BUG: Add support for installation of distribute and pip

Connect the signal "systemExitExceptionRaised" and so that the
application can be cleanup and terminate nicely. This will allow
the installation of distribute to terminate nicely. Indeed "sys.exit"
is called within the "distribute_setup.py" script.

Also add the "isatty" method to PythonQtRedirectStdOut so that logging
framework can check if the output is a tty-like device. Log mechanism
associated with pip install will now be happy since the call "sys.stdout.isatty"
will be valid.

See http://na-mic.org/Mantis/view.php?id=2694

Fixes #2694

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21331 3bd1e089-480b-0410-8dfb-8563597acbee
BUG 2725. Fixed setting transform node reference. Added test Testing/vtkMRMLTransformableNodeReferenceSaveImportTest.cxx


git-svn-id: http://svn.slicer.org/Slicer4/trunk@21332 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Add "vtkMRMLTransformableNodeReferenceSaveImportTest" to the list of tests

This is a follow-up of commit r21332

See #2725

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21333 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Ensure application test written in python run serially

Hopefully this will help prevent the factory from crashing
when running the tests.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21334 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Do not pass "--attach-process" when setting sys.argv

It avoid some python script to complain about unknown argument.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21335 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Crash in qMRMLChartView when no array node exist

Credits: Csaba Pinter
Fixes #2742

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21336 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: fix the issue when no multivolumes could be loaded correctly


git-svn-id: http://svn.slicer.org/Slicer4/trunk@21337 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: shorten the names of the loaded volumes to prevent resizing of the module panel node selection widget


git-svn-id: http://svn.slicer.org/Slicer4/trunk@21338 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Make inclusion of .hxx/.txx files consistent.

A long oustanding inconsistentcy in ITKv4 has been made
consistent.  This patch syncronizes all the code
to use the consistent and preferred mechanisms.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21339 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Remove unused file "PlastimatchDVH.s4ext-disabled"

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21344 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: reduce warning messages when loading brain atlas and restoring scenes.

Only call update scene on nodes that are in the scene view.
Use DisableModifiedEventOn instead of Start/EndModify when processing scene view child
nodes since the scene view scene is not in importing state and this reduces
responses to modified events.
Added error checking and tweaked messages when reading model files.

Issue #2513


git-svn-id: http://svn.slicer.org/Slicer4/trunk@21345 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: New brain atlas mrb (uploaded to Nightly dir), cleaned up storage nodes.
STYLE: give feedback about how many model hierarchies and scene views there are to test.

Still to do: clean up the mrml file of extraneous view and camera nodes.

Issue #2513



git-svn-id: http://svn.slicer.org/Slicer4/trunk@21346 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Bump ITKv3 version.

Get fixes to the SpatialObject vessel .tre file reader from hackathon
with Jean-Christophe Fillion-Robin.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21347 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: show self test buttons in alphabetical order

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21348 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: add reloadable self test for DataProbe module

Note: not yet fully implemented.  Requires additional refactoring
of gui into logic, and reloadable code should replace widget in
main gui (not just module gui).

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21349 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: use updated name for download of brain atlas

fix for failing tests related to brain atlas in bug #2513

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21350 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: speed up atlas tests by minimizing delay while printing status

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21351 3bd1e089-480b-0410-8dfb-8563597acbee
ENH; Update ITKv4, SimpleITK, BRAINSTools

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21352 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: remove unused script (performance test cleanup)

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21353 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: issue #2513 avoid a crash when restoring scene view

This change probably speeds things up to - the issue is that without
this change items in the model are being updated while the scene
is in an inconsistent state.  From testing by me and Nicole we saw
no side effects of this call and it allows the brain atlas to
run to completion, although it still crashes when closing the scene
(in a SceneView destructor) which means I believe it is now
the same as issue #2512.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21354 3bd1e089-480b-0410-8dfb-8563597acbee