From: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22599 3bd1e089-480b-0410-8dfb-8563597acbee

Execute the event loop just after queuing the request with the
networkAccessManager.

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22598 3bd1e089-480b-0410-8dfb-8563597acbee

Allocating a single "vtkMRMLScalarVolumeNode" wasn't enough to ensure
that the space previously used by 'vtkMRMLScalarVolumeNode1' wasn't
available again for the restored volume.

See inlined comment for more details.

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22596 3bd1e089-480b-0410-8dfb-8563597acbee

Add list of expected displayable managers and fail test
if returned list doesn't match in size or if returned managers
are not in the list.

From: naucoin <naucoin@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22595 3bd1e089-480b-0410-8dfb-8563597acbee

Since calling GetID() on a newly instantiated node is expected to
return NULL and that attempting to print a NULL string on windows
results in a crash. The test was failing only on windows.

This commit remove the print statement in the test and also add test
test for GetID and GetNodeTagName to EXERCISE_BASIC_MRML_METHODS so that
the default value for every node is verified.

Since there is already a test printing the value if it fails, also
remove extra debug statement printing the number of children in
the hierarchy node.

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22592 3bd1e089-480b-0410-8dfb-8563597acbee

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22591 3bd1e089-480b-0410-8dfb-8563597acbee

This commit makes it easier to read through the different test
associated with the macro.

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22590 3bd1e089-480b-0410-8dfb-8563597acbee

Added getDisplayableManagers on the slice view to mirror the
same call on the 3D view. Added testing.

From: naucoin <naucoin@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22589 3bd1e089-480b-0410-8dfb-8563597acbee

Copy/paste error left an extra comma in the argument list.

From: naucoin <naucoin@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22588 3bd1e089-480b-0410-8dfb-8563597acbee

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22581 3bd1e089-480b-0410-8dfb-8563597acbee

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22580 3bd1e089-480b-0410-8dfb-8563597acbee

Following r22568, the controller has been updated so that the abbreviated
slice name can be dynamically updated after the "LayoutLabel" has been
changed on the associated slice node.

This commit clean up the code removing un-needed ivar "SliceViewLabel" and
fix the test.

Finally, also set "sliceViewLabel" as a property so that is accessible
from python.

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22579 3bd1e089-480b-0410-8dfb-8563597acbee

See inlined comment for details.

This commit will also avoid leaks (and by extension ensure they
pass when leaks detection is enabled) in the following tests:
  py_NeurosurgicalPlanningTutorial
  py_ThresholdThreadingTest
  py_NeurosurgicalPlanningTutorial
  py_ScenePerformance

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22578 3bd1e089-480b-0410-8dfb-8563597acbee

There is currently no automatic/clean mechanism to release the object
created by factory methods.

The only "hack" that exists for now is to decrease the reference
count manually in your code:

For more details, see [1], [2], [3] and [4]

[1] http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/MemoryManagement
[2] http://massmail.spl.harvard.edu/public-archives/slicer-devel/2011/007513.html
[3] http://www.vtk.org/Bug/view.php?id=12139
[4] http://www.vtk.org/pipermail/vtk-developers/2011-April/009757.html

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22577 3bd1e089-480b-0410-8dfb-8563597acbee

This commit ensured that the observer associated with MRMLNodesCallbackCommand
are removed also if the file is successfully loaded.

Warning: In /home/jchris/Projects/Slicer/Libs/MRML/Core/vtkObserverManager.cxx, line 59
vtkObserverManager (0x3b99ce0): The callback is not deleted because there
are still some observation. They seem to not have been registered into
the event broker.

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22576 3bd1e089-480b-0410-8dfb-8563597acbee

This feature is helpful to inform the user of the slice viewer content without
using extra screen space. Resolves issue 3427

From: fedorov <fedorov@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22575 3bd1e089-480b-0410-8dfb-8563597acbee

By using QFile static function each time permission are set/get, we
ensure that the permissions of the file are fully re-stated [1]. Indeed,
internally it create a QFile object for each call.

