BUG: vtkSlicerCommonInterface did not define the right plugin path to plugins when EMSEgmenter was run by installed package

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23329 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: N4ITKBiasFieldCorrection - Change output type to float

Cast of the output to the input type led to occasional overflows. Output of this
module is inherently floating point, as it is a multuplication of the recovered
bias field by the input image.

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23330 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: 3231. Added MRML scene version check and warning on scene load.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23331 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: data() is not part of std::vector on windows compilers

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23332 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Tweak Multi-sampling option

This commits improve the user experience related to
new multi sample option introduced in r23305. It now
allows to specify the number of samples.

Finally the code has been refactored to improve
the flow of changes and to use a cleaner signal/slot
interface.

From: Eric Larson <larson.eric.d@gmail.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23333 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Test failed as MRML node now also include version number in mrml file 

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23334 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Replaced outdated sliceWidgetRed_interactorStyle slicer.sliceWidgetRed_sliceLogic

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23335 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Change default version of VTK to 6

As discussed during June 17 developer hangout and also highlighted on the
Slicer developer list [1], consider that a lot of developer have been
reporting issue and we now have the Slicer application able to build and
run when build against VTK6. This commit changes the default version of VTK.

It is anticipated that some extension will fail to build, error will be
addressed as they come. Additional help will also be provided for
extension developers during the coming project week. See [2]

[1] http://slicer-devel.65872.n3.nabble.com/VTK-6-enabled-by-default-tt4031841.htm

[2] http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23336 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Update ExecutionModelTourTest 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@23337 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Update VTK project to fix build using Xcode 5.1.1

This commit updates the Slicer VTK project to include the following
patch cherry-picked from current VTK development branch.

Thanks to Hans Johnson for suggesting the backport.

8<-----8<-----8<-----8<-----8<-----8<-----8<-----8<-----
Author: Sean McBride <sean@rogue-research.com>
Date:   Thu Feb 13 14:26:42 2014 -0500

    Removed -fobjc-gc from VTK_REQUIRED_OBJCXX_FLAGS

    There are 3 memory management models in Cocoa,
    chronologically by introduction: MRR, GC, ARC.
    VTK supports the first two.
    GC is now deprecated however, and Xcode 5.1 will
    no longer even build GC code.  Therefore
    removed the -fobjc-gc option as a default.
    (It built the libraries as both MRR and GC
    compatible, which was convienent for library code.)
8<-----8<-----8<-----8<-----8<-----8<-----8<-----8<-----

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23338 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Update VTK project to fix CMake 3.0 configuration warnings

This commits updates Slicer VTK fork to include two commits backported
from VTK master. See commit kitware/VTK@7df9a25f and kitware/VTK@d19b4db8

$ git shortlog baa177b..4d7abb2
Brad King (2):
      COMP: Drop invalid custom commands from HDF5
      COMP: Drop missing dependencies of target 'vtkpython_pyc'

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23339 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Update SlicerExecutionModel

This commit both (1) fixes CMake 3.0 config warnings (see below) and
(2) updates the project to include fixes and improvements contributed by
the community:

//------------------------------
$ git shortlog 46f3d89..865e2a7 --no-merges
Jean-Christophe Fillion-Robin (4):
      ENH: Set default value for CMAKE_BUILD_TYPE
      ENH: Add support for CMake 3.0 removing use of LOCATION target property
      ENH: Re-factor GenerateCLP tests to support multi config system
      COMP: By default, disable JsonCpp support.

Jim Miller (2):
      Update README.md
      Update README.md

Julien Finet (1):
      Don't search default path when JsonCpp_DIR is provided

Matt McCormick (3):
      BUG: Output vector argument should not be assigned.
      BUG: Serialize a geometry Parameter with aggregate="true", multiple="true".
      BUG: Fix serialization/deserialization with not Multiple but vector.

Matthew Woehlke (2):
      ENH: Refactor [de]serialize format for brevity
      STYLE: Avoid file(GLOB)

ivmartel (1):
      Allow for reference attribute for geometries.
//------------------------------



This commit fixes the following warning:

//--------------------
CMake Warning (dev) at GenerateCLP/GenerateGenerateCLPConfig.cmake:7 (get_target_property):
  Policy CMP0026 is not set: Disallow use of the LOCATION target property.
  Run "cmake --help-policy CMP0026" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  The LOCATION property should not be read from target "GenerateCLPLauncher".
  Use the target name directly with add_custom_command, or use the generator
  expression $<TARGET_FILE>, as appropriate.

Call Stack (most recent call first):
  GenerateCLP/CMakeLists.txt:201 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.
//--------------------

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23340 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Update EMSegment project to fix VTKv6 build error.

//------------------
r17058 | jcfr | 2014-06-18 09:47:30 -0400 (Wed, 18 Jun 2014) | 9 lines

COMP: Fix compilation against VTKv6.

This commits fixes build error introduced by r17053.

Few tests are still failing due to memory leaks and will
be fixed at a later time:
* EMSegCL_Task_MRIHumanBrain_BRAINS_small
* EMSegCL_Task_MRIHumanBrainFullParcellation_BRAINS_small
//------------------

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23341 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Update CTK to fix build warnings

$ git shortlog 1dbffd..48ef9aeb --no-merges
Jean-Christophe Fillion-Robin (2):
      Fix warning complaining about missing resource with resource list is empty.
      Fix unused variable warnings

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23342 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix Slicer build warnings

This commit addresses two types of warnings:
 - unused variable warnings
 - RCC: Warning: No resources in '/path/to/foo.qrc

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23343 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: On MacOSX, waiting issue #3741 is solved uses VTK 5.10

As illustrated in the bug report [1], the maximum number of linked libraries
is reached  on MacOSX 10.6 (see below for an example of message) but there
are no problem on MacOSX 10.8 (at least when targeting 10.9).

// ---------
ld: warning: duplicate dylib /path/to ...
[...]
ld: warning: duplicate dylib /path/to ...
two level namespace mach-o files can link with at most 253 dylibs, this link would use 287 dylibs
// ---------

Waiting we come up with a solution or understand better the scope of the
problem, this commit force the VTK version to 5.10.

[1] http://na-mic.org/Mantis/view.php?id=3741

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23344 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fixed bug with respect to Image inhomogeneity; included vtkImageLabelPropagation in SlicerCommonInterFaceTest1 so it would fail as this is also the reason for EMSegCL_Task_MRIHumanBrainFullParcellation_BRAINS_small failing

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23345 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Fix 80 char limit in vtkMRMLDiffusionTensorVolumeDisplayNode

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23346 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix vtkTeemEstimateDiffusionTensor

* The nrrd reader did not properly propagate the scalar type to the
pipeline on time.
* vtkTeemEstimateDiffusionTensor did not use a proper pipeline of filters
for the baseline and averagedwi outputs.

Fixes DWIToDTIEstimationTest and DiffusionTensorScalarMeasurementsTest

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23347 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix vtkITKImageToImageFilter for VTK 6

The pipeline of filters was broken.

Fixes DiffusionWeightedVolumeMaskingTest

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23348 3bd1e089-480b-0410-8dfb-8563597acbee