ENH: Adding the capability to process derived items

DerivedItems is a list of file names attributes on the
loadable with the DICOM instances produced by the plugin,
which will be added to the database after loading
the loadable.

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23546 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Create new indexer for each file

Suggested by Steve Pieper as a way to work around potential issues in CTK

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

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23547 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Update VTK6 to include backported bug fixes and tweaks

$ git shortlog 169b37b..6c6e5d3
Andrew Bauer (1):
      Fixing overflow issue that appeared with GCC compilers.

Ben Boeckel (4):
      python: fix leaks when setting constants in wrappers
      STLWriter: Raise an error for non-triangles
      STLReader: Close the file when an error occurs
      STLReader: Fix error signaling when reading files

Bill Lorensen (1):
      BUG0013829: vtkAssembly::GetBounds adds bounds which are uninitialized

Brad King (1):
      Examples: Set required CMake version and policies before project()

Cory Quammen (1):
      Added "sticky" axes mode to vtkCubeAxesActor

David C. Lonie (1):
      Handle empty array initialization in numpy_support.

David Gobbi (7):
      Fix a crash when deleting vtk-python objects.
      Fix warning about trailing comma in enum list.
      In wrappers, guard against #including dirs.
      Fix cell picker for images with negative spacing.
      Fix uninitialized array warnings.
      Bad null pointer check in vtkBSplineTransform.
      Fix bad SetColor/GetColor interaction in vtkProperty.

Jean-Christophe Fillion-Robin (2):
      vtkPythonCommand - Add support for additional call data types
      vtkPythonCommand - Fix indent and variable names

John Stark (1):
      Fix pipeline update issues in vtkImageExport

Julien Finet (2):
      Prevent error message when deep copying vtkGridTransform
      Change GetInputConnection error message into a debug warning message

Sankhesh Jhaveri (1):
      BUG: Border visibility from underlying vtkScalarBar actor

Sean McBride (30):
      Fix clang analyzer warning about passing null to strcmp
      Fixed clang analyzer warning about passing null to memcpy
      Fixed clang analyzer warning about reading uninitialized memory
      Fixed clang analyzer waring about a dead store.
      Fixed clang analyzer warning about dead store
      Fixed clang analyzer warning about dead store.
      Fixed clang analyzer warning about dead store.
      Fixed clang analyzer warning about dead store.
      Fixed clang analyzer warning about dead store.
      Fixed clang analyzer warning about 2 dead stores.
      Fixed clang analyzer warning about dead store.
      Fixed clang analyzer warning about reading past an array.
      Fixed several clang analyzer warnings.
      Fixed clang analyzer warning about reading uninitialized memory.
      Fixed clang analyzer warning about dead store to 'pd'.
      Fixed clang analyzer warning about passing null to memcpy.
      Fixed clang analyzer warning about dead store to 'index'.
      Fixed clang analyzer warning about dead store to 'bestTime'.
      Workaround clang analyzer warning by creating temp variable.
      Fixed clang analyzer warnings about dead stores.
      Misc cleanup of code nearby clang analyzer warnings.
      Fixed clang analyzer warnings about dead stores.
      Fixed clang analyzer warning about dead store at very end of method.
      Fixed clang analyzer warning about dead store to 'itr'.
      Fixed clang analyzer warning about dead store to 'cptr'.
      Fixed null deref found by clang analyzer
      Fixed clang analyzer warnings about dereferences
      Suppress clang analyzer warning
      Fixed clang analyzer warning about null deref
      Fixed clang analyzer warning about reading uninitialized data.

Thomas Vaughan (1):
      Set origin and spacing in vtkSurfaceReconstructionFilter. Ref: Mantis 0002826.

Tristan Coulange (1):
      BUG: Add a missing include for VS 2013

Utkarsh Ayachit (3):
      BUG #14599: Handle double values properly.
      Add support for empty strinngs in SetInputArrayToProcess.
      BUG #14244: Fix stereo image captures.

Will Schroeder (1):
      Fixed bug causing plane to disappear on boundary.

Xabi Riobe (1):
      BUG: The method vtkClipPlanesPainter::UpdateBounds must not be implemented.

xabi riobe (2):
      Fix numerical precision problem in vtkCellLocator::IntersectWithLine
      Add default value for argument

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23548 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: fix force color to children checkbox in Models

When converting the model displayable manager to use
more scalar options, missed using the hierarchy display node
for cases when it over rides the model display node. Cast
the hierarchy display node to a model node and use it if defined.

