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

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master 67c4ae61

2017-04-25 23:17:59

jcfr

Details Diff 		ENH: Remove unused VolumeRenderingReplacements fixed point raycaster override

This specialized implementation was first introduced in r4673 (ENH: Integrated
VTK ray cast classes, started with modifications for incremental update) by
copying the VTK implementation of the FixedPoint volume caster and was
most likely introduced to better support volume rendering compositing
with polygonal data.

Based on the discussion of the Developer meeting from April 25th [1] and
considering that non of the classes found in VolumeRenderingReplacements
are instantiated when using either the CPU or GPU volume mapper currently
available in Slicer, this commit removes them.

[1] https://www.slicer.org/wiki/Developer_Meetings/20170425

They most likely became obsolete with one of these commits:

* r23887 (ENH: Remove unused VTK OpenGL 3D Texture based volume rendering classes)

* r23888 (ENH: Remove unused NCI volume rendering classes)

* r23889 (ENH: Remove unused NCI GPU MultiVolume rendering classes).

Also worth noting that since then, the VTK implementation has matured
and fixes can now easily be contributed upstream.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25972 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/VolumeRendering/CMakeLists.txt Diff File
mod - Modules/Loadable/VolumeRendering/Logic/CMakeLists.txt Diff File
mod - Modules/Loadable/VolumeRendering/Logic/vtkSlicerVolumeRenderingLogic.cxx Diff File
mod - Modules/Loadable/VolumeRendering/MRMLDM/CMakeLists.txt Diff File
mod - Modules/Loadable/VolumeRendering/MRMLDM/vtkMRMLVolumeRenderingDisplayableManager.cxx Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/CMakeLists.txt Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerFixedPointRayCastImage.cxx Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerFixedPointRayCastImage.h Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerFixedPointVolumeRayCastCompositeGOHelper.cxx Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerFixedPointVolumeRayCastCompositeGOHelper.h Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerFixedPointVolumeRayCastCompositeGOShadeHelper.cxx Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerFixedPointVolumeRayCastCompositeGOShadeHelper.h Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerFixedPointVolumeRayCastCompositeHelper.cxx Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerFixedPointVolumeRayCastCompositeHelper.h Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerFixedPointVolumeRayCastCompositeShadeHelper.cxx Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerFixedPointVolumeRayCastCompositeShadeHelper.h Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerFixedPointVolumeRayCastHelper.cxx Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerFixedPointVolumeRayCastHelper.h Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerFixedPointVolumeRayCastMIPHelper.cxx Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerFixedPointVolumeRayCastMIPHelper.h Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerFixedPointVolumeRayCastMapper.cxx Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerFixedPointVolumeRayCastMapper.h Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerOpenGLRayCastImageDisplayHelper.cxx Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerOpenGLRayCastImageDisplayHelper.h Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerRayCastImageDisplayHelper.cxx Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerRayCastImageDisplayHelper.h Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerVolumeRenderingFactory.cxx Diff File
rm - Modules/Loadable/VolumeRendering/VolumeRenderingReplacements/vtkSlicerVolumeRenderingFactory.h Diff File

master 350b63cc

2017-04-25 22:07:47

lassoan

Details Diff 		BUG: Fixed data module subject hierarchy tab checkboxes

Event of show/hide MRML IDs was mixed up with show/hide transforms.
Also updated the checkbox names to match between all tabs.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25971 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Data/Resources/UI/qSlicerDataModuleWidget.ui Diff File
mod - Modules/Loadable/Data/qSlicerDataModuleWidget.cxx Diff File

master ff4ac959

2017-04-25 21:30:37

lassoan

Details Diff 		BUG: Update to latest CTK to fix test errors

The new CTK version contains this fix for multi-value arguments handling in launcher.
When a multi-value argument was passed to the command-line parser, all subsequent parameters were considered part of the argument.
This lead to ignoring --python-script argument when --additional-module-paths argument was specified before.

The patch fixes these Slicer test errors:
* py_nomainwindow_SlicerTestingExitFailureTest
* py_nomainwindow_SlicerUnitTestWithErrorsTest
* py_SlicerTestingExitFailureTest).

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25970 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_CTK.cmake Diff File

master 90f53805

2017-04-25 21:30:35

lassoan

Details Diff 		BUG: Fixed ScreenCapture module test

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25969 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/ScreenCapture/ScreenCapture.py Diff File

master d377d268

2017-04-25 21:30:33

lassoan

Details Diff 		BUG: Fixed SampleData downloadAbdominalCTVolume

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25968 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Scripted/SampleData/SampleData.py Diff File

master cdc0fb83

2017-04-25 21:30:29

lassoan

Details Diff 		BUG: Fixed miniscene import

Fixed premature node reference resolution during miniscene import.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25967 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Logic/vtkSlicerApplicationLogic.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLScene.cxx Diff File

master a3deed45

2017-04-25 19:33:16

jcfr

Details Diff 		BUG: python-setuptools: Remove leftover lock file when starting build.

