BUG: Partial fix for EMSegment/BRAINSFit integration. See #3561, #2741, #3779

This commit is a follow up of EMSegment commit r23496. It updates BRAINSFit
to integrate the fix done by Kent to specifically address the naming
of .h5 transform files written by BRAINSFit.

// ---------------------
commit e46c99795cedd4c6aeec98e881af9c2b28dc5cf5
Author: Kent Williams <norman-k-williams@uiowa.edu>
Date:   Tue Jul 29 15:24:11 2014 -0500

BUG: don't extend composite transform filenames needlessly.there was some deficient logic that
was changing the filename of composit transforms to force them to hdf5 format, even if the filename
given was already for an HDF5 file.
// ---------------------

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23507 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Specify list VTK_MAKE_INSTANTIATOR3 input as list of cxx files only.

This commit fixes a build error introduced by kitware/VTK@5c3241b9d8
It ensures there are no duplicated entries in the instantiator files.

The error (reported below) was first discovered when building Slicer
on MacOSX 10.6 with the option VTK_ENABLE_KITS while working on issue
#3741.

// ------------------------
$ make vtkSlicerTransformsModuleMRMLDisplayableManager/fast
[ 59%] Building CXX object Modules/Loadable/Transforms/MRMLDM/CMakeFiles/vtkSlicerTransformsModuleMRMLDisplayableManager.dir/TransformsInstantiator.cxx.o
/path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx: In function 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager2DNew()':
/path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx:10: error: redefinition of 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager2DNew()'
/path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx:9: error: 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager2DNew()' previously defined here
/path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx: In function 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager3DNew()':
/path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx:12: error: redefinition of 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager3DNew()'
/path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx:11: error: 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager3DNew()' previously defined here
make[1]: *** [Modules/Loadable/Transforms/MRMLDM/CMakeFiles/vtkSlicerTransformsModuleMRMLDisplayableManager.dir/TransformsInstantiator.cxx.o] Error 1
make: *** [vtkSlicerTransformsModuleMRMLDisplayableManager/fast] Error 2
// ------------------------

The content of the associated instantiator file was:

// ---------------
$ cat Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx

[...]

vtkInstantiatorNewMacro(vtkMRMLTransformsDisplayableManager2D)
vtkInstantiatorNewMacro(vtkMRMLTransformsDisplayableManager2D)
vtkInstantiatorNewMacro(vtkMRMLTransformsDisplayableManager3D)
vtkInstantiatorNewMacro(vtkMRMLTransformsDisplayableManager3D)

[...]
// ---------------

This commit avoid the duplicated entries in the instantiator file.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23508 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix VTK6 link error on MacOSX 10.6. Fixes #3741

To reduce the number of libraries passed to the linker, this commit build
VTK6 with the VTK_ENABLE_KITS option enabled.

If building on MacOSX 10.6 without CMake 3.0, it also updated the build
system to output a fatal error message explaining that a more recent
version of CMake is required.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23509 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Remove unused/commented CMake code from Base/Logic/CMakeLists.txt

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23510 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Download openssl-1.0.1e source packages from packages.kitware.com

Since openssl.org is not always up, the source archive has been
mirrored on midas.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23511 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Update VTK6 to include support for VTK_ENABLE_KITS. See #3741

This commit updates the version of VTK so that the changes introduced
in commit r23509 can have an effect.

An attempt to cherry-pick only the commits introducing the VTK_ENABLE_KITS
feature has been done. It turned out that the kits feature and the
introduction of the support for different backend were too much tangled.

After reviewing the list of changes, most them includes bug fixes, addition
of VTK tests, fixes for memory initialization, optimization.
More specifically, here is a list of the one that are of interest
for Slicer are:

  kitware/VTK@504036 : Added "sticky" axes mode to vtkCubeAxesActor
  kitware/VTK@196bbe : Refactor GetRange to compute all ranges at the same time.
                       [...] improves the total runtime by 1.5x to 3x.
  kitware/VTK@87291c : Improve ComputeScalarRange when we have a single component.
                       In testing this takes the ComputeScalarRange on 600^3 from ~430 ms to ~20ms.
  kitware/VTK@cbd488 : Fix a crash when deleting vtk-python objects.
  kitware/VTK@e76153 : BUG: vtkProp3D - Wrong transformation used to restore original parameters

Following discussion with Berk [1], the OpenGL backend remains the
same and the corresponding changes are backward compatible. (There are
some exceptions but Slicer code base is not impacted)

[1] http://www.kitware.com/blog/home/post/703

For a complete list of changes:

  git shortlog 169b37..0d4202 --no-merges

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23512 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix logic setting VTK_ENABLE_KITS. See #3741

This commit ensures that the variable will be set for MacOSX < 10.8

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23513 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Update minimum required VTK version

This commit will fix the following warning:

CMake Error at CMakeLists.txt:701 (find_package):
  Could not find a configuration file for package "VTK" that is compatible
  with requested version "6.1".

  The following configuration files were considered but not accepted:

    /path/to/Slicer-SuperBuild/VTKv6-build/VTKConfig.cmake, version: 6.2.0

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23514 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Update VTK to configure a more friendly VTKConfigVersion file

// -------------------
commit 15fac7625d2b817aee4326376871f2cc2bbf53cd
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Wed Jul 30 06:51:28 2014 -0400

    Configure VTKConfigVersion consistent with VTK's compatibility guarantees

    Since the minimum CMake version required by VTK is 2.8.8, this commit
    uses the module CMakePackageConfigHelpers available in that version of
    CMake.
// -------------------

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23515 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: fix typo in volume slice model attribute

Issue #3718


git-svn-id: http://svn.slicer.org/Slicer4/trunk@23516 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Add logging to extension update check

Add logging messages to report status when checking for updates, and
when an update is scheduled. (In particular, this reports a warning if
the server extension information query fails.)

Issue #3784

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23517 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Update comments in dashboard driver script

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23518 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Remove deprecated variable from CDash driver script

Setting ADDITIONAL_{C|CXX}_FLAGS variables is not the conventional
way of setting additional flags. Setting environment variable
CFLAGS and CXXFLAGS is the recommended way.

Remove variable "WITH_TESTING_EXTENSIONS". This is an advanced variable
that shouldn't be enabled on contributed dashboards. Only the factories
should eventually enable it. That said, the recommended way is to
build a set of s4ext files as explained in [1]

[1] http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Build_ExtensionsIndex

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23519 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix install of VTK6 python modules on MacOSX

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23520 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Update MultiVolumeExplorer - Fix frame scrolling

This fixes an issue due to missing cast from float to int that disabled
frame scrolling. See fedorov/MultiVolumeExplorer@f9222a25a

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23521 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: SimpleITK is now enabled by default.

SimpleITK is a first class citizen in Slicer and is now enabled by default.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23522 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Set slice plane coordinates using plane source filter

Triggering ModifiedEvent on the input polydata does not (yet) propagate
onto the model node.
Closes #3780

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23523 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Propagate ModifiedEvent to volume/modelNode

When setting a raw (vs pipeline filter) input data to a mrml node,
the node was not notified (ProcessMRMLEvents) whenever the data
was changed because the trivial producer internally used
is not forwarding events.

Issue #3780

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23524 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: respect don't show again on fiducials conversion

Define a new button with an AcceptRole to have it saved
in the config file, following the pattern of the Delete
pop up boxes.

Issue #3663



git-svn-id: http://svn.slicer.org/Slicer4/trunk@23525 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Update to latest landmark registration

Improved point placement through transforms

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23526 3bd1e089-480b-0410-8dfb-8563597acbee