COMP: Ensure SlicerExecutionModel variable expected by fixup script is set.

This commit fixes a regression introduced by commit r23413 moving
call to find_package where they are needed. By moving the find_package call
from the top-level CMakeLists.txt, variable expected by fixup script were
not set anymore.

It updates SlicerCPack to call find_package and ensure
variable SlicerExecutionModel_LIBRARY_DIRS expected by the fixup script
is set.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23443 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix "Deleting Unknown Object" warning in all mrml node tests

This commits (1) changes the helper node class name associated with the
hierarchy node to be unique and (2) updates the helper node definitions
to be consistent with the helper node declared in vtkMRMLNodeTest1.

Also remove debug output for vtkMRMLColorNodeTest1 and vtkMRMLUnitNodeTest1.
The extra verbosity was adding "noise" to the test output.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23444 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Re-organize and simplify vtkMRMLColorTableNodeTest1

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23445 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Change vtkMRMLColorNode::GetColor to explicitly accept array of size 4

The function signature is now consistent with vtkLookupTable::GetTableValue.

Let's also note that when wrapped in python, an error will now be returned
if a list not having exactly a size of four is passed.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23446 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix memory initialization in vtkMRMLColorTableNode::SetNumberOfColors

This commit fixes a problem discovered while running the test
vtkMRMLColorTableNodeTest1 through valgrind. It basically ensures that
new table entry are initialized.

==26783== Conditional jump or move depends on uninitialised value(s)
==26783==    at 0x23B631D3: __printf_fp (printf_fp.c:404)
==26783==    by 0x23B62A9B: vfprintf (vfprintf.c:1654)
==26783==    by 0x23B875A4: vsnprintf (vsnprintf.c:119)
==26783==    by 0x2367E01F: ??? (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.18)
==26783==    by 0x23684455: std::ostreambuf_iterator<char, std::char_traits<char> > std::num_put<char, std::ostreambuf_iterator<char, std::char_traits<char> > >::_M_insert_float<double>(std::ostreambuf_iterator<char, std::char_traits<char> >, std::ios_base&, char, char, double) const (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.18)
==26783==    by 0x2368473F: std::num_put<char, std::ostreambuf_iterator<char, std::char_traits<char> > >::do_put(std::ostreambuf_iterator<char, std::char_traits<char> >, std::ios_base&, char, double) const (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.18)
==26783==    by 0x2368FA34: std::ostream& std::ostream::_M_insert<double>(double) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.18)
==26783==    by 0x511352D: vtkMRMLColorNode::SetNameFromColor(int) (vtkMRMLColorNode.cxx:312)
==26783==    by 0x511336F: vtkMRMLColorNode::SetNamesFromColors() (vtkMRMLColorNode.cxx:295)
==26783==    by 0x512245B: vtkMRMLColorTableNode::SetColor(int, char const*, double, double, double, double) (vtkMRMLColorTableNode.cxx:1301)
==26783==    by 0x48750A: vtkMRMLColorTableNodeTest1(int, char**) (vtkMRMLColorTableNodeTest1.cxx:83)
==26783==    by 0x47215C: main (MRMLCoreCxxTests.cxx:616)

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23447 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Update vtkMRMLColorTableNodeTest1 to test against expected output

This commit updates the test to check that color table entry
can be written and read from a color table file.

Some background into ...

Commit r20729 attempted to implement a test checking that the color table
entry could be written to a scene and read from the scene. The issue was
that the test was only displaying value and was not testing against
expected value.
Then, in commit r22344, the color mrml nodes have been updated to
to not write anymore into the mrml scene.

