Documentation/Nightly/Developers/Tutorials/MigrationGuide

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Migration Guide



Contents

Slicer backward incompatible changes

Slicer 5.0: API changes since 4.10

  • Removed protected method vtkMRMLModelDisplayableManager::FindPickedDisplayNodeFromMesh

Python 2 to Python 3

Slicer core has been updated to only support Python 3.

C++ classes and python scripts have been updated to use idioms and constructs only available in Python 3.

Update to python scripts have been done leveraging the CLI provided by https://python-future.org by (1) iteratively applying each one of the associates "fixes", (2) reviewing associated changes and (3) updating as needed.

Updates specific to extensions are discussed in Documentation/Nightly/Developers/Tutorials/MigrationGuide#Slicer_5.0:_Python2_to_Python3

Interactor styles

Limitations of VTK widgets (editable points, lines, curves, etc.) prevented Slicer from having sophisticated user interaction in slice and 3D views. In Slicer5, we replaced VTK widgets with MRML widgets. These widgets are still VTK-based and somewhat similar to VTK widgets, but they operate directly on MRML nodes, they use direct method calls between widgets and their representation, and they use a more efficient and flexible event processing. Instead of hardcoding how viewers behave in response to interaction (mouse move, button click, keyboard, ...) events in an interactor style, all these events are translated to actions and performed in a MRML widget. Most modules are not expected to observe interactor events or styles directly, but if they did, then they may need to be updated accordingly.

  • vtkSliceViewInteractorStyle renamed to vtkMRMLSliceDViewInteractorStyle to reflect that it uses MRML classes directly.
  • vtkThreeDViewInteractorStyle renamed to vtkMRMLThreeDViewInteractorStyle to reflect that it uses MRML classes directly.

Markups

  • vtkCommand::Modified events are no longer invoked when control points are added/removed/modified to improve performance. Modules that need to know If a point position is modified need to add observers to vtkMRMLMarkupsNode::PointAddedEvent, vtkMRMLMarkupsNode::PointRemovedEvent, vtkMRMLMarkupsNode::PointModifiedEvent events.
  • vtkMRMLMarkupsNode::MarkupAddedEvent is renamed to vtkMRMLMarkupsNode::PointAddedEvent
  • vtkMRMLMarkupsNode::MarkupRemovedEvent is renamed to vtkMRMLMarkupsNode::PointRemovedEvent
  • vtkMRMLMarkupsNode::NthMarkupModifiedEvent is replaced by vtkMRMLMarkupsNode::PointModifiedEvent
  • During placement of markups, a preview markup point is created. If number of already placed markup points needs to be determined then check if annulusMarkupDisplayNode.GetActiveComponentType() == slicer.vtkMRMLMarkupsDisplayNode.ComponentControlPoint and if that's the case then subtract -1 from the number of markup points to get the number of already placed points.
  • GetDefaultMarkups...() and SetDefaultMarkups...() methods are removed. Instead default display node can be accessed by GetDefaultMarkupsDisplayNode() method and default values can be get/set in that class.
  • vtkMRMLMarkupsNode::GetNthMarkupSelected() is replaced by GetNthControlPointSelected()
  • For more details, see vtkMRMLMarkupsNode

Slicer 4.11: teem python module renamed to vtkTeem, explicit import required

  • Since the module provides VTK classes interfacing with "teem", the name is now representative of the class it contains.
  • vtkTeem classes are expected to be used by explicitly importing the module.

Replace code like this:

import teem

class CalculateTensorScalars(object):
  def __init__(self):
    self.dti_math = teem.vtkDiffusionTensorMathematics()

By this:

import vtkTeem

class CalculateTensorScalars(object):
  def __init__(self):
    self.dti_math = vtkTeem.vtkDiffusionTensorMathematics()

Slicer 4.11: Display window/level (brightness/contrast) adjustment

  • A new "Window/level" mouse interaction mode was introduced. Volume display window/level can only be changed if this mode is activated by clicking the corresponding button in the toolbar. The new mouse mode prevents accidental modification of volume window/level (when for example the user accidentally clicked too far from a markup) and it also allows more sophisticated window/level adjustments.
  • New region-based auto window/level feature added: activate "Window/level" mouse mode and use Ctrl + left-click-and-drag to highlight a region and optimize window/level for that (pressing Escape or right-click cancels the operation).
  • Auto window/level reset: activate "Window/level" mouse mode and double-click the left mouse button.
  • Improved auto window/level algorithm to prevent too bright display of images. Window/level is set to display values between 0.1th and 99.9th percentile of gray levels. See details here: https://discourse.slicer.org/t/feedback-requested-how-to-improve-mouse-interaction-in-views/6420.
  • Removed class vtkImageBimodalAnalysis

Slicer 4.10: Registration of runTest function done in ScriptedLoadableModule base class

Following r27617:

  • the ScriptedLoadableModule class takes care of registering the runTest function.
  • the runTest function expects msec keyword argument.

