ENH: Remove ITKv3 support

As discussed on the mailing list [1] and reported on the Roadmap [2],
this commit removes all conditional code that was allowing Slicer4 to be
compiled against ITKv3.

Code that was building only against ITKv3 has also been removed. This
includes DicomToNrrdConverter CLI module
and SlicerITKv3N4MRIBiasFieldCorrectionImageFilter class.

[1] http://slicer-devel.65872.n3.nabble.com/Removal-of-ITKv3-support-tt4031364.html

[2] http://wiki.slicer.org/slicerWiki/index.php/Roadmap#Deprecation_.2F_API_Changes

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23077 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: 3121. Added module wiki doc page link

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23078 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Allow loading of bspline transforms with IdentityTransform bulk component

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23079 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: 3618. Changed interpolation mode to linear in the vtkMRMLVolumeNode::ApplyNonLinearTransform()

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23080 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: 2346. Made default fiber solid color to white matter. 

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23081 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: move the User and File node types up to superclass
Support for user and file procedural color nodes requires that these
node types be moved into the color node superclass, not just defined
on the color table node.

Issue: 3573



git-svn-id: http://svn.slicer.org/Slicer4/trunk@23082 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Expand scalar range options

Add the ScalarRangeFlag on the display node, test it, use it in the Model
display node.
Provide a GUI interface for it in the Models Scalars GUI.
Use it in the model displayable manager.
Separate out the auto scalar range setting from updating the poly data
in the model display node.

This expands the options from just using the scalar range of the data
to allowing the user to select using the scalar range defined on the
display node, the range on the color node, or the range of the data
type (use this last with caution, TBD: readjusting the minimum and
maximum values allowed on the range slider). Keeps the default
behaviour of AutoScalarRange and Data. The interaction of Auto/Manual
and the range flags might need some tweaking.
Also keeps the deep copy of the color look up table in the model displayable
manager - monitor for performance issues.
Expands the model displayable manager to work with procedural color nodes,
this required copying the color transfer function to a look up table to
support setting the range. Using a table with 256 entries for now.
UI full change due to having to run dos2unix on it to get it commited
to git without whitespace errors.

Issue #3573



git-svn-id: http://svn.slicer.org/Slicer4/trunk@23083 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Add procedural color storage node and GUI support

Add a new storage node, register it, test it.
Added support for copying procedural nodes so that users can copy
an existing one and then save it to disk.
LoadColorFile expanded to work with both color table and procedural
color node loading.
TBD: add support for .cxml
Added support in the Colors gui to display and edit color transfer
functions (Continuous frame, with a ctkVTKScalarsToColorsWidget).
As well as allowing the scalar bar widget to be set from a procedural
color node.

Issue #3573



git-svn-id: http://svn.slicer.org/Slicer4/trunk@23084 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: unify how add/remove handle error cases

Remove the error print out when removing a view node that
is not in the list, since when adding a view node that is
already in the list no error is printed. The code recovers
gracefully, no need to post an error.

Issue #3216



git-svn-id: http://svn.slicer.org/Slicer4/trunk@23085 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: expand the view combo box to work on abstract view nodes

Removed the limitation on the display node view combo box that
only allowed selecting 3D view nodes, now all subclasses of
abstract view nodes can be used. Slice nodes and chart view
nodes are now allowed. This fixes the issue that while a
display node could have a slice node added to it's list of
view nodes, this combo box would remove it as it wasn't a
3d view node.
Update the volume rendering module widget to use the new combo
box code, limiting the view nodes to 3d ones since volume
rendering can't be shown in slice views.

Issue #3216



git-svn-id: http://svn.slicer.org/Slicer4/trunk@23086 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: add support for markups in different views

Added support in the displayable managers to check if
a markup is visible in a given view. Added testing.
Added a GUI drop down box to allow the user to
manipulate the view node settings (in the Advanced
Display group)

Resolves Issue #3216



git-svn-id: http://svn.slicer.org/Slicer4/trunk@23087 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix windows packaging error disabling GitPython and PyGithub

The problem is that the directory structure is too deep. Some path
have a length greater than 260 characters and seems to be an issue
for the CMake install command due to the windows maximum path
length limitation [1]

Waiting this issue is addressed, this commit disables the package on
Windows to ensure packages will be uploaded.

