Grundlett: Text replacement - "https?:\/\/www.slicer.org\/slicerWiki\/index.php\/([^ ]+) " to "https://www.slicer.org/wiki/$1"

2019-11-27T14:53:01Z

Text replacement - "https?:\/\/www.slicer.org\/slicerWiki\/index.php\/([^ ]+) " to "https://www.slicer.org/wiki/$1"

UpdateBot: Nightly -> 4.8

2017-10-18T07:01:56Z

Nightly -> 4.8

New page

__TOC__

== Migration Guide ==

===Slicer 4.8: Application: isRelease() function not available or deprecated===

Error message similar to:

Missing/deprecated qSlicerCoreApplication::isRelease()

or

Missing/deprecated slicer.app.isRelease()

Solution:

Use <tt>qSlicerCoreApplication::releaseType() == "Stable"</tt>

Summary:

Prior to rXYZ, the variable <tt>Slicer_VERSION_TWEAK</tt> was used to check if a "stable release" was built. The variable value
was set by updating the sources and defining the variable to an integer greater or equal to 0. In other word, if the variable
evaluated to an empty string, a nighty or experimental build was being done, if it evaluated to an integer, a stable release build
was being done.

The approach had few issues:
* the name of the variable was confusing
* identifying a "stable release" only from a source tree revision was not enough. Indeed the environment defining a "release" is the one found on the build machines used to generate the installer.
* nightly build are also considered as release

To address this, the CMake variable <tt>Slicer_RELEASE_TYPE</tt> was introduced. As of 2017-10-04, it can be set to <tt>Experimental</tt>, <tt>Nightly</tt>
or <tt>Stable</tt> with <tt>Experimental</tt> being the value hard-coded in the source.

Identifying a build as "stable" is now explicitly done by setting <tt>Slicer_RELEASE_TYPE</tt> to <tt>Stable</tt> at configure time.

Also, since the concept of release types was introduced, the function <tt>isRelease()</tt> has been removed in favor of <tt>releaseType()</tt>.

References:

https://github.com/Slicer/Slicer/pull/354

===Slicer Python Module: modulewidget and others removed.===

 Summary
Python classes formerly in "slicer.moduledm", "slicer.modulelogic", "slicer.modulemrml"
and "slicer.modulewidget" are now directly available in the slicer module.

See example of change [https://github.com/QIICR/LongitudinalPETCT/pull/11 here].

Rational:

See comments in commit messages referenced blow.

References:

https://github.com/Slicer/Slicer/commit/628f83fe7a6f4e0710e306bcaf7c04b9e3e5e6bd

https://github.com/Slicer/Slicer/commit/9cb5668fde1abc8f0430a91ca37fc29277ceeb4e

===MRML: Slicer 4.6: Moved up vtkMRMLStorableNode in the MRML node hierarchy.===

Rational:

vtkMRMLStorableNode is not a children of vtkMRMLTransformable node anymore,
but directly a children of vtkMRMLNode.

This allows making a node storable without requiring it to be also
transformable. It is important for several node types (color maps, tables,
etc), which require separate storage node but are not transformable.

References:
* Changed introduced in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24891 r24891]

Error message similar to:

/tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx: In member function ‘void vtkMRMLLongitudinalPETCTStudyNode::ObserveRegistrationTransform(bool)’:
/tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx:478:28: error: ‘class vtkMRMLVolumePropertyNode’ has no member named ‘GetParentTransformNode’
&& propNode->GetParentTransformNode()
^
/tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx:480:23: error: ‘class vtkMRMLVolumePropertyNode’ has no member named ‘SetAndObserveTransformNodeID’
propNode->SetAndObserveTransformNodeID(
^
/tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx:503:23: error: ‘class vtkMRMLVolumePropertyNode’ has no member named ‘SetAndObserveTransformNodeID’
propNode->SetAndObserveTransformNodeID(NULL);
^

Solution:

Removes lines and/or refactor code

===MRML: Slicer 4.5: Introduction of vtkMRMLLabelMapVolumeNode===

Rational:

Before <tt>vtkMRMLScalarVolumeNode</tt> was used for both scalar and label map
volumes and the LabelMap custom MRML node attribute was used for
distinguishing between them (0=scalar; 1=label map volume).

