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2145-support-for-installing-extension-from-file a6f16a90

2013-05-07 08:51:51

pieper

Details Diff 		BUG: disable the ChangeTracker test when the module is not available

ChangeTracker is now an extension, so it won't typically be
available when tests are being run.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21967 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/Testing/Python/RSNA2012Quant.py Diff File

2145-support-for-installing-extension-from-file cebfae84

2013-05-06 18:51:52

pieper

Details Diff 		BUG: fix memory leak of vtkIntArray related to node references

Leak was exposed by commit 21957, but was originally introduced
in revision 21810.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21966 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLNode.h Diff File

2145-support-for-installing-extension-from-file 9de236d8

2013-05-06 09:21:08

fedorov

Details Diff 		ENH: added capability to parse multivolume data by TemporalPositionIdentifier
tag (0020,0100)


git-svn-id: http://svn.slicer.org/Slicer4/trunk@21965 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_MultiVolumeImporter.cmake Diff File

2145-support-for-installing-extension-from-file 518f8844

2013-05-01 00:58:14

jcfr

Details Diff 		STYLE: Remove obsolete comment from External_python.cmake

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21964 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_python.cmake Diff File

2145-support-for-installing-extension-from-file a9dd3c38

2013-05-01 00:45:20

jcfr

Details Diff 		COMP: Use internally consistent zlib

The zlib libraries are used by many differnt packages
includeing ITKv4, LibArchive, VTK, python, and teem.

This patchset builds a single version of zlib
that is mangled with a slicer namespace, and uses
that one library for all zlib operation through the
"USE_SYSTEM_ZLIB" options.

The mangling for vtk_zlib is disabled for teem because
it is not needed when using the External_zlib build.

From: Hans Johnson <hans-johnson@uiowa.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21963 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMakeLists.txt Diff File
mod - Libs/FreeSurfer/CMakeLists.txt Diff File
mod - SuperBuild.cmake Diff File
mod - SuperBuild/External_DCMTK.cmake Diff File
mod - SuperBuild/External_ITKv4.cmake Diff File
mod - SuperBuild/External_LibArchive.cmake Diff File
mod - SuperBuild/External_VTK.cmake Diff File
mod - SuperBuild/External_python.cmake Diff File
mod - SuperBuild/External_teem.cmake Diff File
mod - SuperBuild/External_zlib.cmake Diff File

2145-support-for-installing-extension-from-file afc064c4

2013-04-30 23:51:15

jcfr

Details Diff 		COMP: Prevent confusion removing unused "weave" external project

It was initially been introduced in r14346

The files have also been added to the Slicer attic for future reference.
See https://github.com/Slicer/Attic

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21962 3bd1e089-480b-0410-8dfb-8563597acbee
rm - SuperBuild/External_weave.cmake Diff File
rm - SuperBuild/weave_configure_step.cmake.in Diff File
rm - SuperBuild/weave_make_step.cmake.in Diff File

2145-support-for-installing-extension-from-file 0cd4e614

2013-04-30 23:42:27

jcfr

Details Diff 		STYLE: Remove unused files

Follow up of previous commit r21960

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21961 3bd1e089-480b-0410-8dfb-8563597acbee
rm - SuperBuild/python_patch_step.cmake.in Diff File
rm - SuperBuild/pythonrun.c.in Diff File
rm - SuperBuild/pythonrun.h.in Diff File

2145-support-for-installing-extension-from-file 78aeed78

2013-04-30 23:34:50

jcfr

Details Diff 		COMP: Remove python patch step related to "dll boundaries" hack

As explained in r21863, patching pythonrun.h and pythonrun.c was
required to prevent crash (related to dll boundaries [1][2]) when
building Slicer debug against a released python.

[1] http://stackoverflow.com/questions/2322095/why-does-this-program-crash-passing-of-stdstring-between-dlls
[2] http://social.msdn.microsoft.com/Forums/en-US/vcgeneral/thread/57e0d522-a42c-4add-963d-c87c6e76f161

Applying the approach discussed on the Blender mailing list[3], the
hack is not required anymore. This is made possible by using
"PyRun_String" function combined with the "execfile" statement.

[3] http://lists.blender.org/pipermail/bf-python/2008-May/005253.html

When transitioning to Python3 [4], use of "exec" and "compile" could be
considered:

with open('foo.py', 'r') as fh:
code = compile(fh.read(), 'foo.py', 'exec'); exec(code);

[4] http://stackoverflow.com/questions/436198/what-is-an-alternative-to-execfile-in-python-3-0

Approach making use of the "imp" module could also be investigated [5][6]

[5] http://www.ragestorm.net/blogs/?tag=execfile
[6] http://docs.python.org/2/library/imp.html

Finally, let's note that overall approach to load module could be
revised to prevent side effect as the one described in
"qSlicerScriptedFileDialog::setPythonSource"