Error message similar to:

Traceback (most recent call last):
  File "/path/to/Slicer-SuperBuild/Slicer-build/bin/Python/slicer/ScriptedLoadableModule.py", line 205, in onReloadAndTest
    test(msec=int(slicer.app.userSettings().value("Developer/SelfTestDisplayMessageDelay")), **kwargs)
TypeError: runTest() got an unexpected keyword argument 'msec'
Reload and Test: Exception!

runTest() got an unexpected keyword argument 'msec'

Replace code like this:

class sceneImport2428(ScriptedLoadableModule):
  [...]
  def __init__(self, parent):
    ScriptedLoadableModule.__init__(self, parent)
    parent.title = "..."
    [...]
    parent.acknowledgementText = "..."
    self.parent = parent 	 
	  	 
    # Add this test to the SelfTest module's list for discovery when the module 	 
    # is created.  Since this module may be discovered before SelfTests itself, 	 
    # create the list if it doesn't already exist. 	 
    try: 	 
      slicer.selfTests 	 
    except AttributeError: 	 
      slicer.selfTests = {} 	 
    slicer.selfTests['sceneImport2428'] = self.runTest 	 
 
  def runTest(self): 	 
    tester = sceneImport2428Test() 	 
    tester.runTest()

  [...]

By this:

class sceneImport2428(ScriptedLoadableModule):
  [...]
  def __init__(self, parent):
    ScriptedLoadableModule.__init__(self, parent)
    parent.title = "..."
    [...]
    parent.acknowledgementText = "..."

  [...]

Slicer 4.9: Update of VTK version from 9.0 to 8.2

Following kitware/VTK@b703d78be, VTK has updated to use version number 8.2 instead of 9.0. This was discussed in on the VTK mailing list in http://vtk.1045678.n5.nabble.com/Discussion-OK-to-change-VTK-s-version-number-from-9-0-to-8-2-tt5748702.html

At first, this VTK commit and its companion kitware/VTK@8a00b357e were both reverted from the Slicer/VTK fork. Then, since having the corresponding changes reverted in VTK was not possible, it was decided to also update Slicer. This was done in the following commits:

  • r27472: COMP: Update c++ classes to support building against VTK >= 9 and VTK >= 8.2
  • r27473: COMP: Update VTK to include version change from 9.0 to 8.2. Fixes #4623

This means that code depending on VTK must also be updated to include similar fixes.

Replace this:

 #if VTK_MAJOR_VERSION >= 9

By this:

 #if VTK_MAJOR_VERSION >= 9 || (VTK_MAJOR_VERSION >= 8 && VTK_MINOR_VERSION >= 2)

and

Replace this:

 #if VTK_MAJOR_VERSION < 9

By this:

 #if VTK_MAJOR_VERSION <= 7 || (VTK_MAJOR_VERSION <= 8 && VTK_MINOR_VERSION <= 1)


Slicer 4.9: ITK_LEGACY_REMOVE is now OFF

In preparation to switch to ITK 5.0, we disable legacy functionality in ITK. This might affect some modules which rely on ITK. Take a look at ITK 4 migration guide before ITK 5 migration guide.

Slicer 4.9: vtkMRMLPlotDataNode renamed to vtkMRMLPlotSeriesNode

Plotting was improved in this commit

Replace this:

 vtkMRMLPlotDataNode

By this:

 vtkMRMLPlotSeriesNode

Slicer 4.9: CMake: Module MIDAS not available

The test infrastructure of your project should be updated to use ExternalData built-in CMake module instead of the specific MIDAS module.

See EMSegment commit r17150 for an example of transition.

This means that instead of using midas_add_test with the MIDAS{path/to/file.ext.md5} syntax for addressing the test data, the function ExternalData_add_target is used by specifying both DATA{path/to/file.ext} and a download target name.

Replace this:

 midas_add_test(NAME test1 COMMAND ...)
 midas_add_test(NAME test2 COMMAND ...)

By this:

 ExternalData_add_test(EMSegmentData NAME test1 COMMAND ...)
 ExternalData_add_test(EMSegmentData NAME test2 COMMAND ...)
 
 [...]
 
 ExternalData_add_target(EMSegmentData)


A key difference with the former approaches is that instead of adding two tests (one named <testName>_fetchData to downoad the data and one running the test command), only one test is added but a common download target is added at the end using ExternalData_add_target function.

This means that test data can now be downloaded in parallel (and cached) at build time instead of testing time.

Slicer 4.9: CMake: Module SlicerMacroCheckExternalProjectDependency not available

Since the module was removed in r26992, consider updating your build system to use CMake module ExternalProjectDependency

Slicer 4.9: CMake: Module SlicerMacroEmptyExternalProject not available

Since the module was removed in r26991

Replace this:

include(SlicerMacroEmptyExternalProject)

[...]

