BUG: 3660. Fixed faulty logic checking for coordinate changes in the vtkMRMLMarkupsFiducialDisplayableManager3D.cxx

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23108 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Store a list of disabled plugins when user disable plugins in
advanced mode. All plugins would be enabled by default (both in simple and
advanced mode).

From: Alireza Mehrtash <mehrtash@bwh.harvard.edu>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23109 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: Added comments describing the grid transform reader behavior

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23110 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: add coordinates to right click menu

When select rows in the Markups table, right click will now add the
coordinate points to the top of the context menu. Works for
multi select, and will work for multiple points per markup.
Adds the label of the markup if there are multiple rows selected.
Adds a separator after the coordinates and before the command
actions.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23111 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: add check box to show/hide coordinate columns

When box is checked, hide the markup coordiante columns in the
table, when unchecked show them.

Issue #3667

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23112 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: label change from XYZ to RAS

After discussion on Slicer Developer hangout, change the GUI
coordinate labels to RAS instead of XYZ.

Issue #3367

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23113 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: fix behaviour of gui when markup inside transform

When editing the coordinates of a markup that's inside of a
transform, the pairing of getting the untransformed
coordinate and then saving it as transformed was leading to
incorrect values.
Added in a checkbox to select if the GUI table shows the
markup coordinates in transformed or untransformed versions.

Issue #3632

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23114 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: remove compiler warnings

Remove unused variable, mark parameter as unused.

Issue #3632


git-svn-id: http://svn.slicer.org/Slicer4/trunk@23115 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix dashboard submission removing subproject settings

When copied over from CTK, some of the setting related to
"SubProject" were still set. This was causing some issue on the CDash
server. This commit is an attempt to fix the submission error.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23116 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: disable alternate color editors

The color module was just collapsing the color table and
continuous color transfer viewer/editors when the other type
of node was active. User feedback showed this to be confusing
as valid looking data was visible if the sections were
expanded. This change disables the invalid editor on
selection of a color node.

Issue #3573


git-svn-id: http://svn.slicer.org/Slicer4/trunk@23117 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: fix fiber bundle color display

Check for fiber bundle display nodes and use the old method,
igoring the new scalar range options for models. Fixes bug
introduced with issue #3573 in svn revision 23083

Issue #3672


git-svn-id: http://svn.slicer.org/Slicer4/trunk@23118 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Remove VTK 4 backwards compatibility

Removed vtkSource, vtkProcessObject and subclasses.
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Overview#Removal_of_VTK_4_Backwards_Compatibility_Superclasses
http://www.vtk.org/Wiki/VTK/Tutorials/New_Pipeline#Converting_an_Existing_Filter_to_the_New_Pipeline

Closes #3485
From Yuzheng Zhou <yuzheng.zhou@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23119 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix VTK 4 backward compatibility removal

Issue #3485

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23120 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Add VTK 6 support 1/2

1) Support vtk6 to build system.
http://www.vtk.org/Wiki/VTK/Build_System_Migration
Give users a build option between vtk5 and vtk6.
Solve vtk library python wrapping for VTK 6
Use system zlib (this is a hack)
Use system png (this is a hack)

2) Update dependency projects in superbuild including VTK, CTK, OpenIGTLinkIF, MultiVolumeExplorer.

3) Remove deprecated Macro.
The following two macros were deprecated in VTK 5.0 that were still supported, but have now been eliminated:
vtkTypeRevisionMacro has been replaced with vtkTypeMacro; vtkCxxRevisionMacro has been removed.
http://www.visitusers.org/index.php?title=VTK_6.0_Upgrade

The following two macros were deprecated in VTK 6.0 if VTK_LEGACY_REMOVE is on:
VTK_LARGE_INTEGER and VTK_LARGE_FLOAT
https://github.com/Kitware/VTK/blob/9a0fbb8da1a1701dc1b44c71467b969b3302efad/Common/Core/vtkType.h#L158-159

vtkFloatingPointType is replaced with double.
http://review.source.kitware.com/#/t/1667/

vtkType deprecations
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/vtkType_deprecations

4) Replace SetInput() with SetInputData() and SetInputConnection(), the same kind of functions include SetInput1(), SetInput2(), AddInput() and SetSource().
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Replacement_of_SetInput

5) Remove GetProducerPort() from vtkDataObject.
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_GetProducerPort

6) Remove Execute
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_Execute

7) Remove SetWholeExtent() from vtkDataObject
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_SetWholeExtent

8) Remove Methods for Manipulating Update Extent
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_Methods_for_Manipulating_Update_Extent

9) Change AllocateOutputData() in vtkImageAlgorithm.
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Change_to_AllocateOutputData

10) Remove CopyInformation and CopyTypeSpecificInformation from vtkDataObject and vtkImageData.
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_CopyInformation

11) Remove GetPipelineInformation and GetExecutive from vtkDataObject.
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_GetPipelineInformation

12) VTK6 requires #include <vtkVersion.h> to use the VTK_xxx_VERSION preprocessor directives.
http://vtk.org/Wiki/VTK/VTK6/Migration/WikiExamples#Improve

13) Remove Methods for Manipulating Update Extent.
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_Methods_for_Manipulating_Update_Extent.
http://vtk.org/Wiki/VTK/VTK6/Migration/WikiExamples#Improve.

14) Change scalars manipulation functions
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Changes_to_Scalars_Manipulation_Functions.
http://vtk.org/Wiki/VTK/VTK6/Migration/WikiExamples#Improve.

15) Remove Pipeline Update Methods from vtkDataObject.
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_Update

16) Remove Pipeline Update Methods from vtkDataObject.
http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Removal_of_Update.

17) Refactor functions in vtkMRMLModelNode and sublcasses.

18) Refactor functions in vtkMRMLVolumeNode and its subclasses.
Use ImageDataPort instead of ImageData

Issue #3514

From Yuzheng Zhou <yuzheng.zhou@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23121 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Add VTK 6 support 2/2

Issue #3514

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23122 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Add FindFontConfig.cmake

FindFontConfig.cmake is from VTK.

VTKv6 was not built with the module vtkRenderingFreeTypeFontConfig because
it could not find FontConfig. However, once VTK was downloaded and
configured. Any find_package(FontConfig) call (e.g. in CTK) would succeed
because FindFontConfig.cmake is now in the CMake search path.

Issue #3514

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23123 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix vtkMRMLDiffusionWeightedVolumeDisplayNode pipeline

Issue #3514

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23124 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix crash in vtkMRMLModelDisplayableManager

Regression from r23118

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23125 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Restore slice views when building with VTK v5

Issue #3514

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23126 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix uninitialized pointer in vtkMRMLModelDisplayDisplayableManager

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23127 3bd1e089-480b-0410-8dfb-8563597acbee