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master 81951bb8

2016-06-10 19:55:12

jcfr

Details Diff 		BUG: Extension packaging: Ensure @rpath is not applied at build time

Having the ids of library set as full path is mandatory to ensure
fixup bundle script works properly.

Setting CMAKE_MACOSX_RPATH to 0 ensures that @rpath will not be automatically
be applied to extension module libraries where the CMake minimum required
version >= 3.0.

CMake 3.0 is the version where CMP0042 is set to NEW by default.

CMP0042 set to NEW means that CMAKE_MACOSX_RPATH is ON by default.

Notes: Existing workarounds within Slicer core (e.g use of patched version
of ITK forcing CMP0042 to OLD) will be removed and a similar change will
also be applied to SlicerCPack.cmake.

See SBU-BMI/SlicerOpenCV#30

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25180 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/UseSlicer.cmake.in Diff File

master bd4ccceb

2016-06-10 13:43:56

msmolens

Details Diff 		BUG: Fix py_nomainwindow_SlicerOptionIgnoreSlicerRCTest

This commit fixes an error when running py_nomainwindow_SlicerOptionIgnoreSlicerRCTest. On Windows the error message is similar to:

File "C:/D/N/Slicer-0/Applications/SlicerApp/Testing/Python/SlicerOptionIgnoreSlicerRCTest.py", line 79, in <module>
os.remove(slicerrc)
WindowsError: [Error 32] The process cannot access the file because it is being used by another process: 'c:\\users\\slicer~1\\appdata\\local\\temp\\tmpqu7b2u'

The issue is that tempfile.mkstemp() returns an OS-level handle to an open file.
Using Python's open() function on the filename opens the file a second time.
Therefore, an error occurs when attempting to remove the file, because the
handle opened by tempfile.mkstemp() has not been closed.

Replacing open() with os.fdopen() is one way to fix the issue. In that case, the
file is opened only once.

From: Max Smolens <max.smolens@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25179 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/SlicerOptionIgnoreSlicerRCTest.py Diff File

master 1f4fa0a8

2016-06-10 01:20:23

jcfr

Details Diff 		BUG: Fix logging warning message when slicer.vtkPVScalarBarActor doesn't exist

This commit fixes a bug with logging a warning message. Because 'slicer.logging'
doesn't exist, the call to 'slicer.logging.warning()' failed with an error like:

File "/path/to/Slicer-build/lib/Slicer-4.5/qt-scripted-modules/DataProbeLib/SliceViewAnnotations.py", line 25, in __init__
slicer.logging.warning("SliceAnnotations: Disable features relying on vtkPVScalarBarActor")
AttributeError: 'module' object has no attribute 'logging'

Now the code calls 'logging.warning()'.

This warning was added in r24058. As described in that commit, the warning can
be triggered by starting Slicer with '--disable-builtin-loadable-modules'.

From: Max Smolens <max.smolens@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25178 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/DataProbe/DataProbeLib/SliceViewAnnotations.py Diff File

master acc9915c

2016-06-09 14:50:18

jcfr

Details Diff 		BUG: Update VTK: Support InvokeEvent with param from python. Fixes 0004181

Currently it only supports strings, floats and ints.

Infrastructure to support vtkObjects is also in place, but cherry-picking
the wrapping infrastructure patches to support it are too involved
to be reliably done.

Doing the following is now expected to work:

paramNode = slicer.vtkMRMLScriptedModuleNode()
paramNode.InvokeEvent(vtk.vtkCommand.ModifiedEvent, 4)

$ git shortlog 4b9957b..f08b7db --no-merges
Hastings Greer (1):
Allow pyvtkObjects to have InvokeEvent called on them with calldata


Thanks: Hastings Greer <hastings.greer@kitware.com>
Thanks: David Gobbi <david.gobbi@gmail.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25177 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_VTKv6.cmake Diff File

master e6188f5c

2016-06-08 22:53:09

jcfr

Details Diff 		STYLE: slicer.util.getFirstNodeByName: Extend test case.

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25176 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Python/slicer/tests/test_slicer_util_getNodes.py Diff File

master ce917bab

2016-06-08 22:53:07

jcfr

Details Diff 		BUG: slicer.util.getFirstNodeByName: Should not return only visible nodes

This commits updates "getFirstNodeByName()" to leverage changes
integrated in r25160 (ENH: Update VTK to handle default values
for array parameters in python)

Now wrapping of methods with pointer parameter having a NULL default value
are supported, there is no need to hardcode the value of "byHideFromEditors"
to either [0] or [1].

From: Francois Budin <francois.budin@gmail.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25175 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Python/slicer/util.py Diff File

master fe589e82

2016-06-08 22:53:06

jcfr

Details Diff 		BUG: Fix test_getNodesMultipleNodesSharingName. See 0004186

This commit fixes a regression introduced in r25155 (BUG: slicer.util.GetNodes:
Support multiple node with same name. Fix 0004186) by properly adding the
nodes sharing the same name.