If build is interrupted before a lock is released, the associated lock file
needs to be explicitly removed to avoid following build from waiting
indefinitely.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25966 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_python-setuptools.cmake Diff File

master ae6f222b

2017-04-25 18:24:41

jcfr

Details Diff 		COMP: CTestCustom: Add warning exceptions to avoid false positive

This commit prevents the following warnings from being reported as error
on CDash:

C:\D\S4R\python-install\Lib\distutils\dist.py:267: UserWarning: Unknown distribution option: 'test_suite'
C:\D\S4R\python-install\Lib\distutils\dist.py:267: UserWarning: Unknown distribution option: 'tests_require'
C:\D\S4R\python-install\Lib\distutils\dist.py:267: UserWarning: Unknown distribution option: 'install_requires'
C:\D\S4R\python-install\lib\site-packages\setuptools-35.0.1.post20170425-py2.7.egg\setuptools\dist.py:334: UserWarning: Normalizing '0.30.0.a0' to '0.30.0a0'

Reported-by: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25965 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/CTestCustom.cmake.in Diff File

master 81741d7e

2017-04-25 15:24:16

pinter

Details Diff 		STYLE: Removed CLI-style documentation for Data module

- The documentation stored in the XML file is mostly for CLIs, and it appears in the wiki as "Parameters: ...", while this module is not for processing
- Content is outdated and need to be updated, and it is more complex than what the XML structure allows
- New content on the wiki page: https://www.slicer.org/wiki/Documentation/Nightly/Modules/Data

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25964 3bd1e089-480b-0410-8dfb-8563597acbee
rm - Modules/Loadable/Data/Documentation/Data.dox Diff File
rm - Modules/Loadable/Data/Documentation/Data.xml Diff File

master 2dbed562

2017-04-25 15:11:53

pinter

Details Diff 		STYLE: Changing order of contributors of Data module

The wiki page and so the author list is automatically generated, and none of the original contributors work on Slicer core any more, so if somebody wants to contact a developer, they find an active one

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25963 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Modules/Loadable/Data/qSlicerDataModule.cxx Diff File

master ecf5636f

2017-04-25 14:51:13

pinter

Details Diff 		BUG: Fixed issue when deleting virtual branches from subject hierarchy

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25962 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/Core/vtkMRMLSubjectHierarchyNode.cxx Diff File

master e52ad0af

2017-04-25 14:13:46

pinter

Details Diff 		ENH: Integration of Subject hierarchy into the Data module

The name of the subject hierarchy is not indicative to a user at all, and they may have difficulties finding out what the name actually covers. In the same time there is the Data module with an indicative name, but which has limited uses, and is mostly used to build transform hierarchies and for development purposes. It seems to make sense to "merge" the two modules, so that the now stable and fast subject hierarchy can be used where it is easiest to find.
- Made the Data module widget tabbed, with "Subject hierarchy", "Transform hierarchy", and "All node" tabs. Transform hierarchy contains the MRML tree from the previous Data module, showing only the transformable nodes. Note that ModelHierarchy and Displayable modes were not migrated, as Model hierarchies are supported by subject hierarchy, and if display properties are to be set, then the Models module is needed anyway. All nodes contains a flat list of MRML nodes showing all types of nodes
- Subject hierarchy made a hidden module, and all content removed from its module widget (so that it does not need to be maintained in two places
- Data module icon replaced with the subject hierarchy icon, and Subject hierarchy replaced by Data in the favorite module toolbar
- Added a button to "Explore Loaded Data" in Welcome module, and also updated text

