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master 9e230ada

2013-12-31 17:21:06

pieper

Details Diff 		ENH: update LandmarkRegistration to support RegistrationPlugins

Still some work to do on the built-in plugins, but the framework
is now in place for extensions (like SlicerRT/Plastimatch) to provide
registration plugins.

Affine registration is now a plugin and it works like the previous
version of LandmarkRegistration which supported only Affine.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22792 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master 95fd51ff

2013-12-19 22:21:24

jcfr

Details Diff 		ENH: Fix module history to keep most recent selected module last

The current implementation is a dysfunctional mix between
a "module history navigator" and "fixed workflow navigator".

This commit implements "module history navigator" behavior,
which is useful for generic Slicer use.

A "fixed workflow navigator" is a very special case, it is only
applicable when all the modules are part of the workflow,
there are no loops, skipping of steps, auxiliary modules, etc.

Considering the following convention, the update is illustrated
below.

Legend:

-> X : Go to module X
P : List of module in the "previous stack"
N : List of module in the "next stack"

Current behaviour:

A P: - | N: -
-> B P: A | N: -
-> C P: BA | N: -
-> D P: CBA | N: -
-> A P: - | N: BCD
-> E P: A | N: -

After integrating this commit, the behaviour is then:

A P: - | N: -
-> B P: A | N: -
-> C P: BA | N: -
-> D P: CBA | N: -
-> A P: DCB | N: -
-> E P: ADCB | N: -

where

A: Welcome module
B: Annotations
C: Data
D: DataStore
E: SampleData

Fixes 0003533

From: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22791 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerModuleSelectorToolBar.cxx Diff File

master b2a88002

2013-12-19 21:47:04

jcfr

Details Diff 		STYLE: Update doxygen comment of vtkMRMLScene::AddReferencedNodeID

The comment document the changes introduced by commit r22669

From: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22790 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLScene.h Diff File

master e70b1b07

2013-12-19 21:46:54

jcfr

Details Diff 		STYLE: Improve readability of vtkMRMLScene::AddReferencedNodeID method

This commit does not introduced any functional change, it just makes
the code cleaner.

From: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22789 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLModelNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLScene.cxx Diff File

master 19bc562f

2013-12-19 21:46:42

jcfr

Details Diff 		BUG: Added missing node references update to scene->AddNode methods

Fixes http://na-mic.org/Mantis/view.php?id=3539.

Problem was that node references were not updated in the scene when
node->SetScene(scene) was called for the node before scene->AddNode(node).

From: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22788 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLScene.cxx Diff File

master af65ff60

2013-12-18 16:40:09

jcfr

Details Diff 		ENH: Add 'DataStore' to top-level module category.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22787 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master 63fef02a

2013-12-18 10:30:42

fedorov

Details Diff 		BUG: check that the frame image has been initialized

Fixes 0003535


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22786 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master e7102b54

2013-12-17 18:42:15

pieper

Details Diff 		ENH: Add prototype LandmarkRegistration and CompareVolumes modules

These are still work-in-progress modules, but should be usable to
support interatcive registration.

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22785 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master a44d8757

2013-12-17 16:05:36

jcfr

Details Diff 		COMP: Remove 'python_install_chmod_library' external project install step

Since the transition to CMake'ified python, this extra step is not
required anymore because the installed file has the expected
permissions.

Because the timestamp of the library is not systematically modified, it
will avoid the systematic recompilation of all project linking against
python library and speed up the overall MacOSX developer experience.


Before the update:

[...]
-- Installing: /path/to/python-install/lib/python2.7/zipfile.py
Performing python_install_chmod_library step for 'python'
Performing python_customPython_configure step for 'python'
Completed 'python'
$ ls -als python-install/lib/
total 3688
0 drwxr-xr-x 5 kitware staff 170 Dec 17 16:00 .
0 drwxr-xr-x 6 kitware staff 204 Dec 17 16:00 ..
3688 -rwxr-xr-x 1 kitware staff 1886288 Dec 17 16:00 libpython2.7.dylib
0 drwxr-xr-x 5 kitware staff 170 Dec 17 16:00 pkgconfig
0 drwxr-xr-x 234 kitware staff 7956 Dec 17 16:00 python2.7


After the update:

[...]
-- Installing: /path/to/python-install/lib/python2.7/zipfile.py
[ 18%] Performing python_customPython_configure step for 'python'
[ 18%] Completed 'python'
$ ls -als python-install/lib/
total 3688
0 drwxr-xr-x 5 kitware staff 170 Dec 17 16:02 .
0 drwxr-xr-x 6 kitware staff 204 Dec 17 16:02 ..
3688 -rwxr-xr-x 1 kitware staff 1886288 Dec 17 16:02 libpython2.7.dylib
0 drwxr-xr-x 5 kitware staff 170 Dec 17 16:02 pkgconfig
0 drwxr-xr-x 234 kitware staff 7956 Dec 17 16:02 python2.7

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22784 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_python.cmake Diff File

master 35f3bf01

2013-12-17 12:09:54

jcfr

Details Diff 		COMP: Fix build issue 0003522 due to nice() and getpid() calls.