The test wasn't reporting that no color could be read but was still
passing, this commit updates the test and check for expected values instead
of just displaying them.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23448 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Update SlicerExecutionModel - Update GenerateCLP to avoid confusing CDash

$ git shortlog ecb58ad..4e61f6c --no-merges
Jean-Christophe Fillion-Robin (1):
      BUG: Output GenerateCLP arguments on stdout instead of stderr

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23449 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Silence unused variable warning in qMRMLTransformInfoWidget

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23450 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Silence widget name already in use in qSlicerSettingsModulesPanel

This commit fixes the following warning:

/path/to/Slicer/Base/QTGUI/Resources/UI/qSlicerSettingsModulesPanel.ui: Warning: The name 'horizontalLayout_4' (QHBoxLayout) is already in use, defaulting to 'horizontalLayout_41'

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23451 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Update Doxygen minimum required version to 1.8.4

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23452 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix doxygen warnings and tweak doxygen layout

This commit also updated the main page to include an "important link"
section. It has been inspired by the Blender main page.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23453 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Improve error checking in vtkMRMLDiffusionWeightedVolumeNode

This commit:

* updates function taking the number of gradient as input
parameter to also check if that number if negative.

* updates function taking a pointer to vtkMatrix4x4 and check for
null value.

* fixes indent.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23454 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Update MRMLIDImageIO - Add comment line separator

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23455 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: MRMLIDImageIO - Invoke modified event at the end of gradient update

This commit reduce the number of modified event invoked by
vtkMRMLDiffusionWeightedVolumeNode by using StartModify/EndModify

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23456 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix memory initialization in vtkMRMLDiffusionWeightedVolumeNode

This commits fixes a problem discovered while running the test
vtkMRMLDiffusionWeightedVolumeNodeTest1 through valgrind. It
ensures that each time the number of gradient is set, the DiffusionGradients
and BValues double arrays are initialized with zeros. To do so,
a protected function "SetNumberOfGradientsInternal" is introduced, it is
doesn't invoke the modified event, set the double array value to zeros.

The redundant ivar "NumberOfGradients" has also been removed. Instead
the function "GetNumberOfGradients" return the number of tuples in
the DiffusionGradients array.

[...]

Conditional jump or move depends on uninitialised value(s)
==32492==    at 0x23B631D3: __printf_fp (printf_fp.c:404)
==32492==    by 0x23B62A9B: vfprintf (vfprintf.c:1654)
==32492==    by 0x23B875A4: vsnprintf (vsnprintf.c:119)
==32492==    by 0x2367E01F: ??? (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.18)
==32492==    by 0x23684455: std::ostreambuf_iterator<char, std::char_traits<char> > std::num_put<char, std::ostreambuf_iterator<char, std::char_traits<char> > >::_M_insert_float<double>(std::ostreambuf_iterator<char, std::char_traits<char> >, std::ios_base&, char, char, double) const (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.18)
==32492==    by 0x2368473F: std::num_put<char, std::ostreambuf_iterator<char, std::char_traits<char> > >::do_put(std::ostreambuf_iterator<char, std::char_traits<char> >, std::ios_base&, char, double) const (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.18)
==32492==    by 0x2368FA34: std::ostream& std::ostream::_M_insert<double>(double) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.18)
==32492==    by 0x5143A38: vtkMRMLDiffusionWeightedVolumeNode::PrintSelf(std::ostream&, vtkIndent) (vtkMRMLDiffusionWeightedVolumeNode.cxx:394)
==32492==    by 0x17BF4BD7: vtkObjectBase::Print(std::ostream&) (vtkObjectBase.cxx:149)
==32492==    by 0x4B78B4: vtkMRMLDiffusionWeightedVolumeNodeTest1(int, char**) (vtkMRMLDiffusionWeightedVolumeNodeTest1.cxx:24)
==32492==    by 0x4729AC: main (MRMLCoreCxxTests.cxx:616)

[...]

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23457 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix memory initialization in vtkMRMLGlyphableVolumeDisplayNode

This commits fixes a problem discovered while running the test
vtkMRMLGlyphableVolumeDisplayNodeTest through valgrind. It ensures
that the ivar "VisualizationMode" is initialized.