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25961 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMakeLists.txt Diff File
mod - Libs/MRML/Widgets/qMRMLSortFilterProxyModel.cxx Diff File
mod - Modules/Loadable/Data/CMakeLists.txt Diff File
add - Modules/Loadable/Data/Resources/Icons/SubjectHierarchy.png Diff File
mod - Modules/Loadable/Data/Resources/UI/qSlicerDataModuleWidget.ui Diff File
mod - Modules/Loadable/Data/Resources/qSlicerDataModule.qrc Diff File
mod - Modules/Loadable/Data/qSlicerDataModule.cxx Diff File
mod - Modules/Loadable/Data/qSlicerDataModuleWidget.cxx Diff File
mod - Modules/Loadable/Data/qSlicerDataModuleWidget.h Diff File
mod - Modules/Loadable/SlicerWelcome/Resources/HTML/AdjustingDataDisplay.html Diff File
mod - Modules/Loadable/SlicerWelcome/Resources/Images/WelcomeModules.png Diff File
mod - Modules/Loadable/SlicerWelcome/Resources/UI/qSlicerWelcomeModuleWidget.ui Diff File
mod - Modules/Loadable/SlicerWelcome/qSlicerWelcomeModuleWidget.cxx Diff File
mod - Modules/Loadable/SlicerWelcome/qSlicerWelcomeModuleWidget.h Diff File
mod - Modules/Loadable/SubjectHierarchy/Resources/UI/qSlicerSubjectHierarchyModule.ui Diff File
mod - Modules/Loadable/SubjectHierarchy/Widgets/qMRMLSortFilterSubjectHierarchyProxyModel.h Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModule.h Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModuleWidget.cxx Diff File
mod - Modules/Loadable/SubjectHierarchy/qSlicerSubjectHierarchyModuleWidget.h Diff File

master c9dc6c80

2017-04-25 01:05:03

lassoan

Details Diff 		BUG: Fixed test errors

Recent changes removed extra spaces that were put in scene files when they were saved.
Baseline scene files had to be updated accordingly.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25960 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Libs/MRML/DisplayableManager/Testing/Data/vtkMRMLCameraDisplayableManagerTest1.mrml Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLWindowLevelWidgetEventTranslatorPlayerTest1.xml Diff File
mod - SuperBuild.cmake Diff File

master 7b5ee468

2017-04-24 23:58:22

jcfr

Details Diff 		STYLE: ExtensionManager: Add PYTHON_SITE_PACKAGES_SUBDIR to launcher settings

This commit ensures that python path is updated after installing extension
bundling python packages.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25959 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCore/qSlicerExtensionsManagerModel.cxx Diff File
mod - CMake/vtkSlicerConfigure.h.in Diff File

master 58275e6d

2017-04-24 23:58:20

jcfr

Details Diff 		STYLE: ExtensionManager: Add Slicer_THIRDPARTY_ vars to launcher settings

For sake of consistency, this commit explicitly add directory associated
with third-party libraries packages to the launcher settings.

Related commits:

* r25288 (BUG: Add the extension third party directories to
additional launcher settings)

* r25182 (BUG: Extension packaging: Support fixup of 3rd-party (external
proj) libs)

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25958 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/QTCore/qSlicerExtensionsManagerModel.cxx Diff File
mod - CMake/SlicerConfig.cmake.in Diff File
mod - CMake/vtkSlicerConfigure.h.in Diff File
mod - CMakeLists.txt Diff File

master 766c61b7

2017-04-24 23:58:17

jcfr

Details Diff 		ENH: Install wheel and pip python packages

These packages will enable use of pip to install python dependencies.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25957 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File
add - SuperBuild/External_python-pip.cmake Diff File
add - SuperBuild/External_python-wheel.cmake Diff File

master 3e131d70

2017-04-24 23:58:15

jcfr

Details Diff 		ENH: Update from Python 2.7.11 to 2.7.13

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25956 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_python.cmake Diff File

master 45606be4

2017-04-24 23:58:14

jcfr

Details Diff 		ENH: Update python-cmake-buildsystem version

$ git shortlog 39ccab0..30b0d56 --no-merges
David Brooks (2):
Correctly name the installed include and library configuration directories.
Set PLATFORM_TRIPLET as per Python's `configure` script.

Jean-Christophe Fillion-Robin (9):
ConfigureChecks: Add support for system not expecting "libutil" (e.g VxWorks)
ConfigureChecks: Ensure LIBUTIL_LIBRARIES is set after first configure
circleci: simplify load/pull/save of docker images using scikit-ci-addons
extension_ctypes: Fix compilation on linux-x86
circleci: Use dockcross scripts
cmake: Change version built by default from 2.7.12 to 3.5.2
circleci: Enable parallel build using circleci-matrix
circleci: Speed-up build using system python
Add support for Python 2.7.13

Jérémy Viau-Trudel (1):
change default python version on readme.md

Marcel Metz (1):
Replace remaining instances of BUILD_{SHARED,STATIC} control variable

Martin Oberhuber (2):
ConfigureChecks: libutil is now optional. See 0000163
ConfigureChecks: VxWorks: Disable _XOPEN_SOURCE due to "sys/select.h" failing

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25955 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/External_python.cmake Diff File

master 376e00f6

2017-04-24 23:58:12

jcfr

Details Diff 		ENH: Support execution of python binaries using SlicerPython launcher env

Running the python executable (or any binaries installed by python) using
SlicerPython launcher environment will now resolve to the correct binary.

For example, here are after/before results associated with a linux Slicer
build tree.

