ENH: explicit selection of the secondary multivolume using the module GUI


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22416 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: adding default method for initializing of the node-specific display node


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22420 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: print out widget projections

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22421 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: fixing a Markups merge error for the active place node

The more general activePlaceNodeID is to be used instead of a specific 
Annotations or Markups variable name.

Fixed while working on issue #3296 for the 4.3.1 release.



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22422 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix missing conversion of fiducials in scene views

Annotation fiducials in scene view scenes were coming up as unsaved in the Save
data dialog when loaded from a scene with scene views where only the current
scene had had it's fiducials conerted to markups. This was due to the change
Alex made to save data that only appears in scene views, so added in
iterating over the current scene and scene views when converting fiducials. 
Added in looking for end scene restore events in the GUI so that it will
be updated properly even if there wasn't an active place node id in the saved scene view. 
Expanded the AddNewFiducialNode method to support adding to a passed in scene so
that the converted markups can be added to the scene view scenes.

Issue #3296



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22423 3bd1e089-480b-0410-8dfb-8563597acbee
STYLE: update Annotatons module documentation for 4.3

Removed references to fiducials as they've been moved into the Markups module.



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22424 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix memory mgt in PythonQt, ENH: Config of dicom log level from python

// ---------------------------------------

CTK Commits:

Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Tue Sep 10 04:27:56 2013 -0400

    Re-factor ctkDICOMUtil to be consistent with ctkUtil

    Add the methods dicomLogLevel and setDICOMLogLevel to "ctk" namespace

    Update PythonQt external project to include fix allowing to wrap
    QFlags.

    The DICOM log level can be set from python doing:

     >>> import ctk
     >>> ctk.ctk.dicomLogLevel()
     16
     >>> ctk.ctk.dicomLogLevelAsString()
     u'Info'
     >>> ctk.ctk.setDICOMLogLevel(ctk.ctkErrorLogLevel.Critical)
     >>> ctk.ctk.dicomLogLevel()
     256
     >>> ctk.ctkErrorLogLevel.logLevelAsString(ctk.ctk.dicomLogLevel())
     u'Critical'
     >>> ctk.ctkErrorLogLevel.logLevelAsString(32)
     u'Warning'
     >>> ctk.ctk.setDICOMLogLevel(64)
     >>> ctk.ctk.dicomLogLevelAsString()
     u'Error'

commit 637da4b68ed93741a4c8cf73b406d66986dbe864
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Tue Sep 10 04:12:10 2013 -0400

    Define ctkErrorLogLevel::logLevelAsString as static for easier re-use

    Explicitly add associated decorator. See code comment for explanation.

commit 8542108ef7d15a39d4d302aa64f4ecc2d15bf3e5
Author: Isaiah Norton <inorton@bwh.harvard.edu>
Date:   Wed Aug 28 11:20:31 2013 -0400

    Add ctkDICOMUtil and ::setDICOMLogLevel helper

    This function allows to set the DICOM log level for
    diagnostic purposes.

// ---------------------------------------

PythonQt commits:


commit e1f1c77d9675c3c5fb1cba19d2a32ace483eda2c
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Tue Sep 10 02:49:23 2013 -0400

    Revert part of r91 preventing QFlags from being wrapped

    By checking if an enum member has already been cached it is not required
    anymore to skip it if is a QFlags.

    Additionally, the wrapping of QFlags can now be done by using
    only Q_FLAGS without having a corresponding Q_ENUMS.

commit 5d5600c4d3134e69b51442a58b58e14c7fd47e54
Author: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>
Date:   Tue Sep 10 02:36:26 2013 -0400

    Add CMake testing support

    Disabled by default to keep behavior consistent with previous
    CMake'ified version.


[...]

commit 7af5c8a4d2194db388ac67f340e3f555e02fea78
Author: florianlink <florianlink@ea8d5007-eb21-0410-b261-ccb3ea6e24a9>
Date:   Wed Jul 3 14:54:20 2013 +0000

    improved wrapper check to avoid crashes on virtual methods while python object gets deleted

    git-svn-id: http://svn.code.sf.net/p/pythonqt/code/trunk@245 ea8d5007-eb21-0410-b261-ccb3ea6e24a9

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22425 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Add close button to "About dialog". Fixes #3172

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22426 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Update Editor extension template to use scripted module macro

Discussion: http://slicer-devel.65872.n3.nabble.com/Issues-with-Editor-effect-extension-td4029730.html

Fixes #3392

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22427 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Simplify editor extension template

This is a follow up of commit r22067 [1] where it should have been done
as described in r22063 [2].