[...]

==32528== Conditional jump or move depends on uninitialised value(s)
==32528==    at 0x23682EF0: std::ostreambuf_iterator<char, std::char_traits<char> > std::num_put<char, std::ostreambuf_iterator<char, std::char_traits<char> > >::_M_insert_int<long>(std::ostreambuf_iterator<char, std::char_traits<char> >, std::ios_base&, char, long) const (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.18)
==32528==    by 0x236834BC: std::num_put<char, std::ostreambuf_iterator<char, std::char_traits<char> > >::do_put(std::ostreambuf_iterator<char, std::char_traits<char> >, std::ios_base&, char, long) const (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.18)
==32528==    by 0x2368EFAD: std::ostream& std::ostream::_M_insert<long>(long) (in /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.18)
==32528==    by 0x53A4422: vtkMRMLGlyphableVolumeDisplayNode::PrintSelf(std::ostream&, vtkIndent) (vtkMRMLGlyphableVolumeDisplayNode.cxx:153)
==32528==    by 0x17BF4BD7: vtkObjectBase::Print(std::ostream&) (vtkObjectBase.cxx:149)
==32528==    by 0x508DBD: vtkMRMLGlyphableVolumeDisplayNodeTest1(int, char**) (vtkMRMLGlyphableVolumeDisplayNodeTest1.cxx:22)
==32528==    by 0x4729AC: main (MRMLCoreCxxTests.cxx:616)

[...]

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23458 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix memory initialization in vtkMRMLScalarVolumeNodeTest2

This commits fixes a problem discovered while running the test
 vtkMRMLScalarVolumeNodeTest2 through valgrind. It ensure the image
data is initialized with zeros.

[...]

==32668== Conditional jump or move depends on uninitialised value(s)
==32668==    at 0x1BC3DE03: void vtkImageAccumulateExecute<unsigned short>(vtkImageAccumulate*, vtkImageData*, unsigned short*, vtkImageData*, int*, double*, double*, double*, double*, long long*, int*) (vtkImageAccumulate.cxx:197)
==32668==    by 0x1BC34531: vtkImageAccumulate::RequestData(vtkInformation*, vtkInformationVector**, vtkInformationVector*) (vtkImageAccumulate.cxx:313)
==32668==    by 0x16C94CB7: vtkImageAlgorithm::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) (vtkImageAlgorithm.cxx:103)
==32668==    by 0x16C8A6AD: vtkExecutive::CallAlgorithm(vtkInformation*, int, vtkInformationVector**, vtkInformationVector*) (vtkExecutive.cxx:745)
==32668==    by 0x16C85002: vtkDemandDrivenPipeline::ExecuteData(vtkInformation*, vtkInformationVector**, vtkInformationVector*) (vtkDemandDrivenPipeline.cxx:497)
==32668==    by 0x16C7E07E: vtkCompositeDataPipeline::ExecuteData(vtkInformation*, vtkInformationVector**, vtkInformationVector*) (vtkCompositeDataPipeline.cxx:175)
==32668==    by 0x16C8476E: vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) (vtkDemandDrivenPipeline.cxx:279)
==32668==    by 0x16CA9B25: vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) (vtkStreamingDemandDrivenPipeline.cxx:346)
==32668==    by 0x16C801BA: vtkCompositeDataPipeline::ForwardUpstream(vtkInformation*) (vtkCompositeDataPipeline.cxx:712)
==32668==    by 0x16C846DD: vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) (vtkDemandDrivenPipeline.cxx:265)
==32668==    by 0x16CA9B25: vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) (vtkStreamingDemandDrivenPipeline.cxx:346)
==32668==    by 0x16C84E5B: vtkDemandDrivenPipeline::UpdateData(int) (vtkDemandDrivenPipeline.cxx:448)

[...]