After:

$ eval $(SlicerPython --launcher-show-set-environment-commands)
$ which python
/path/to/python-install/bin/python

Before:

$ eval $(SlicerPython --launcher-show-set-environment-commands)
$ which python
/usr/bin/python

Note that within a Slicer package, python executable is currently
renamed to "python-real". See r23057 (BUG: Rename installed python
executable to account for case-insistive system) for the rational.

Background:

The python project built by Slicer is installed in
/path/to/Slicer-SuperBuild/python-install, in addition to the python executable,
a launcher named "SlicerPython" is also configured and set as PYTHON_EXECUTABLE
CMake variable to ensure build step relying on python built by Slicer resolve
to the expected environment.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25954 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild/python_customPythonLauncherSettings.ini.in Diff File

master 7213951b

2017-04-24 23:58:11

jcfr

Details Diff 		ENH: Support custom additional launcher settings in extension external proj

This commit allows external project used within SuperBuild based
extensions to configured custom Paths, LibraryPaths and PythonPaths used
within the AdditionalLauncherSettings.ini.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25953 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Extensions/CMake/SlicerBlockAdditionalLauncherSettings.cmake Diff File

master 11f8aefb

2017-04-24 23:58:09

jcfr

Details Diff 		BUG: Configure extension AdditionalLauncherSettings only once

In case of SuperBuild extension the settings were
configured in both the top-level and the inner-build directories.

This commit ensures the settings are configured only in the top-level
directory for regular extension and in the inner-build directory for
superbuild ones.

Example of outputs:

* Regular extension:

```
[...]
-- Setting EXTENSION_NAME ......................: LoadableExtensionTemplate
-- Adding ConfigureAdditionalLauncherSettings target
-- Adding ConfigureAdditionalLauncherSettings target - yes
[...]
```


* Superbuild extension (top-level configuration):

```
[...]
-- Setting EXTENSION_NAME ......................: SuperBuildExtensionTemplate
[...]
-- Adding ConfigureAdditionalLauncherSettings target
-- Adding ConfigureAdditionalLauncherSettings target - no (because configuring top-level project)
[...]
```

* Superbuild extension (inner-build configuration):

```
[...]
-- Setting EXTENSION_NAME ......................: SuperBuildExtensionTemplate
[...]
-- Adding ConfigureAdditionalLauncherSettings target
-- Adding ConfigureAdditionalLauncherSettings target - yes (because configuring inner-build)

```

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25952 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Extensions/CMake/SlicerBlockAdditionalLauncherSettings.cmake Diff File

master 3fc888e6

2017-04-24 23:58:07

jcfr

Details Diff 		STYLE: SlicerBlockCTKAppLauncherSettings: Add comment and re-organize code

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25951 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerBlockCTKAppLauncherSettings.cmake Diff File

master 1e9cc24c

2017-04-24 23:58:06

jcfr

Details Diff 		ENH: Allow extension to check Slicer_USE_SYSTEM_python

This commit adds support for explicitly associating Slicer_USE_SYSTEM_*
variables with a label of the same name so that they are automatically
added to SlicerConfig.

This will allow to easily build Slicer extension against a system python
where extension python dependencies are already available.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25950 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerConfig.cmake.in Diff File
mod - CMake/SlicerGenerateSlicerConfig.cmake Diff File
mod - SuperBuild/External_python.cmake Diff File

master 55581c89

2017-04-24 23:58:03

jcfr

Details Diff 		STYLE: Slicer(Extension)CPackBundleFixup: Fix typo in variable name

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25949 3bd1e089-480b-0410-8dfb-8563597acbee
mod - CMake/SlicerCPackBundleFixup.cmake.in Diff File
mod - CMake/SlicerExtensionCPackBundleFixup.cmake.in Diff File

master 10c23a49

2017-04-24 23:58:02

jcfr

Details Diff 		ENH: Improve generation of extension AdditionalLauncherSettings.ini

This commit updates the CMake module SlicerBlockAdditionalLauncherSettings
so that it reuses the function "ctkAppLauncherListToQtSettingsArray"

To allow the CMake function "ctkAppLauncherListToQtSettingsArray" to be
usable from the extension build system, "CTKAPPLAUNCHER_DIR" is added to
SlicerConfig by specifying the "FIND_PACKAGE" label.

Note that the "FIND_PACKAGE" label is used to automatically configure
the associated variables in "CMake/SlicerGenerateSlicerConfig.cmake"

git-svn-id: http://svn.slicer.org/Slicer4/trunk@25948 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Extensions/CMake/SlicerBlockAdditionalLauncherSettings.cmake Diff File
mod - SuperBuild/External_CTKAPPLAUNCHER.cmake Diff File
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