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
STYLE: fix coding style to match superclass (VTK)

Indentation and curly brace placement needs to match
the parent class!

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21628 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: add hook for patient hierarchy testing (from Csaba)

This hook will allow testing but will later be refactored when
the patient hieararchy work is finalized.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21629 3bd1e089-480b-0410-8dfb-8563597acbee
PERF: handle boundary case when DICOM files have empty strings as tag values

When evaluating DICOM Plugins, and empty string triggered a reload
of the file, when if fact the empty string was valid, and not
an indication of uncached tag data.

https://github.com/commontk/CTK/commit/e96b581c23c7bf9cdb10a05ef35b22aca6bbc512

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21630 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Update ExtensionsManager webview when ExtensionsServer url is updated in the settings panel

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21631 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: For consistency, rename "*[Ee]xtensionManager*" methods into "*[Ee]xtensionsManager*"

Note the extra "s" added to the word "Extension".

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21632 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Add qMRMLTreeView::setSortFilterProxyModel function to be able to set custom proxy models to the tree view

Signed-off-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21633 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Add deprecated warning message to "slicerMacroBuildCLI"

"SEMMacroBuildCLI" should be used instead.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21634 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Add convenience macro "SlicerMacroBuildScriptedModule"

This will ease the maintenance and prevent developer from having to
update their CMakeLists.txt each time the process to build scripted
module change (for example value associated with parameter DESTINATION_DIR
and INSTALL_DIR of ctkMacroCompilePythonScript)

See http://www.na-mic.org/Bug/view.php?id=2647

Fixes #2647

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21635 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Remove unused file

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21636 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Simplify DICOM2FullBrainTractography CMakeLists.txt

Remove unused and obsolete extension related CMake code

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21637 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Remove WebGLExport module from Slicer core - Will be distributed as extension.

See https://github.com/xtk/SlicerWebGLExport/pull/2

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21638 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Ensure optimized atlas, blas, mkl or lapack libraries are not discovered

When building NUMPY, it causes more harm than it helps to have the automatic
discovery of these libraries. Especially due to Fortran ABI mismatch [1].

It is also agree that compiling against an optimized version of these libraries
would probably make sens, it should be handled on a case by case basis by the
developer. A variable named NUMPY_ENABLE_OPTIMZED_LIBRARY or similar could
then be added.

[1] http://docs.scipy.org/doc/numpy/user/install.html#fortran-abi-mismatch

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21639 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: fix calculation for snapping to center of slice (fixes #2878)

When performing pixel level operations, as with the Editor module,
or even when rendering multiple layers, the result can be ambiguous
when the slice plane is exactly at the border between two pixels due
to rounding differences accumulated through transforms.  This can lead
to inconsistent rendering or operations being applied in a differnt
location than expected.

A regression from 4.1 had crept in by which the slice plane was
being consistently adjusted to be exactly on the pixel boundary,
leading to the potential issues.  This fix ensures that the plane
is adjusted to the middle of the pixel.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21640 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: find dicom helper apps when DCMTK is build outside of CTK

Check in both CTK and DCMTK directories to find executables.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21641 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: fix dicom data bundle export/import

* Fix syntax of zip file size for dump2dcm call (use UL not IS)
* Fix UIDs by having dump2dcm generate new ones to overwrite reference
* Use app logic Zip/Unzip rather than python for consistency
* Fix some stylistic issues

git-svn-id: http://svn.slicer.org/Slicer4/trunk@21642 3bd1e089-480b-0410-8dfb-8563597acbee