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25174 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Python/slicer/tests/test_slicer_util_getNodes.py Diff File

master 63c6d2ae

2016-06-08 19:10:26

jcfr

Details Diff 		COMP: LandmarkRegistration: Update to use expected git tag

This commit update the git tag to effectively use the version of
the project mentioned in previous commit.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25173 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master acc642d8

2016-06-08 16:56:04

pieper

Details Diff 		PERF: 0004191 update landmark registration

New version avoids some duplicated work when interacting
with fiducial lists and displayable managers.

See:
https://github.com/pieper/LandmarkRegistration/commit/b6198147a57f2fe50aa9ac40194e67064a14a524

From: Steve Pieper <pieper@isomics.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25172 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master a0c599a6

2016-06-08 16:08:41

jcfr

Details Diff 		ENH: Add support for managing slice orientation presets

This commit generalizes the concept of slice orientation known as
Axial, Sagittal and Coronal so that it is possible to add, rename and
delete new ones.

Default presets (Axial, Sagittal and Coronal) are associated to a default
slice node in the application logic.

Handle orientation as 3x3 because maintaining sliceOrigin information
in matrices that are orientation presets is not relevant.

Notes:

(1) Mark Get/SetOrientationReference as protected: These methods are only
used internally and could ultimately be removed by refactoring
"RotateToVolumePlane()"

(2) Remove unused SetOrientationString: The method is not used in any Slicer
extensions.

(3) Explicitly setting the orienation string to "Reformat" is
not needed anymore because "GetOrientation()" or "GetOrientationString()"
will return "Reformat" if the SliceToRAS matrix is not one of the preset.

(4) For sake of consistency, in the RenameSliceOrientationPreset, the
orientation reference is also renamed.

(5) In "Copy()" method, Orientation and OrientationReference are set
after the presets.

(6) Remove unused SetOrientationToReformat() function. At the time of this
commit, it was used only in "SlicerRT/ExternalBeamPlanning/Logic/vtkSlicerExternalBeamPlanningModuleLogic"
and the maintainer of the module planned on removing the call.

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Co-authored-by: Andras Lasso <lasso@queensu.ca>

From: Davide Punzo <punzodavide@hotmail.it>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25171 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/CMakeLists.txt Diff File
add - Applications/SlicerApp/Testing/Python/SlicerOrientationSelectorTest.py Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLSceneTest2.cxx Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLSliceNodeTest1.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLCoreTestingUtilities.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLSliceNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLSliceNode.h Diff File
mod - Libs/MRML/Logic/Testing/Cxx/vtkMRMLApplicationLogicTest1.cxx Diff File
mod - Libs/MRML/Logic/vtkMRMLApplicationLogic.cxx Diff File
mod - Libs/MRML/Logic/vtkMRMLSliceLayerLogic.cxx Diff File
mod - Libs/MRML/Logic/vtkMRMLSliceLogic.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLSceneDisplayableModelTest2.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLSceneModelHierarchyModelTest2.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLSceneTransformModelTest2.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLSliceControllerWidgetEventTranslatorPlayerTest1.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLSliceControllerWidgetTest.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLSliceWidgetTest1.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLSliceWidgetTest2.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLTreeViewEventTranslatorPlayerTest1.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLTreeViewTest1.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLVolumeThresholdWidgetEventTranslatorPlayerTest1.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLVolumeThresholdWidgetTest1.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLVolumeThresholdWidgetTest2.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLWindowLevelWidgetEventTranslatorPlayerTest1.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLWindowLevelWidgetTest1.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLSliceControllerWidget.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLSliceControllerWidget_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLSliceInformationWidget.cxx Diff File
mod - Modules/Loadable/Reformat/qSlicerReformatModuleWidget.cxx Diff File
mod - Modules/Loadable/Units/Testing/Cxx/vtkSlicerUnitsLogicTest1.cxx Diff File

master 1642a45e

2016-06-08 13:58:12

jcfr

Details Diff 		STYLE: vtkMRMLSliceNode: Tweak doxygen of SetOrientationTo methods

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25170 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLSliceNode.h Diff File

master 4c241888

2016-06-08 11:53:06

alexy

Details Diff 		BUG: 4204. Fixed output CLI parameters <file> and <directory> so that users are able to enter file/directory names.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25169 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCLI/qSlicerCLIModuleUIHelper.cxx Diff File

master 07d56668

2016-06-08 03:43:43

jcfr

Details Diff 		ENH: vtkMRMLApplicationLogicTest1: Add test for Set/GetSliceLogics()

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25168 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/Testing/Cxx/vtkMRMLApplicationLogicTest1.cxx Diff File
mod - Libs/MRML/Logic/vtkMRMLApplicationLogic.cxx Diff File

master d43b2585

2016-06-08 03:43:41

jcfr

Details Diff 		STYLE: vtkMRMLApplicationLogicTest1: Refactor code to allow adding new tests