Doing so fix the test ensuring the call to:

  QFile(this->Tmp.absolutePath()).permissions() & QFile::WriteUser)

returns the expected value just after permission has been set.

This is a know Qt issue. See https://bugreports.qt-project.org/browse/QTBUG-7211

[1] http://en.wikipedia.org/wiki/Stat_%28system_call%29

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22567 3bd1e089-480b-0410-8dfb-8563597acbee

Following Qt 4.8.1, setting permission on a folder with a parent folder
not being executable leads to an error.

As it should always have:

$ mkdir bar/foo
$ chmod u-x bar
$ chmod u-x bar/foo
chmod: cannot access ‘bar/foo’: Permission denied

This commit implement the correct behavior by setting flags in the
right order depending if Executable but is passed or not.

Since it is not possible to change permission of directory without executable
bit set to off, if flag "with executable bit off" is recursively set to
path /a/b/c/d, permission should be set to d, c, b and then a.

[1] and probably 4.8.0 but this hasn't been tested.

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22566 3bd1e089-480b-0410-8dfb-8563597acbee

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22565 3bd1e089-480b-0410-8dfb-8563597acbee

After checking with the author of the class, it makes sense to remove the
code related to the unused "gradientRange" variable.

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22561 3bd1e089-480b-0410-8dfb-8563597acbee

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22560 3bd1e089-480b-0410-8dfb-8563597acbee

$ git shortlog 90000c32..f64b68acd
Andras Lasso (1):
      Prevent reentrant calling of ctkProxyStyle::ensureBaseStyle()

Jean-Christophe Fillion-Robin (1):
      Merge pull request #372 from lassoan/371-ensure-base-style-infinite-recursion-crash

Fixes #3129

From: Andras Lasso <lasso@cs.queensu.ca>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22557 3bd1e089-480b-0410-8dfb-8563597acbee

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22556 3bd1e089-480b-0410-8dfb-8563597acbee

Simplify code removing tests for null object already being done
in the helper macro "EXERCISE_BASIC_OBJECT_METHODS"

For example, the following should not be needed:

  vtkNew<vtkFoo> foo;
  if (foo.GetPointer() == 0)
  {
    std::cerr << "Failed to instantiate vtkFoo" << std::endl;
  }

Instead, the following should be used:

  EXERCISE_BASIC_OBJECT_METHODS(foo.GetPointer())

Remove use of unnecessary vtkSmartPointer to check return value. Indeed,
since the operator "==" of the vtkSmartPointer is overloaded to compare with
the pointed object, there is no need to used a smart pointer. [1]

// ---------
vtkSmartPointer<vtkMRMLDisplayableNode> pnode = node1->GetDisplayableNode();
std::cout << "GetDisplayableNode returned "
          << (pnode == NULL ? "null" : "not null")
          << std::endl;
// ---------

has been changed into

// ---------
vtkMRMLDisplayableNode* pnode = node1->GetDisplayableNode();
std::cout << "GetDisplayableNode returned "
          << (pnode == NULL ? "null" : "not null")
          << std::endl;
// ---------

[1] https://github.com/Kitware/VTK/blob/0e0674a3695fdeaf01ce87dfc04e32111b7402e0/Common/vtkSmartPointerBase.h#L104

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22555 3bd1e089-480b-0410-8dfb-8563597acbee

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22554 3bd1e089-480b-0410-8dfb-8563597acbee

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22553 3bd1e089-480b-0410-8dfb-8563597acbee

Factor out code into convenience functions:
 - checkViewArrangement
 - checkNumberOfItems

Use vtkNew when possible

There is no need to explicitly delete the layout manager since
it was a QWidget instantiated on the stack as a parent.

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22552 3bd1e089-480b-0410-8dfb-8563597acbee

Ensure ModelDisplayableManager properly delete resources when
a new scene is set.

Ensure the slicer logic set the scene on layers when a new
scene is set a second time.