[1] http://msdn.microsoft.com/en-us/library/windows/desktop/aa365247%28v=vs.85%29.aspx#maxpath

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23088 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Update ITK to v4.5.2

$ git shortlog 754278cb7ab50ae3e64dc0a413aef4b9ff0ff1f0..v4.5.2 --no-merges
Bill Lorensen (2):
      BUG: Tiff compression was broken and untested
      COMP: Missing breaks in swithc

Bradley Lowekamp (12):
      COMP: fix unused variable warning in abort test
      BUG: Do not throw exception in Probes with mis-matched Stop
      BUG: Address Shared Library issues with SCIFIO
      COMP: fix failing voronoi segmentation tests
      COMP: export required in explicitly defined NumbericTraits consts
      BUG: Fix linkage for SmartPointerForwardReference for clang 4
      BUG: Add support for system libtiff 4.0.0-4.0.2
      BUG: remove second wrapping of BinShrink for scalars
      BUG: Fix LabelStatistics and LabelOverlap to require same image size
      COMP: Fix checks for system libtiff
      BUG: Add mutex lock to MersenneTwister GetInstance
      BUG: Same test function in different file causes conflict

Brian Helba (3):
      BUG: Fix uninitialized variable in GradientRecursiveGaussianImageFilter
      BUG: Make all specializations NumericTrails::SetLength re-zero contents
      BUG: Update SmoothingRecursiveYvvGaussianFilter remote module

Gib Bogle (1):
      BUG: Windows BigTIFF errors: stat failure and lack of COMPRESSION_DEFLATE

Hans Johnson (2):
      BUG: Missing Modified() call
      PERF: Reviewing code for facilitating compiler optimizations

Luke Bloy (2):
      BUG: Fixes itkBoxSpatialObject part of issue ITK-3153
      BUG: Fixes itkImageMaskSpatialObject part of issue ITK-3153

Matthew McCormick (9):
      BUG: Remove unused itkAffineTransformXX.txt content links.
      COMP: Do not use -fno-ipa-cp-clone with clang.
      ENH: Bump ITK version to 4.5.1.
      COMP: Wrap OptimizerParameterScalesEstimatorTemplate.
      BUG: Wrap TransformFileReader, TransformFileWriter.
      COMP: Duplicated VectorContainer wrapping for real types.
      BUG: GDCM Series does not write z-spacing.
      BUG: Invalid read during ImageIOBase SetDirection.
      ENH: Bump version to 4.5.2.

Michka Popoff (5):
      BUG: Fix for the WrapITK.pth destination path
      COMP: Fixed itkQuasiNewtonOptimizerv4 wrapping warnings
      COMP: Fixed itkGradientDescentOptimizerv4 wrapping warnings
      COMP: Duplicated wrapping for double in Array2D
      ENH: Bump SCIFIO for OS X installation

Sean McBride (1):
      BUG: initialize m_SmallBlock ivar in ctor; fixes garbage read

Vladimir S. FONOV (1):
      COMP: Improved MINCIOTransform tests

Wei Liu (1):
      BUG: Fixed a bug in ExpectationMaximiationMixtureModelEstimator.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23089 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Update SimpleITK to release branch and simplify build system

This commit partially reverts r23052 that was adding workaround for
SimpleITK issues 517 and 518.

$ git shortlog v0.8.0..9cc5382466a945ded055bcd1a4f64bced810656d --no-merges
Bradley Lowekamp (8):
      ENH: Adding UseHistograms options to LabelStatistics
      Add initialization to the new parameter member variable.
      Adding UseHistograms option to procedure and Execute methods
      COMP: fix extraneous semi-colons at end of member function definitions
      BUG: Fix potential missing library dependency in last BasicFilters library
      BUG: Add SimpleITK_VERSION variable defined after find_package
      Require SimpleITK major version to match for compatible version
      BUG: Specify "Development" component for all headers

Hans Johnson (1):
      COMP: Header guard typo mis-match

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23090 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix sign compararison warnings

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23091 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Remove now unneeded SimpleITK build system hack introduced in r23052

This commit implements the change that commit r23090 is describing.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23092 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fixed Windows build error

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23093 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Merged to latest trunk and resolved conflicts

Merge branch 'master' of https://github.com/Slicer/Slicer into TransformDisplayableManagerInteg

Conflicts:
	Libs/MRML/Core/vtkMRMLProceduralColorNode.cxx
	Libs/MRML/Core/vtkMRMLProceduralColorNode.h
	Libs/MRML/Core/vtkMRMLScene.cxx
ENH: Merged to latest trunk and resolved conflicts

Merge branch 'master' of https://github.com/Slicer/Slicer into TransformDisplayableManagerInteg

Conflicts:
	Libs/MRML/Core/vtkMRMLProceduralColorNode.cxx
	Libs/MRML/Core/vtkMRMLProceduralColorNode.h
	Libs/MRML/Core/vtkMRMLScene.cxx