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22428 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Set module name / objectName in GenericTests

In addition to be consistent with what is done in the "instantiateModule"
method of the "qSlicerAbstractModuleFactoryManager".

It also ensure that the "ModuleShareDirectory" set in the "logic" method
of the "qSlicerAbstractCoreModule" class is done using the expected
value for the module name.

This will allow generic tests instantiating module using
"GetModuleShareDirectory" method to get the correct value (i.e Reporting
module)

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22429 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Allow extension to easily use "SlicerMacroExtractRepositoryMacro"

As consequence the code within the Reporting will be simplified and
duplicated macro will be removed.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22430 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: add missing StartPlaceMode method

Laurent's extension was using the Annotation module logic
StartPlaceMode call and it wasn't working. Added it to
Markups logic and debugged it to work to set the mouse
mode to place Markup fiducials. Added a return boolean
to check success. Updated testing.



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22431 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: finish steps for the Neurosurgical Planning Tutorial

Added the editor steps and label map seeding.
Added the screen capture functionality to the template file.

Issue #3328



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22432 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: fix error on start up from SurfaceToolbox

Add in import string to fix start up error when 
trying to load the SurfaceToolbox scriptable module:

Traceback (most recent call last):
  File "/projects/birn/nicole/Slicer42/Slicer4-SuperBuild-Debug/Slicer-build/lib/Slicer-4.3/qt-scripted-modules/SurfaceToolbox.py", line 11, in __init__
    parent.helpText = string.Template("""
NameError: global name 'string' is not defined



git-svn-id: http://svn.slicer.org/Slicer4/trunk@22433 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix CTKConfig.cmake to properly set _{LIBRARY,INCLUDE}_DIRS variable

For example, within CTKConfig.cmake:

* Before this commit:

[...]
set(CTKVisualizationVTKCore_LIBRARY_DIRS "VTK_LIBRARY_DIRS;/path/to/VTK-build/bin")
[...]

set(CTKVisualizationVTKWidgets_INCLUDE_DIRS
  [...]
  "/path/to/CTK-build/Libs/Core;"
  "/path/to/CTK/Libs/Visualization/VTK/Core;
  "/path/to/CTK-build/CTK-build/Libs/Visualization/VTK/Core;"
  "VTK_INCLUDE_DIRS;"
  "/path/to/VTK-build;"
  "/path/to/VTK-build/Common;"
  [...]
  )

* After this commit:

[...]
set(CTKVisualizationVTKCore_LIBRARY_DIRS "/path/to/VTK-build/bin")
[...]

set(CTKVisualizationVTKWidgets_INCLUDE_DIRS
  [...]
  "/path/to/CTK-build/Libs/Core;"
  "/path/to/CTK/Libs/Visualization/VTK/Core;
  "/path/to/CTK-build/CTK-build/Libs/Visualization/VTK/Core;"
  "/path/to/VTK-build;"
  "/path/to/VTK-build/Common;"
  [...]
  )

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22434 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix EMSegment test "EMSeg_MRML_DiffReadWriteNodes"

Update EMSegment project to account for backward incompatible changes
made in r22310

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22435 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fix Slicer crash on DTIVolume reload after scene is closed.

Handle the case when newVolumeDispalyNode is NULL in setMRMLVolumeNode().
Fixes #3380

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22436 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix superbuild when using Xcode 5.0 or Xcode 5.0 command line tools

Xcode no longer ships with MacOSX10.7.sdk (or earlier) from version 5.0,
which is the most recent version specified in
CMake/SlicerBlockSetCMakeOSXVariables.cmake. Therefore the superbuild
fails when attempted to build Python and NumPy due to a missing version
number or SDK location. Manually setting CMAKE_OSX_DEPLOYMENT_TARGET
to 10.8 and CMAKE_OSX_SYSROOT to ${SDK_ROOT}/MacOSX10.8.sdk or
editing SlicerBlockSetCMakeOSXVariables.cmake fixes the issue.

Fixes #3402

From: Jamie Snape <jamie.snape@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22454 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Fix launch of Slicer-real on MacOSX adding rpath to libarchive

Fixes #3189

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22455 3bd1e089-480b-0410-8dfb-8563597acbee