BUG: Update launcher to version 0.1.14. Fixes #3771

// -------------------
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Tue Jul 22 18:19:04 2014 -0400

    Ensure 'additionalPathVariables' is not overridden. Fixes #56

    Commit 714981 generalized how environment variables dealing with paths
    were managed. This commit fixes a regression where environment variables
    set in the main settings file where not considered is additional settings
    where found.
// -------------------

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23475 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Wrap setuptools module installation to avoid false-positive error.

This commit ensure the build and install output of setuptools module is
redirected into files to avoid warning like the following one to be
falsely categorized as error:

15>removing 'build\bdist.win-amd64\egg' (and everything under it)
15>C:\D\C\Slicer-1-build\python-setuptools\setuptools\command\easy_install.py:316: UserWarning: Unbuilt egg for setuptools [unknown version] (c:\d\c\slicer-1-build\python-setuptools)
15>  self.local_index = Environment(self.shadow_path + sys.path)

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23476 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Add "python-" prefix to GitPython, Github and pydicom module

Consistently name python package.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23477 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Update SlicerExecutionModel - Fixes #2712

This commit updates SlicerExecutionModel to include an updated version
of ModuleDescription::ReadParameterFile function that support string
parameter without value. The Slicer/SlicerExecutionModel@05af78d also
adds corresponding test checking that parameter file with and without
value can still be read.

$ git shortlog feef59e..a6616b52 --no-merges
Jean-Christophe Fillion-Robin (1):
      BUG: Support parameter file with empty value

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23478 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix missing icons in extension manager

Update qSlicerBaseQTGUI.qrc[1] to include icons for new tool menu in
extension manager. This fixes the button for the same having no icon on
systems that lack the themed icon, as the non-themed icon was being
specified and exists in the source tree, but was missing from the
aforementioned .qrc.

(1: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Build_system/Qt_resource_files)

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23479 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Ensure MultiVolume modules work with VTK 5 and 6

This commit updates the modules to check for the version
of VTK (using `vtk.VTK_MAJOR_VERSION`). This is required
because the MacOSX factory is still building against VTK5.

For more details see:

  fedorov/MultiVolumeExplorer@1053c40
  fedorov/MultiVolumeImporter@351226a

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23480 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Ensure extension wizard can find git executable provided by Git Bash

This commit explicit set the environment variable "GIT_PYTHON_GIT_EXECUTABLE"
to ensure GitPython finds and uses the git executable provided by Git Bash.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23481 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Properly serialize python paths when installing extension. Fixes #3772

Following r23036 environment variable specifying list of path were
handled differently. This commit ensures that python paths associated
with extension are also serialized into the settings by following the
new convention introduced in r23036.

For example, before this commit, after installing an extension named
"Foo", the settings contained:

// ----------------------
[Modules]
AdditionalPaths=/home/jchris/.config/NA-MIC/Extensions-23473/Foo/lib/Slicer-4.3/qt-scripted-modules

[...]

[EnvironmentVariables]
PYTHONPATH=/home/jchris/.config/NA-MIC/Extensions-23473/Foo/lib/Slicer-4.3/qt-scripted-modules
// ----------------------

whereas the following is now written:

// ----------------------
[Modules]
AdditionalPaths=/home/jchris/.config/NA-MIC/Extensions-23473/Foo/lib/Slicer-4.3/qt-scripted-modules

[...]

[PYTHONPATH]
1\path=/home/jchris/.config/NA-MIC/Extensions-23473/Foo/lib/Slicer-4.3/qt-scripted-modules
size=1
// ----------------------

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23482 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fixed accented character display of series and studies in subject hierarchy

Fixes #3688

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23483 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Removed testing code from previous commit

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23484 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fixed error with intensity sampling; removed code not used under Slicer4

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23485 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: cli-modules were not included in PATH of installed version of MAC so added it to search path

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23486 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix IconEngine and d&d of QStandardItems with icons

When doing drag&drop, the mime data failed to stream the QIcon because
qSlicerIconEnginePlugin was not a subclass of QIconEngineV2.
Regression when adding Qt5 support in CTK.
Closes #3778

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23487 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix CheckForLabelVolumeValidity warning. Fixes #3776

This commit fixes a regression introduced in r23406 [1]
where calling CheckForLabelVolumeValidity with two volumes that have
the same dimension was returning a wrong warning, e.g. "IJKToRAS mismatch
at [0, 3] (-89.6207 != -89.6207)", "IJKToRAS mismatch
at [1, 1] (0.000542851 != 0.000542851)", and "IJKToRAS mismatch
at [2, 0] (4.32616e-09 != 4.32616e-09) IJKToRAS mismatch
at [2, 2] (0.0752821 != 0.0752821)", and "IJKToRAS mismatch
at [2, 3] (176.197 != 176.197)".

Thanks to "safir" for reporting the problem and suggesting a solution.

[1] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23406

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23488 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Subject hierarchy UI update issues fixed
Fixes #3714

- qMRMLSceneSubjectHierarchyModel::nodeIndex rewritten to generate correct indices, parentNode also fixed. Workarounds removed
- New subject hierarchy nodes get simpler names
- Setting icons is not so simple as it should be due to a bug in Qt (https://bugreports.qt-project.org/browse/QTBUG-20248), which raises the need to check if the icon to be set is the same as the current icon of an item. This introduces one more thing to remember to the developer. Thus, instead of having the plugins set icons on items, they just return it (or an empty one), and the model does the check. This way developing plugins is not harder than before.
- Changed copyright information in all subject hierarchy files
- Instead of having the potential nodes list on the bottom of the module, those nodes are shown in the subject hierarchy tree on the top-level without icons. They can be shown/hidden with a checkbox under the tree, and can be handled the same way as in the potential list before.


git-svn-id: http://svn.slicer.org/Slicer4/trunk@23489 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Add HDF5 and Matlab TransformIO to ITKFactoryRegistration

This commit explicitly lists these transform to ensure the associated
files can be read/write.

This should help in fixing error related to the integration of
BRAINSFit and EMSegment.

Co-authored-by: Bradley Lowekamp <blowekamp@mail.nih.gov>
Co-authored-by: Steve Pieper <pieper@isomics.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23490 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Added a method in VolumesLogic class to resample volume node.

Also changed the LabelStatistics.py to use the new resample logic to make labelmap same as input volume.

From: Kevin Wang <kevin.wang@rmp.uhn.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23491 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Added a method in VolumesLogic class to resample volume node.

Also added a new CloneVolume method which does not clone the imageData. Changed the LabelStatistics.py to use the new resample logic to make labelmap same as input volume.

From: Kevin Wang <kevin.wang@rmp.uhn.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23492 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: test for active camera before enabling fiducials

Removes the error message that world to view and view to world
can't compute result due to a missing active camera. Delaying
setting the handles and widgets to be enabled if there's
no active camera defined on their renderers seems to work well
since the next time through the update code once the layout
has stabilised and the renderers are updated, the seeds 
will get positioned and enabled.

Issue #3761


git-svn-id: http://svn.slicer.org/Slicer4/trunk@23493 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: check for valid transform pointers to avoid crash

On scene close and possibly other circumstances there can be transform
nodes that don't have valid transforms, so check the pointers.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23494 3bd1e089-480b-0410-8dfb-8563597acbee