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21960 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Logic/vtkSlicerScriptedLoadableModuleLogic.cxx Diff File
mod - Base/QTGUI/qSlicerScriptedFileDialog.cxx Diff File
mod - Base/QTGUI/qSlicerScriptedFileDialog.h Diff File
mod - Base/QTGUI/qSlicerScriptedLoadableModule.cxx Diff File
mod - Base/QTGUI/qSlicerScriptedLoadableModuleWidget.cxx Diff File
mod - CMake/vtkSlicerConfigure.h.in Diff File
mod - Libs/MRML/Core/vtkMRMLConfigure.h.in Diff File
mod - Libs/MRML/DisplayableManager/vtkMRMLScriptedDisplayableManager.cxx Diff File
mod - SuperBuild.cmake Diff File
mod - SuperBuild/External_python.cmake Diff File

2145-support-for-installing-extension-from-file 8be840cb

2013-04-30 15:53:11

alexy

Details Diff 		BUG: 3094. Update ROI selection widget after an ROI is selected


git-svn-id: http://svn.slicer.org/Slicer4/trunk@21959 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/TractographyDisplay/Widgets/qSlicerTractographyEditorROIWidget.cxx Diff File

2145-support-for-installing-extension-from-file 4e135908

2013-04-30 15:49:39

pieper

Details Diff 		ENH: add more keyboard shortcuts in Editor

Per request from Sonia, give shortcuts for paint, draw, wand, and
rectangle effects.

See full list here:

http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Editor#Editor_Wide_Keystrokes

Also STYLE: some dead code removal and end-of-line space removal.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21958 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/Editor/Editor.py Diff File
mod - Modules/Scripted/EditorLib/EditBox.py Diff File

2145-support-for-installing-extension-from-file 6c839bb0

2013-04-30 15:10:56

alexy

Details Diff 		BUG: 3072. Observe TransformModifiedEvent in the vtkMRMLTransformableNode.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21957 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLTransformableNode.cxx Diff File

2145-support-for-installing-extension-from-file 6fef5754

2013-04-30 11:55:02

finetjul

Details Diff 		BUG: Fix ApplyAndWait Completed CLI node status

By not observing the application logic, the cli logic was never notified
when the CLI node was completed and could not set the status accordingly.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21956 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCLI/vtkSlicerCLIModuleLogic.cxx Diff File

2145-support-for-installing-extension-from-file 4ff8a57b

2013-04-29 19:28:39

pohl

Details Diff 		BUG: Skull stripping in test mode did not work

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21955 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_EMSegment.cmake Diff File

2145-support-for-installing-extension-from-file aa699729

2013-04-29 18:56:04

pohl

Details Diff 		BUG: QInputdialog does not exist - changed it to QInputDialog

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21954 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerIOManager.cxx Diff File

2145-support-for-installing-extension-from-file df58ed05

2013-04-29 11:35:13

pieper

Details Diff 		COMP: fix duplicate metatype declaration (Issue 0003081)

See also r21951

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21953 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerFileDialog.h Diff File

2145-support-for-installing-extension-from-file df694809

2013-04-29 11:02:53

pieper

Details Diff 		ENH: 0002761 Add CTCTDentalSurgery example

One click to get pre- and post- surgery scans, but the
logic API allows access to individual scans if desired.

http://na-mic.org/Bug/view.php?id=2761

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21952 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/SampleData/SampleData.py Diff File

2145-support-for-installing-extension-from-file 35b30817

2013-04-29 10:12:03

finetjul

Details Diff 		ENH: Add qSlicerScriptedFileDialog

* Add qSlicerFileDialog::description
* Add input dialog to select reader when multiple readers accept the same mime data


How to create a FileDialog in python?

+class XYZFileDialog:
+ def __init__(self, parent):
+ self.parent = parent
+ parent.fileType = 'XYZ'
+ parent.description = 'XYZ'
+ parent.action = slicer.qSlicerFileDialog.Read
+ def isMimeDataAccepted(self):
+ accept = self.parent.mimeData().hasFormat("text/uri-list")
+ self.parent.acceptMimeData(accept)
+ def dropEvent(self):
+ self.parent.dropEvent().accept()
+ def execDialog(self):
+ print 'exec'

How to order the list (make the module reader by default):
Make the module depend on "Data" -> instantiated after "Data" module
def __init__(self, parent):
+ parent.dependencies = ["Data"]

Issue 0003081

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21951 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCore/qSlicerCoreApplication.cxx Diff File
mod - Base/QTGUI/CMakeLists.txt Diff File
mod - Base/QTGUI/qSlicerDataDialog.cxx Diff File
mod - Base/QTGUI/qSlicerDataDialog.h Diff File
mod - Base/QTGUI/qSlicerFileDialog.cxx Diff File
mod - Base/QTGUI/qSlicerFileDialog.h Diff File
mod - Base/QTGUI/qSlicerIOManager.cxx Diff File
mod - Base/QTGUI/qSlicerModelsDialog.cxx Diff File
mod - Base/QTGUI/qSlicerModelsDialog.h Diff File
mod - Base/QTGUI/qSlicerSaveDataDialog.cxx Diff File
mod - Base/QTGUI/qSlicerSaveDataDialog.h Diff File
add - Base/QTGUI/qSlicerScriptedFileDialog.cxx Diff File
add - Base/QTGUI/qSlicerScriptedFileDialog.h Diff File
mod - Base/QTGUI/qSlicerScriptedLoadableModule.cxx Diff File
mod - Base/QTGUI/qSlicerScriptedLoadableModule.h Diff File

2145-support-for-installing-extension-from-file c4a16fba

2013-04-27 18:35:11

jcfr

Details Diff 		BUG: Ensure ITK IOFactory are registered for EXECUTABLE_ONLY cli modules

The library wrapper are now used when compiling either the [executable] or
[executable + shared library] cli module. It allows to call the
"itk::itkFactoryRegistration();" in both cases.