Issue #3784


git-svn-id: http://svn.slicer.org/Slicer4/trunk@23549 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: Fixed issue of DICOM browser not closed after loading a volume

Browser was not closed after loading a volume even if "Persistent" checkbox was unchecked.

Also added a settings (DICOM/BrowserPersistent) to remember the checkbox setting.

From: Andras Lasso <lasso@queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23550 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Added SceneViews and Segment plugins to subject hierarchy

SceneViews is a role plugin for scene view nodes. Provides an icon and allows restoring scene views (request of Sonia)
Segment is a function plugin that adds a context sub-menu ("Segment this using...") to volumes. There is only one action under the sub-menu so far that takes the user to the Editor module, sets the volume as master and creates a labelmap as merge volume.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23551 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Add support for building on windows using Qt 4.8.6 and OpenSSL 1.0.1h

For more details see inlined comment. Also copied below for convenience:

8<----8<----8<----8<----8<----8<----8<----8<----8<----
# Starting with Qt 4.8.6, we compiled [1] OpenSSL binaries specifically for each
# version of Microsoft Visual Studio. To understand the motivation, read below.
#
# As explained in [2][3], if a library meets these two conditions:
#   (a) exposes a pure C interface
#   (b) is linked against static version of the CRT
# the version of the compiler and runtime used to build the library
# shouldn't matter.
#
# That said, since OpenSSL is built as a shared library using the '/MD' [4]
# flag, it is not possible to use the same library with different runtime
# libraries.
#
# We found out that '/MD' was used by inspecting the the file 'ms/ntdll.mak'
# generated atfer configuring OpenSSL.
#
# If you find mistake in this explanation, do not hesitate to submit a patch
# to fix this text. Thanks.
#
# [1] Script used to compile OpenSSL: https://gist.github.com/jcfr/6030240
# [2] http://siomsystems.com/mixing-visual-studio-versions/
# [3] http://bytes.com/topic/net/answers/505515-compile-different-versions-visual-studio
# [4] http://msdn.microsoft.com/en-us/library/2kzt1wy3.aspx
8<----8<----8<----8<----8<----8<----8<----8<----8<----

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23552 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: External_OpenSSL - Fix typo introduced in previous commit r23552

Use "OpenSSL_(URL|MD5)" instead of "OPENSSL_(URL|MD5)" variables.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23553 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Update Slicer.crt based on Base/QtCore/Resources/Certs/README

Update summary:

$ ./make-ca.sh                                         &&
>  ./remove-expired-certs.sh certs                      &&
>  REVISION=$(grep CVS_ID certdata.txt | cut -f4 -d'$') &&
>  VERSION=$(echo $REVISION | cut -f2 -d" ")            &&
>  mv "BLFS-ca-bundle-${VERSION}.crt"  "Slicer.crt"     &&
>  unset REVISION VERSION
rm: cannot remove ‘certs/*’: No such file or directory
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certs/ce026bf8.pem expired on 20131024! Removing...

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23554 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: For sake of consistency, systematically load Slicer SSL certificates

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23555 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Exclude crt extension from git hook line lengths check

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23556 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Do not log when module UI is successfully displayed

Displaying that everything went well is not useful and add extra "noise"
to the regular Slicer output.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23557 3bd1e089-480b-0410-8dfb-8563597acbee
ENH: Update CTK to remove extra debug statements related to ctkDICOMDatabase

Before this commit:

// -------
$ ./Slicer
Number of registered modules: 142
Register compression libraries
TagCacheDatabase not open

TagCacheDatabase verified!

Number of instantiated modules: 142
Number of loaded modules: 142
// -------

After:

// -------
$ ./Slicer
Number of registered modules: 142
Number of instantiated modules: 142
Number of loaded modules: 142
// -------


Summary of changes:

$ git shortlog 9e1c0258..62675d0 --no-merges
Jean-Christophe Fillion-Robin (2):
      Remove qDebug statement from registerCompressionLibraries()
      Do not display debug info when tagCacheExists method works as expected.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23558 3bd1e089-480b-0410-8dfb-8563597acbee
COMP: Ensure designer plugin provided by Qt are also fixed up

In r23042, install rules have been modified to install designer plugin
provided by Qt but the corresponding pattern to select plugins candidate
for fixup has not been adapted. This commit takes care of it.

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23559 3bd1e089-480b-0410-8dfb-8563597acbee