From: Junichi Tokuda <tokuda@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22783 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Logic/vtkSlicerApplicationLogic.cxx Diff File

master 10f2c02c

2013-12-17 12:09:05

jcfr

Details Diff 		BUG: Fix "No handleSslErrors" slot run time error

Since by default moc (MetaObject compiler) doesn't understand ifdef, let
simply expect that SSL headers are available and unconditionally include
the "handleSslErrors". For this to work, we would have to associated a
compile definition with moc.

Since the QSslError header was already unconditionally included, defining
the slot is not a problem.

Error was:
Object::connect: No such slot qSlicerWebWidget::handleSslErrors(QNetworkReply*, const QList<QSslError> & ) in /home/jchris/Projects/Slicer/Base/QTGUI/qSlicerWebWidget.cxx:99
Object::connect: (receiver name: 'qSlicerWebWidget')

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22782 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTGUI/qSlicerWebWidget.cxx Diff File
mod - Base/QTGUI/qSlicerWebWidget.h Diff File

master eb412957

2013-12-17 10:16:17

jcfr

Details Diff 		COMP: Fix configuration adding missing parameter to ExternalProject_Add_Source

Following commit r22776, the macro ExternalProject_Add_Source has been
added and jqPlot retrieved using it but the URL and URL_MD5 parameters
were not considered. This probably happens because the jqPlot directory
was already existing.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22781 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/ExternalProjectAddSource.cmake Diff File

master 19b6b1a6

2013-12-17 05:36:40

jcfr

Details Diff 		COMP: Add DataStore module as remote module.

See [1] for details about remote module.

Fixes 0003400

[1] http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Build_system/Remote_Module

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22780 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

master ee51fd4f

2013-12-17 05:24:34

jcfr

Details Diff 		COMP: Configure include directories into SlicerConfig.cmake

This commit adds the following variables to the config file:

For each module:

- <Module>_INCLUDE_DIRS
- <ModuleLogic>_INCLUDE_DIRS
- <ModuleMRML>_INCLUDE_DIRS
- <ModuleWidget>_INCLUDE_DIRS

and for MRMLLogic:

- MRMLLogic_INCLUDE_DIRS

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22779 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerConfig.cmake.in Diff File
mod - CMake/SlicerGenerateSlicerConfig.cmake Diff File
mod - CMake/SlicerMacroBuildModuleLogic.cmake Diff File
mod - CMake/SlicerMacroBuildModuleMRML.cmake Diff File
mod - CMake/SlicerMacroBuildModuleWidgets.cmake Diff File
mod - CMake/SlicerMacroBuildQtModule.cmake Diff File

master 17028999

2013-12-17 02:30:53

jcfr

Details Diff 		COMP: Export qMRMLTreeViewPrivate class

Associated discussion: http://slicer-devel.65872.n3.nabble.com/Export-qMRMLTreeViewPrivate-tt4030532.html#a4030536

From: Csaba Pinter <csaba.pinter@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22778 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Widgets/qMRMLTreeView_p.h Diff File

master 41be19df

2013-12-17 02:30:49

jcfr

Details Diff 		STYLE: Add warning in pimpl headers explaining it is not part of Slicer API

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22777 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCLI/qSlicerCLIModuleWidget_p.h Diff File
mod - Base/QTCore/qSlicerCoreApplication_p.h Diff File
mod - Base/QTCore/qSlicerIOOptions_p.h Diff File
mod - Base/QTGUI/qSlicerDataDialog_p.h Diff File
mod - Base/QTGUI/qSlicerModelsDialog_p.h Diff File
mod - Base/QTGUI/qSlicerMouseModeToolBar_p.h Diff File
mod - Base/QTGUI/qSlicerSaveDataDialog_p.h Diff File
mod - Base/QTGUI/qSlicerViewersToolBar_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLChartViewControllerWidget_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLChartView_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLColorModel_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLEventLogger_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLLayoutManager_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLNodeComboBox_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLSceneDisplayableModel_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLSceneHierarchyModel_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLSceneModel_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLSceneViewMenu_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLSliceControllerWidget_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLSliceInformationWidget_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLSliceView_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLSliceWidget_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLThreeDViewControllerWidget_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLThreeDView_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLTreeView_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLViewControllerBar_p.h Diff File
mod - Libs/MRML/Widgets/qMRMLVolumeWidget_p.h Diff File

master bb38caff

2013-12-17 01:07:46

jcfr

Details Diff 		COMP: Easier maintenance simplifying process to add remote module source

Following this commit, adding a remote module source to Slicer can
simply be done calling:

Slicer_Remote_Add(Foo
GIT_REPOSITORY git://github.com/john/foo
GIT_TAG abcdef
OPTION_NAME Slicer_BUILD_Foo
LABELS REMOTE_MODULE
)

As a side effect, (1) the option "Slicer_BUILD_Foo" will automatically be
added as an advanced option and (2) the CMake variables "Slicer_BUILD_Foo"
and "Foo_SOURCE_DIR" will be passed to Slicer inner build.