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25167 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Logic/Testing/Cxx/vtkMRMLApplicationLogicTest1.cxx Diff File

master 6b905e04

2016-06-08 02:48:13

jcfr

Details Diff 		ENH: vtkAddonMathUtilities: Add GetOrientationMatrix() function

Co-authored-by: Davide Punzo <punzodavide@hotmail.it>

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25166 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkAddon/Testing/vtkAddonMathUtilitiesTest1.cxx Diff File
mod - Libs/vtkAddon/vtkAddonMathUtilities.cxx Diff File
mod - Libs/vtkAddon/vtkAddonMathUtilities.h Diff File

master d3060819

2016-06-08 02:48:11

jcfr

Details Diff 		ENH: vtkAddon: Add "CHECK_DOUBLE" testing macro

Co-authored-by: Davide Punzo <punzodavide@hotmail.it>

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25165 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkAddon/vtkAddonTestingMacros.h Diff File

master 49b352f0

2016-06-08 02:48:08

jcfr

Details Diff 		ENH: vtkAddon: Add method to compare 3x3 matrices

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

From: Davide Punzo <punzodavide@hotmail.it>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25164 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/vtkAddon/Testing/vtkAddonMathUtilitiesTest1.cxx Diff File
mod - Libs/vtkAddon/vtkAddonMathUtilities.cxx Diff File
mod - Libs/vtkAddon/vtkAddonMathUtilities.h Diff File

master 745ca048

2016-06-08 02:48:06

jcfr

Details Diff 		STYLE: Rename "Matrix4x4AreEqual" to "MatrixAreEqual"

Anticipating the addition of method comparing matrices of different types,
this commit renames the method with a more general name.

Co-authored-by: Davide Punzo <punzodavide@hotmail.it>

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25163 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/Testing/vtkMRMLTransformNodeTest1.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLSliceNode.cxx Diff File
mod - Libs/MRML/Logic/vtkMRMLSliceLayerLogic.cxx Diff File
mod - Libs/vtkAddon/Testing/vtkAddonMathUtilitiesTest1.cxx Diff File
mod - Libs/vtkAddon/vtkAddonMathUtilities.cxx Diff File
mod - Libs/vtkAddon/vtkAddonMathUtilities.h Diff File

master 4a213169

2016-06-08 02:48:03

jcfr

Details Diff 		STYLE: vtkMRMLSliceNode: Fix typo in doxygen comment

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25162 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLSliceNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLSliceNode.h Diff File

master bc7ca08a

2016-06-03 16:57:04

jcfr

Details Diff 		ENH: qMRMLThreeDViewControllerWidget: Set ctkAxesWidget labels from view node

This commit updates the code using feature integrated in
r24961 (ENH: Made view axis labels configurable) and
r25157 (ENH: Update CTK to include ctkAxesWidget support for
setting AxesLabels)

From: Davide Punzo <punzodavide@hotmail.it>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25161 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Widgets/qMRMLThreeDViewControllerWidget.cxx Diff File

master 694291df

2016-06-03 16:57:02

jcfr

Details Diff 		ENH: Update VTK to handle default values for array parameters in python

Without this commit, one must specify parameters like (,int array[3]=0) when
the method is called from python.

$ git shortlog 1c30cb0..4b9957b --no-merges
David Gobbi (2):
Fix wrapping pointer parameters with default value 0.
Handle default values for array parameters in python.

From: Francois Budin <francois.budin@gmail.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25160 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_VTKv6.cmake Diff File

master 1bff66d6

2016-06-03 16:38:20

jcfr

Details Diff 		STYLE: qMRMLSliceControllerWidget: Refactor code introducing mrmlOrientation()

Co-authored-by: Davide Punzo <punzodavide@hotmail.it>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25159 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Widgets/qMRMLSliceControllerWidget.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLSliceControllerWidget_p.h Diff File

master 77140777

2016-06-03 16:38:17

jcfr

Details Diff 		STYLE: vtkMRMLSliceNode: Keep reference to matrix using smart pointers

Co-authored-by: Davide Punzo <punzodavide@hotmail.it>
Suggested-by: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25158 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Logic/vtkSlicerApplicationLogic.h Diff File
mod - Libs/MRML/Core/vtkMRMLSliceNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLSliceNode.h Diff File

master 146e7592

2016-06-03 02:11:49

jcfr

Details Diff 		ENH: Update CTK to include ctkAxesWidget support for setting AxesLabels

$ git shortlog --no-merges adc88bf..5b7dc1a
Davide Punzo (1):
ENH: ctkWidgetAxes: Add setter for AxisLabels

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25157 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTK.cmake Diff File

master 6551e17d

2016-06-03 01:16:13

jcfr

Details Diff 		STYLE: slicer.util.getFirstNodeByName: Refactor code to use C++ implementation

From: Francois Budin <francois.budin@gmail.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25156 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Python/slicer/tests/test_slicer_util_getNodes.py Diff File
mod - Base/Python/slicer/util.py Diff File
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