This made conversion between labelmap/scalar volumes very easy but made
it difficult to customize behavior, display, processing of segmentation
information.

Now a new <tt>vtkMRMLLabelMapVolumeNode</tt> class is used for storing segmentation
information (still using <tt>vtkMRMLScalarVolume</tt> used as base class for backward
compatibility; but in the future the base class may be changed to reflect
that segmentation can be represented in various ways, not just as volumes).

Error message similar to:

error: ‘class vtkMRMLScalarVolumeNode’ has no member named ‘SetLabelMap’
outputVolumeNode->SetLabelMap(1);
^

Solution (part1: down cast to <tt>vtkMRMLLabelMapVolumeNode</tt>, remove call to <tt>SetLabelMap</tt>)

Replace lines like:

vtkMRMLNode* outputNode = d->OutputLabelVolumeMRMLNodeComboBox->currentNode();
vtkMRMLScalarVolumeNode* outputVolumeNode = vtkMRMLScalarVolumeNode::SafeDownCast(outputNode);
[...]
outputVolumeNode->SetLabelMap(1);

with:

vtkMRMLLabelMapVolumeNode* outputVolumeNode =
vtkMRMLLabelMapVolumeNode::SafeDownCast(d->OutputLabelVolumeMRMLNodeComboBox->currentNode());
[...]

Solution (part2: Update UI file):

Replace lines like:

<widget class="qMRMLNodeComboBox" name="InputLabelVolumeMRMLNodeComboBox">
<property name="nodeTypes">
<stringlist>
<string>vtkMRMLScalarVolumeNode</string>
</stringlist>
</property>
[...]
</widget>

with:

<widget class="qMRMLNodeComboBox" name="InputLabelVolumeMRMLNodeComboBox">
<property name="nodeTypes">
<stringlist>
<string>vtkMRMLLabelMapVolumeNode</string> <------------- Update Here
</stringlist>
</property>
[...]
</widget>

Solution (part3: Update node selector configuration):

Replace lines like:

nodeSelector.setNodeTypes(QStringList("vtkMRMLScalarVolumeNode"));
nodeSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap", "1");

with:

nodeSelector.setNodeTypes(QStringList("vtkMRMLLabelMapVolumeNode"));

References:
* http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/Segmentations#vtkMRMLLabelMapVolumeNode_integration
* http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24291

===CLI: Slicer 4.3: Add ITKFactoryRegistration library centralizing ITK IO factory registration===

Rational:

Linking against <tt>ITKFactoryRegistration</tt> ensures that ITK IO factory are properly registered on all supported platforms.

Error message similar to:

Undefined symbols for architecture x86_64:
"itk::itkFactoryRegistration()", referenced from:
_main in ImageMakerTest.cxx.o
ld: symbol(s) not found for architecture x86_64

Solution:

Replace lines like:

target_link_libraries(${CLP}Test ${CLP}Lib)

with:

target_link_libraries(${CLP}Test ${CLP}Lib ${SlicerExecutionModel_EXTRA_EXECUTABLE_TARGET_LIBRARIES})

References:

* http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21592
* https://issues.slicer.org/view.php?id=2813

← Older revision		Revision as of 14:53, 27 November 2019
Line 171:		Line 171:

	<b>References:</b>		<b>References:</b>
−	* ~~http~~://www.slicer.org/~~slicerWiki/index.php~~/Documentation/Labs/Segmentations#vtkMRMLLabelMapVolumeNode_integration	+	* https://www.slicer.org/wiki/Documentation/Labs/Segmentations#vtkMRMLLabelMapVolumeNode_integration* http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24291
−	* http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24291

Documentation/4.8/Developers/Tutorials/MigrationGuide/Slicer - Revision history

Grundlett: Text replacement - "https?:\/\/www.slicer.org\/slicerWiki\/index.php\/([^ ]+) " to "https://www.slicer.org/wiki/$1"

UpdateBot: Nightly -> 4.8