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23459 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix memory initialization in vtkMRMLVolumeHeaderlessStorageNode

This commits fixes a problem discovered while running the test
vtkMRMLVolumeHeaderlessStorageNodeTest1 through valgrind.

[...]

==423== Conditional jump or move depends on uninitialised value(s)
==423==    at 0x53AB10F: vtkMRMLVolumeHeaderlessStorageNode::SetFileDimensions(int, int, int) (in /home/jchris/Projects/Slicer-2-SuperBuild-Debug/Slicer-build/bin/libMRMLCore.so)
==423==    by 0x53A762A: vtkMRMLVolumeHeaderlessStorageNode::vtkMRMLVolumeHeaderlessStorageNode() (vtkMRMLVolumeHeaderlessStorageNode.cxx:56)
==423==    by 0x53A7480: vtkMRMLVolumeHeaderlessStorageNode::New() (vtkMRMLVolumeHeaderlessStorageNode.cxx:39)
==423==    by 0x621EBF: vtkNew<vtkMRMLVolumeHeaderlessStorageNode>::vtkNew() (vtkNew.h:66)
==423==    by 0x61BC65: vtkMRMLVolumeHeaderlessStorageNodeTest1(int, char**) (vtkMRMLVolumeHeaderlessStorageNodeTest1.cxx:21)
==423==    by 0x4729AC: main (MRMLCoreCxxTests.cxx:616)

[...]

==423== Conditional jump or move depends on uninitialised value(s)
==423==    at 0x53AB10F: vtkMRMLVolumeHeaderlessStorageNode::SetFileDimensions(int, int, int) (in /home/jchris/Projects/Slicer-2-SuperBuild-Debug/Slicer-build/bin/libMRMLCore.so)
==423==    by 0x53A762A: vtkMRMLVolumeHeaderlessStorageNode::vtkMRMLVolumeHeaderlessStorageNode() (vtkMRMLVolumeHeaderlessStorageNode.cxx:56)
==423==    by 0x53A7480: vtkMRMLVolumeHeaderlessStorageNode::New() (vtkMRMLVolumeHeaderlessStorageNode.cxx:39)
==423==    by 0x53A7523: vtkMRMLVolumeHeaderlessStorageNode::CreateNodeInstance() (vtkMRMLVolumeHeaderlessStorageNode.cxx:39)
==423==    by 0x61BD63: vtkMRMLVolumeHeaderlessStorageNodeTest1(int, char**) (vtkMRMLVolumeHeaderlessStorageNodeTest1.cxx:25)
==423==    by 0x4729AC: main (MRMLCoreCxxTests.cxx:616)

[...]

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23460 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Update CameraDisplayableManagerTest1 input scene to include MRML version

This commit updates the test input data to account for commit r23331
including MRML version in the mrml file.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23461 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Update VTKv6 external project - Fix test MarkupsInCompareViewersSelfTest

$ git shortlog 4d7abb2..169b37b
Nicole Aucoin (1):
      BUG: fix null pointer crash in view to world with no active camera

This commit prevent the test from failing but it doesn't avoid the
following error from being displayed:

//------------
338: ERROR: In /home/jchris/Projects/Slicer-2-SuperBuild-Debug/VTKv6/Rendering/Core/vtkRenderer.cxx, line 1252
338: vtkOpenGLRenderer (0x741a1d0): ViewToWorld: no active camera, cannot compute view to world, returning 0,0,0
338:
338:
338: MH Head in background, scrolled to a fiducial
[...]
338: Switched back to conventional layout
338: Switched to Compare grid
338: ERROR: In /home/jchris/Projects/Slicer-2-SuperBuild-Debug/VTKv6/Common/ExecutionModel/vtkAlgorithm.cxx, line 1421
338: vtkOpenGLImageMapper (0x7548770): Attempt to get connection index 0 for input port 0, which has 0 connections.
//------------

See #3761

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23462 3bd1e089-480b-0410-8dfb-8563597acbee