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22551 3bd1e089-480b-0410-8dfb-8563597acbee

This commit will fix the following warnings:

147: Warning: In /home/jchris/Projects/Slicer/Libs/MRML/DisplayableManager/vtkMRMLAbstractDisplayableManager.cxx, line 583
147: vtkMRMLThreeDReformatDisplayableManager (0x2c92750): CreateIfPossible - MRMLScene does NOT contain any InteractionNode
147:
147: Warning: In /home/jchris/Projects/Slicer/Libs/MRML/DisplayableManager/vtkMRMLAbstractDisplayableManager.cxx, line 591
147: vtkMRMLThreeDReformatDisplayableManager (0x2c92750): CreateIfPossible - MRMLScene does NOT contain any SelectionNode

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22550 3bd1e089-480b-0410-8dfb-8563597acbee

see issue 2384

From: fedorov <fedorov@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22549 3bd1e089-480b-0410-8dfb-8563597acbee

In the situations when Yellow/Green/Red viewers are present, the additional viewers should be numbered starting from 4.

From: fedorov <fedorov@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22548 3bd1e089-480b-0410-8dfb-8563597acbee

Per comment from Jim, see issue 2384

From: fedorov <fedorov@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22547 3bd1e089-480b-0410-8dfb-8563597acbee

From: alexy <alexy@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22546 3bd1e089-480b-0410-8dfb-8563597acbee

$ git shortlog 0e21d85e..90000c3

Jean-Christophe Fillion-Robin (1):
      Merge pull request #366 from finetjul/294-fix-ctkconsole-copy-paste

Julien Finet (5):
      Fix copy/paste in ctkConsole
      Add private implementation to ctkCoordinatesWidget
      Merge branch '355-ctkcoordinateswidget-pimpl'
      Add ctkCoordinatesWidget_p.h
      Merge branch '355-ctkcoordinateswidget-pimpl'

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22545 3bd1e089-480b-0410-8dfb-8563597acbee

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22544 3bd1e089-480b-0410-8dfb-8563597acbee

From: alexy <alexy@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22543 3bd1e089-480b-0410-8dfb-8563597acbee

BUG: 3388. Added observer events parameter to the vtkMRMLNode::AddNodeReferenceRole() method, so that the events can be set only once in subclasses. Added observed events to DisplayableNode and TransformableNode. Simplified and unified reference implementation in TransformableNode

From: alexy <alexy@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22542 3bd1e089-480b-0410-8dfb-8563597acbee

$ git shortlog a8429da..97a08e0

Matthew McCormick (3):
      BUG: Enable MRC IO in UseITK whenever the ITKReview module is enabled.
      Merge branch 'MRC-UseITK' into release
      COMP: Fix NIFTI CMake variable separation warning.

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22522 3bd1e089-480b-0410-8dfb-8563597acbee

In case either the Slicer settings file or, the extensions install
directory are not readable/writable, a nicely formatted message will
be displayed to the user instead of the app-store page,

Note that the associated messages are also logged.

Fixes #3179

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22520 3bd1e089-480b-0410-8dfb-8563597acbee

The compile issue hasn't been detected earlier because only a visual check
between the original patch (Slicer/itkMGHImageIO@13f5e11ef) and
the back-ported one has been done (r22485).

This commit fixes the build issue and also confirm that the associated
Slicer tests now pass:

// --------------
Start 545: py_nomainwindow_test_slicer_mgh
[...]
test_saveShortCompressedNode (test_slicer_mgh.SlicerUtilLoadSaveMGHTests) ... ok
test_saveUnCompressedNode (test_slicer_mgh.SlicerUtilLoadSaveMGHTests) ... ok
// --------------

From: jcfr <jcfr@3bd1e089-480b-0410-8dfb-8563597acbee>

git-svn-id: http://svn.slicer.org/Slicer4/branches/Slicer-4-3@22519 3bd1e089-480b-0410-8dfb-8563597acbee