Additionally, by associating the "REMOTE_MODULE" label, the corresponding
source directory will be added automatically using a call 'add_directory'
similar to this one:

add_directory(
/path/to/Slicer-build/Foo
/path/to/Slicer-build/Slicer-build/Module/Remote/Foo)

This happen in the Slicer/Modules/Remote/CMakeLists.txt file.

Finally, note that a new module named "ExternalProjectAddSource" has been
added, it is still experimental and should be considered as
internal to Slicer without any promise to keep backward compatibility.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22776 3bd1e089-480b-0410-8dfb-8563597acbee
add - CMake/ExternalProjectAddSource.cmake Diff File
mod - CMakeLists.txt Diff File
mod - Modules/Remote/CMakeLists.txt Diff File
mod - SuperBuild.cmake Diff File
rm - SuperBuild/External_BRAINSTools.cmake Diff File
rm - SuperBuild/External_EMSegment.cmake Diff File
rm - SuperBuild/External_MultiVolumeExplorer.cmake Diff File
rm - SuperBuild/External_MultiVolumeImporter.cmake Diff File
rm - SuperBuild/External_OpenIGTLinkIF.cmake Diff File
rm - SuperBuild/External_SimpleFilters.cmake Diff File
rm - SuperBuild/External_jqPlot.cmake Diff File

master 7c772699

2013-12-15 18:09:45

jcfr

Details Diff 		COMP: Update CTK - Unconditionally rebuild "CTK-build" inner project.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22775 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTK.cmake Diff File

master 89e8c0d2

2013-12-15 17:13:22

jcfr

Details Diff 		COMP: Fix CTK inner build configuration. See commontk/CTK@a91b2b2

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22774 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTK.cmake Diff File

master bbc5e1f9

2013-12-15 03:02:44

jcfr

Details Diff 		COMP: Simplify external project includes & passing of CMake vars to project

A new module named "ExternalProjectDependency" has been introduced, it is
equivalent to the Artichoke module at revision commontk/Artichoke@70ed903.

This new module is now used within Slicer to support its build system. To
maintain backward compatibility with existing extensions, the modules
"SlicerMacroEmptyExternalProject" and "SlicerMacroCheckExternalProjectDependency"
are kept around.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22773 3bd1e089-480b-0410-8dfb-8563597acbee
add - CMake/ExternalProjectDependency.cmake Diff File
mod - CMake/SlicerConfig.cmake.in Diff File
mod - CMake/SlicerGenerateSlicerConfig.cmake Diff File
mod - CMake/UseSlicer.cmake.in Diff File
mod - CMakeLists.txt Diff File
mod - Extensions/Testing/SuperBuildExtensionTemplate/CMakeLists.txt Diff File
mod - Extensions/Testing/SuperBuildExtensionTemplate/SuperBuild.cmake Diff File
mod - Extensions/Testing/SuperBuildExtensionTemplate/SuperBuild/External_Foo.cmake Diff File
mod - SuperBuild.cmake Diff File
mod - SuperBuild/External_BRAINSTools.cmake Diff File
mod - SuperBuild/External_BatchMake.cmake Diff File
mod - SuperBuild/External_CTK.cmake Diff File
mod - SuperBuild/External_CTKAPPLAUNCHER.cmake Diff File
mod - SuperBuild/External_DCMTK.cmake Diff File
mod - SuperBuild/External_EMSegment.cmake Diff File
mod - SuperBuild/External_ITKv3.cmake Diff File
mod - SuperBuild/External_ITKv4.cmake Diff File
mod - SuperBuild/External_LibArchive.cmake Diff File
mod - SuperBuild/External_MultiVolumeExplorer.cmake Diff File
mod - SuperBuild/External_MultiVolumeImporter.cmake Diff File
mod - SuperBuild/External_NUMPY.cmake Diff File
mod - SuperBuild/External_OpenIGTLink.cmake Diff File
mod - SuperBuild/External_OpenIGTLinkIF.cmake Diff File
mod - SuperBuild/External_OpenSSL.cmake Diff File
mod - SuperBuild/External_PCRE.cmake Diff File
mod - SuperBuild/External_SciPy.cmake Diff File
mod - SuperBuild/External_SimpleFilters.cmake Diff File
mod - SuperBuild/External_SimpleITK.cmake Diff File
mod - SuperBuild/External_SlicerExecutionModel.cmake Diff File
mod - SuperBuild/External_Swig.cmake Diff File
mod - SuperBuild/External_VTK.cmake Diff File
mod - SuperBuild/External_curl.cmake Diff File
mod - SuperBuild/External_incrTcl.cmake Diff File
mod - SuperBuild/External_jqPlot.cmake Diff File
mod - SuperBuild/External_python.cmake Diff File
mod - SuperBuild/External_qRestAPI.cmake Diff File
mod - SuperBuild/External_tcl.cmake Diff File
mod - SuperBuild/External_teem.cmake Diff File
mod - SuperBuild/External_tk.cmake Diff File
mod - SuperBuild/External_zlib.cmake Diff File

