fixes 0002571

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22376 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/CMakeLists.txt Diff File

2145-support-for-installing-extension-from-file edbb6ffa

2013-08-30 22:32:38

jcfr

Details Diff 		COMP: Suggest "insteadof" git config only for ITKv3.

Since ITKv4 doesn't use submodule (see fab42d0ef) it only applies to ITKv3.

Fixes 0002751

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22375 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

2145-support-for-installing-extension-from-file f0d00170

2013-08-30 22:08:13

jcfr

Details Diff 		COMP: Fix building of Slicer on MacOSX when cronjob is used

Extending PATH with /usr/sbin will allow the OpenSSL config script to
properly find 'sysctl' executable so that the configuration succeed.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22374 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/OpenSSL_patch_and_configure_step.cmake.in Diff File

2145-support-for-installing-extension-from-file 204de168

2013-08-30 18:33:45

jcfr

Details Diff 		BUG: Apply "ShowToolButtonText" settings to mainwindows on restart

While the slot qSlicerSettingsStylesPanel::onShowToolButtonTextToggled()
is properly called when the settings is registered at startup, it failed
to disable/enable the toolButton property because the mainwindow is not
instantiated.

This commit ensure this is the case in the main windows readSettings()
function.

Fixes 0002164

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22373 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/qSlicerAppMainWindow.cxx Diff File

2145-support-for-installing-extension-from-file fe43894c

2013-08-30 18:33:44

jcfr

Details Diff 		STYLE: Refactor function onShowToolButtonTextToggled re-using existing code

See 0002164

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22372 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerSettingsStylesPanel.cxx Diff File

2145-support-for-installing-extension-from-file c5a2bad9

2013-08-30 16:59:45

jcfr

Details Diff 		BUG: Update SimpleFilters for Marksup Fiducials

ceb1a61 ENH: Update single Point and index types for Markups
4241d7b ENH: update the filter's seed list to use Markups nodes

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22371 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_SimpleFilters.cmake Diff File

2145-support-for-installing-extension-from-file ab2fc916

2013-08-30 16:59:44

jcfr

Details Diff 		COMP: Fix unused variable warning in vtkSlicerMarkupsLogicTest3

From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22370 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Markups/Testing/Cxx/vtkSlicerMarkupsLogicTest3.cxx Diff File

2145-support-for-installing-extension-from-file 20882931

2013-08-30 14:41:01

naucoin

Details Diff 		BUG: update WriteCLI to fill a vector of strings, honor mutiple = false

Because Markups define multiple markups (with potentially multiple points) in one node,
it was writting multiple instances of a string + coordinates to the string stream passed
in to WriteCLI. This causes a problem for the parsing of the arguments in CLIs such as
FiducialRegistration which needed a separate string for each point.
With this change, the markup points are writen into a vector of strings, one string
for each point in each Markup.
Added the multipleFlag to be passed to WriteCLI, and if it's false, only write the
first selected markup to the output vector. If that markup has multiple points, it will
write all of those points.
Updated the Annotation control point to use the new WriteCLI signature, but because
of the way the points are written, it will only write the first point in a multi point
annotation (such as a ruler) if multiple is false, so it ignores it and the
CLI module logic takes care of ensuring that only the first child in an
annotation hierachy is written out. Write out a warning message if this is the case.
Added a test for FiducialRegistration, updated the Markups node test 1 to test the single point flag.
Removed trailing white spaces.

Issue 0001910 0003345 0003340



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22369 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCLI/vtkSlicerCLIModuleLogic.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLDisplayableNode.h Diff File
mod - Modules/CLI/FiducialRegistration/FiducialRegistration.cxx Diff File
mod - Modules/CLI/FiducialRegistration/Testing/CMakeLists.txt Diff File
add - Modules/CLI/FiducialRegistration/Testing/FiducialRegistrationTest.cxx Diff File
mod - Modules/Loadable/Annotations/MRML/vtkMRMLAnnotationControlPointsNode.cxx Diff File
mod - Modules/Loadable/Annotations/MRML/vtkMRMLAnnotationControlPointsNode.h Diff File
mod - Modules/Loadable/Markups/MRML/vtkMRMLMarkupsNode.cxx Diff File
mod - Modules/Loadable/Markups/MRML/vtkMRMLMarkupsNode.h Diff File
mod - Modules/Loadable/Markups/Testing/Cxx/vtkMRMLMarkupsNodeTest1.cxx Diff File

2145-support-for-installing-extension-from-file 8a24d04a

2013-08-30 14:36:28

jcfr

Details Diff 		COMP: Support build with Slicer_BUILD_DICOM_SUPPORT "on" then "off"

In commit r21598, the option Module_ITKIODCMTK was conditionally added
depending on the value of Slicer_BUILD_DICOM_SUPPORT.

To support build tree where Slicer_BUILD_DICOM_SUPPORT is first enabled
and then disabled, the options should be directly added so that ITK
is rebuilt with the module turned off.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22368 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_ITKv4.cmake Diff File
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