BUG: fix a crash caused by an overlay file with unassigned labels.

When loading some FreeSurfer scalar overlay files, the reader 
returns a warning that some labels were unassigned. This was being
treated as an error, but a valid node was being returned from the
Models logic instead of NULL, causing a crash in the IO file. 
Fixed that issue then changed the response to that warning
to return valid nodes and color tables and that seemed to 
fix the issue.

Issue #2851



git-svn-id: http://svn.slicer.org/Slicer4/trunk@21608 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: avoid hangs/crashes when importing - fixes #2839, #2871

See CTK bug #292
https://github.com/commontk/CTK/issues/292

Multithreading of the indexing operation removed.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21609 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Avoid build error on windows by shortening filename of generated pythonqt files

This commit is a follow-up on r21605 and applies on Slicer base libraries
instead of slicer module libraries.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21610 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Don't crash on designer startup

Closes #2874

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21611 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Ensure EMSegment is build with default option and available in nightly package.

This commit ensures that "Slicer_BUILD_EMSegment" is properly set after
the first CMake configuration

Following r21598, the option "Slicer_BUILD_BRAINSTOOLS" has been moved after
declaring the option "Slicer_BUILD_EMSegment". Since option "Slicer_BUILD_EMSegment"
is depending on the value of Slicer_BUILD_BRAINSTOOLS, Slicer_BUILD_QTLOADABLEMODULES and
Slicer_USE_PYTHONQT, EMSegment wasn't build by default.

Thanks to Ron Kikinis for reporting the issue.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21612 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Renamed qSlicer{MODULE_NAME}Module.ui into qSlicer{MODULE_NAME}ModuleWidget.ui

See na-mic.org/Mantis/view.php?id=2247

Fixes #2247

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21613 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: add FiberBundleToLabelMap module and test

Per request from Ron, this was added as a core diffusion module
rather than as an extension.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21614 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Ensure module widget listen to mrmlSceneChanged signal

This is a follow-up on commit r21613 where the connections haven't been
updated as expected.

Fixes #2247

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21615 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Remove redundant connections from qSlicerWelcomeModuleWidget

Fix warning:

Object::connect: No such slot qSlicerWelcomeModuleWidget::loadData() in /home/jchris/Projects/Slicer-AHM-Superbuild-Debug/Slicer-build/Modules/Loadable/SlicerWelcome/ui_qSlicerWelcomeModuleWidget.h:293
Object::connect: (sender name: 'LoadNonDicomDataButton')
Object::connect: (receiver name: 'qSlicerWelcomeModuleWidget')


See #2247

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21616 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Update QtTesting XML files to reference the appropriate module widget

This is a follow-up on commit r21613 where the xml files haven't been
updated as expected.

See #2247

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21617 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Associated icon with copy, cut and paste action

Icons are licensed under Creative Commons License (CC-BY-SA 3.0)
See http://creativecommons.org/licenses/by-sa/3.0/

They have respectivaly been downloaded from:
 http://openiconlibrary.sourceforge.net/gallery2/?./Icons/actions/edit-copy-6.png
 http://openiconlibrary.sourceforge.net/gallery2/?./Icons/actions/edit-cut-6.png
 http://openiconlibrary.sourceforge.net/gallery2/?./Icons/actions/edit-paste-6.png

Before being uploaded on "openiconlibrary", the icons originally have
been obtained from http://www.oxygen-icons.org/

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21618 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: copy the correct model display node, fixing a copy/paste error

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21619 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: add a new test for importing model heirarchies.

Test that when a model hierarchy is imported that changes to model ids
are reflected in the parent node ids of child hierarchies.



git-svn-id: http://svn.slicer.org/Slicer4/trunk@21620 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: add the ability to import multi level model hierarchies from CLIs

Added to support passing a template scene to the Model Maker 
that contains a multi level model hierarchy. 

TODO: decide the best practice when a hierarchy is imported twice (for 
example, running the model maker on the same label map more than once)
right now this will make a new hierarchy rather than over writing
the old one.



git-svn-id: http://svn.slicer.org/Slicer4/trunk@21621 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Remote filter-end and filter-type from CLI output

Because filter-type was not removed, filter-end couldn't be removed.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21622 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Remove wrong signed/unsigned warning to ThresholdScalarVolume

As of r10439, the CLI doesn't force the output to be signed.
Update the documentation.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21623 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Add Negate property to Treshold Scalar Volume CLI

As of today, there is no easy mechanism in ITK to do so.
See ITK issues:
https://issues.itk.org/jira/browse/ITK-2991
https://issues.itk.org/jira/browse/ITK-2993

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21624 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Don't enforce un-necessary limitation on output signed image type

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21625 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: avoid warning about point locator

Don't try to update the vtkPointLocator with null points or
it will generate a warning message.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21626 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: handle fact that tensors input can come with either 6 or 9 components

Internally slicer (vtk) always represents tensors as 9 component, but
that conversion happens after the data is read in.  So this optimization
needs to check for both cases.

Note that the py_SlicerMRBTest failed as a result of this optimization,
but nobody checked (it happened during the SLC project week, so
things were busy and other things broke as well).

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21627 3bd1e089-480b-0410-8dfb-8563597acbee