master 7d2b554b

2013-12-11 16:52:13

pieper

Details Diff 		BUG: 0003524 check for valid images in Editor

This generates a warning for situations that are thought to be
invalid. Since some tools may still be workable, we let the user
go ahead, but include some suggestions in the warnings about how
to fix the volumes.

http://na-mic.org/Bug/view.php?id=3524

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22772 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/EditorLib/HelperBox.py Diff File

master 475d972f

2013-12-10 19:53:38

pieper

Details Diff 		COMP: update CTK version

Brings in improvements to SuperBuild (Artichoke) process.

Brings in fixes for DICOM Database changes for 0003528.

Plus some other things:

https://github.com/commontk/CTK/compare/36fb628b14e9eba019ac877c14903dbe09ec903c...8fabf8129582d7a609a8bc7c1d9b22ceb9bf3c13

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22771 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTK.cmake Diff File

master d4c9a1c0

2013-12-06 16:28:59

jcfr

Details Diff 		COMP: Fix VTK Maverick MacOSX 10.9 compile error. Fixes 0003521

$ git shortlog adc1327551527dfbcc953ce73c5155d18edf7649..f387593148a8bc49cf46c1e27537674d5b779f49
Dave DeMarle (5):
Merge topic 'release-5.10-windowRect-size' into release-5.10
Merge topic 'tcl86-compatibility-rel5.10' into release-5.10
Merge topic 'dont-define-inline' into release-5.10
Merge branch 'libcxx-error-rel5.10' into integration
Merge branch 'llvm-libc++-fixes-rel5.10' into integration

David Cole (1):
Rendering: Use AdjustWindowRect to ensure pixel perfect client size

Goodwin Lawlor (6):
Backport using Tcl_GetErrorLine with Tcl8.6
Let macro find TclTk version 8.6
Update the TclTk internal files for 8.6
Backport using Tcl_GetErrorLine with Tcl8.6
Let macro find TclTk version 8.6
Update the TclTk internal files for 8.6

Jean-Christophe Fillion-Robin (1):
Merge branch 'osx-10.6.fixes' into slicer-v5.10.1

Sean McBride (5):
Conditionalize insane "#define inline" in libtiff
added missing #include, fixing compiler error with llvm's libc++
Fixed compile error with llvm libcxx
COMP: fixed compilation error using llvm's libc++
COMP: fixed llvm libc++ build error by removing invalid 'operator<<'


Co-authored-by: Junichi Tokuda <tokuda@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22769 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_VTK.cmake Diff File

master 9002247d

2013-12-06 14:14:16

jcfr

Details Diff 		ENH: Remove redundant vtkImageAccumulateDiscrete already provided by VTK

Using Slicer implementation of the ImageAccumulate filter is equivalent
to the VTK implementation after setting ComponentExtent and ComponentOrigin
appropriately to account for signed 16-bit images.

Output of the filter have been verified for both MRHead and ChestCT
sample data.

Associated discussion: http://slicer-devel.65872.n3.nabble.com/Slicer-vtkImageAccumulateDiscrete-Should-we-just-use-the-class-provided-by-VTK-tp4030447p4030451.html

See 0003485

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22768 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/CMakeLists.txt Diff File
rm - Libs/MRML/Core/vtkImageAccumulateDiscrete.cxx Diff File
rm - Libs/MRML/Core/vtkImageAccumulateDiscrete.h Diff File
mod - Libs/MRML/Core/vtkImageBimodalAnalysis.h Diff File
mod - Libs/MRML/Core/vtkMRMLScalarVolumeDisplayNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLScalarVolumeDisplayNode.h Diff File

master d7e53510

2013-12-05 10:04:13

jcfr

Details Diff 		COMP: Remove unused ivar from vtkMRMLScalarVolumeNode

Following commit r17798, calculation of [Scalar]AutoLevels has been
moved into vtkMRMLScalarVolumeDisplayNode. Therefore, the file has been
updated.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22766 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLScalarVolumeNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLScalarVolumeNode.h Diff File
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