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
COMP: memory allocation on windows

Issue #3573



git-svn-id: http://svn.slicer.org/Slicer4/trunk@23094 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: revert windows compilation change

A fix was already checked in



git-svn-id: http://svn.slicer.org/Slicer4/trunk@23095 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix unix installation of SSL libraries

This commit ensures that only the ssl libraries are installed without
additional empty directories.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23096 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Fix python source URL.

The Python tarball http URL sends a 301 Moved Permanently response to
the https version.

Placing the real URL makes errors such as:

-- downloading...
     src='http://www.python.org/ftp/python/2.7.3/Python-2.7.3.tgz'
     dst='/home/matt/bin/Slicer-GCC-MinSizeRel/Python-2.7.3.tgz'
 timeout='none'
CMake Error at
python-source-prefix/src/python-source-stamp/download-python-source.cmake:9
(file):
  file DOWNLOAD HASH mismatch

   for file: [/home/matt/bin/Slicer-GCC-MinSizeRel/Python-2.7.3.tgz]
   expected hash: [2cf641732ac23b18d139be077bd906cd]
     actual hash: [d41d8cd98f00b204e9800998ecf8427e]
          status: [1;"unsupported protocol"]

More informative (HTTPS is not supported).

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23097 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: add view node combo box for models

Gives users a GUI element to set models visible in selected
views. 
Updated the displayable manager so that the model slice intersection
honors the overall display node visibility setting.

Issue #3216



git-svn-id: http://svn.slicer.org/Slicer4/trunk@23098 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix CMake 3.x configuration warnings

Test done using CMake 3.0.20140413 (g94d5a)

Since project version is explicitly set, avoid warning by setting
policy CMP0048

Since ITKConfig.cmake append value to "ITK_LIBRARIES" and "ITK_INCLUDE_DIRS"
variables, let's make sure that "ITKFactoryRegistration" is not in the list
when configuring "ITKFactoryRegistration". This fixes the following
warnings:

//--------------
CMake Warning (dev) at Libs/ITKFactoryRegistration/CMakeLists.txt:55 (add_library):
  Policy CMP0038 is not set: Targets may not link directly to themselves.
  Run "cmake --help-policy CMP0038" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  Target "ITKFactoryRegistration" links to itself.
This warning is for project developers.  Use -Wno-dev to suppress it.
//--------------

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23099 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Update CTK project to include CMake configuration speedup

On Ubuntu 13.10 using CMake 2.8.11.2, an improvement of ~10%
can be observed.

Without CTK tweaks:

real	2m32.996s
user	2m26.225s
sys	0m6.820s

With CTK tweak:

real	2m19.957s
user	2m15.908s
sys	0m3.768s


$ git shortlog 233d87..909073a --no-merges
Jean-Christophe Fillion-Robin (18):
      Remove unused FindCTK.cmake module
      Ensure CTK_ENABLE_Python_Wrapping remain set when CTK_BUILD_ALL is ON
      Print message if CTK_{APP, LIB, PLUGIN} options set to ON because of BUILD_ALL options
      Fix dependency of Scripting/Python/{Core, Widgets} options
      Remove code referencing unexisting variable. See #449
      Remove 'CTK_WRAP_PYTHONQT_FULL' obsolete option. See #449
      Remove setting of INCLUDE_DIRS variable specific to PythonQtGenerator
      Move all PythonQt wrapping code into one script. See #449
      Optimize ctkMacroWrapPythonQt creating required source list in a single loop.
      Configure module init file at configure times. See #449
      Simplify how path of generated file are specified. See #449
      Simplify moc'ing of generated PythonQt wrapper. See #449
      Remove Light wrapping CMake script and directly invoke python executable
      Do not log PythonQt wrapping output. See #449
      Optimize QT4_GENERATE_MOCS macro getting moc flags only when needed
      Simplify QT4_GENERATE_MOCS. See #449
      Re-create python compile script only if needed and fix dependency. See #449
      Fix python script compilation removing inputs from custom target deps. See #449

Julien Finet (2):
      Fix ctkPushButton text alignment with no icon
      Emit ctkSearchBox::textEdited() signal when clear icon is clicked

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23100 3bd1e089-480b-0410-8dfb-8563597acbee