Associated SlicerExecutionModel commit is:

// ---------------------------------------------------
ENH: Use library wrapper in the "EXECUTABLE_ONLY" case
This will allow custom wrapper to execute some code before the main
entry point in both the [exec + shared lib] and [exec only] cases.

The macro "MODULE_STATIC" has also been introduced and can be tested
within the wrapper to discriminate both cases.

Change the component associated with Archive target from RuntimeLibraries
to Development. That way, static library won't be packaged.
// ---------------------------------------------------


See http://na-mic.org/Bug/view.php?id=3008
Fixes 0003008

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21950 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/CLI/SEMCommandLineLibraryWrapper.cxx.in Diff File
mod - SuperBuild/External_SlicerExecutionModel.cmake Diff File

2145-support-for-installing-extension-from-file 63e9b477

2013-04-26 19:54:24

pieper

Details Diff 		COMP: fix packaging for linux DCMTK shared libraries

Be sure to include the symbolic links for the versioning.

Also remove APPLE branch since this is not called/needed for apple.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21949 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerBlockInstallDCMTKLibs.cmake Diff File

2145-support-for-installing-extension-from-file cc18ef43

2013-04-26 18:17:12

jcfr

Details Diff 		COMP: Fix config error introduced in r21943 by using PYTHON_LIBRARY_PATH

See issue 0001180 - http://www.na-mic.org/Bug/view.php?id=1180

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21948 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/CMakeLists.txt Diff File

2145-support-for-installing-extension-from-file 9feb3bd2

2013-04-26 18:01:17

jcfr

Details Diff 		COMP: Tweak installation of DCMTK libraries for MacOSX packaging

Following commit r21914, DCMTK libraries are build as shared
library. Commit r21944 ensured that they were installed. Since on MacOSX
the fixup process takes care of copying the library associated with
external projects, this commit exclude the systematic installation
of DCMTK libraries and teach the fixup script where these libraries
are located.

See issue 0003040

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21947 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerCPack.cmake Diff File
mod - CMake/SlicerCPackBundleFixup.cmake.in Diff File

2145-support-for-installing-extension-from-file 518e1f22

2013-04-26 17:52:30

jcfr

Details Diff 		BUG: Fix hook error specific Git bash/GUI using an old version of BASH.

Thanks Sankhesk for his help.

See http://www.na-mic.org/Bug/view.php?id=3086
Fixes 0003086

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21946 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Utilities/SetupForDevelopment.sh Diff File

2145-support-for-installing-extension-from-file 5804ab8d

2013-04-26 17:52:28

jcfr

Details Diff 		STYLE: Simplify CMake code re-using already set variable

As of r16822, the variable PYTHON_LIBRARY_PATH is set in the top-level
CMakeLists.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21945 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerBlockInstallPython.cmake Diff File

2145-support-for-installing-extension-from-file 800445da

2013-04-26 17:22:32

pieper

Details Diff 		COMP: Include DCMTK shared libraries in packages

Now that DCMTK is built as shared rather than static, the
dlls need to be copied into the install tree for packaging.

See also commit 21914 and bug 0003040.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21944 3bd1e089-480b-0410-8dfb-8563597acbee
add - CMake/SlicerBlockInstallDCMTKLibs.cmake Diff File
mod - CMake/SlicerCPack.cmake Diff File

2145-support-for-installing-extension-from-file 689851c3

2013-04-26 17:19:08

jcfr

Details Diff 		BUG: Fix startup crash due to improper dynamic linking of python dll

This problem affect the a windows build tree of Slicer.

On windows, as explained in [1], system path are searched before path
appended to PATH variable.

[1] Title: Search Path Used by Windows to Locate a DLL
Link: http://msdn.microsoft.com/en-us/library/7d83bc18(v=vs.90).aspx

Following the introduction of CMake'ified python (r21863), python 2.7.3 is
now used. Since developer also have a similar version installed on their
system, this is causing Slicer to crash due to binary incompatibility
between the patched version build by Slicer (r21848) and the one
installed on the system.

While this commit address the immediate issue specific to python, the same
problem would occur with VTK, Qt, ITK or any other Slicer external projects
is already installed in the system. The solution implemented by this commit
will have to be revisited.

See http://www.na-mic.org/Bug/view.php?id=1180
Fixes 0001180

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21943 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Applications/SlicerApp/CMakeLists.txt Diff File
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