SlicerMacroEmptyExternalProject("${proj}" "${${proj}_DEPENDENCIES}")

By this:

include(ExternalProjectDependency)

[...]

ExternalProject_Add_Empty(${proj} DEPENDS ${${proj}_DEPENDENCIES})

Slicer 4.9: CMake: Module SlicerBlockSetCMakeOSXVariables not available

Since it was renamed to SlicerInitializeOSXVariables in r26982

Replace this:

include(SlicerBlockSetCMakeOSXVariables)

By this:

include(SlicerInitializeOSXVariables)

Slicer 4.9: Application: isRelease() function not available

See #Slicer_4.8:_Application:_isRelease.28.29_function_not_available_or_deprecated

Slicer 4.9: slicer.util.getNode() raises exception if node not found

If slicer.util.getNode() is called and the node is not found then instead of just returning None (Slicer 4.8 behavior), the method now raises a MRMLNodeNotFoundException. This makes code debugging easier (the error is reported when it happens), and in general more consistent with Python conventions.

How to update existing code:

It is advisable to only use slicer.util.getNode in tests, or interactively in the Python console, as its behavior is somewhat unpredictable (it may either found a node by name or ID, and result of wildcard search is even less deterministic). In general, it is recommended to use the MRML scene's GetFirstNodeByName and GetNodeByID methods instead.

Replace this:

n = slicer.util.getNode(nodeNameOrID)

By one of these:

If node is to be found by name:

  n = slicer.mrmlScene.GetFirstNodeByName(nodeName)

If node is to be found by ID:

  n = slicer.mrmlScene.GetNodeByID(nodeID)

If node is to be found by name or ID (slower, less predictable, recommended for testing only):

try:
  n = slicer.util.getNode(nodeNameOrID)
except slicer.util.MRMLNodeNotFoundException:
  n = None

More information: https://github.com/Slicer/Slicer/commit/b63484af1b1b413f35396f8f7efb73e870448bd4

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 qSlicerCoreApplication::releaseType() == "Stable"

Summary:

Prior to r26420, the variable Slicer_VERSION_TWEAK 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 Slicer_RELEASE_TYPE was introduced. As of 2017-10-04, it can be set to Experimental, Nightly or Stable with Experimental being the value hard-coded in the source.

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

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

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 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:

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 vtkMRMLScalarVolumeNode 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 vtkMRMLLabelMapVolumeNode class is used for storing segmentation information (still using vtkMRMLScalarVolume 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 vtkMRMLLabelMapVolumeNode, remove call to SetLabelMap)

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:


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

Rational:

 Linking against ITKFactoryRegistration 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:

Slicer Extension updates

Slicer 5.0: ITKv4 to ITKv5

To remove support for ITKv4 and only support ITKv5. See Documentation/Nightly/Developers/Tutorials/MigrationGuide#Transition_from_ITK4_to_ITK5, it includes the following sections:

If completely removing support for ITKv4 and only supporting ITKv5 is not possible. It is possible to conditionally include the ITKv4 code.

For example:

#if ITK_VERSION_MAJOR >= 5
  itk::ITK_THREAD_RETURN_TYPE
#else
  ITK_THREAD_RETURN_TYPE
#endif

Example of commits:

Slicer 5.0: Python2 to Python3

Depending on the complexity of the extension, two approaches shall be considered:

  • code base common to Slicer 4.10 and Slicer 5.0. This means backward compatibility with the latest release is maintained.
  • specific branch for each Slicer version (e.g master-4.10 and master)


Example of commits


Step 1

Understanding the scope of changes needed to support Python 3 can be done by:

  1. installing future package (see https://python-future.org/)
    Slicer_DIR=/path/to/Slicer-SuperBuild/Slicer-build
    ${Slicer_DIR}/../python-install/bin/PythonSlicer -m pip install future
    
  2. applying all fixes
      for f in `find ./ -name "*.py"`; do \
        ${Slicer_DIR}/../python-install/bin/PythonSlicer \
          --launch futurize --nobackups --write $f; \
      done
    

    Note Alternatively the future package could be installed in a regular python environment and used from there.

      for f in `find ./ -name "*.py"`; do \
        futurize --nobackups --write $f; \
      done
    

This first step will apply the following transformations:

lib2to3.fixes.fix_apply
lib2to3.fixes.fix_dict
lib2to3.fixes.fix_except
lib2to3.fixes.fix_exec
lib2to3.fixes.fix_exitfunc
lib2to3.fixes.fix_filter
lib2to3.fixes.fix_funcattrs
lib2to3.fixes.fix_getcwdu
lib2to3.fixes.fix_has_key
lib2to3.fixes.fix_input
lib2to3.fixes.fix_intern
lib2to3.fixes.fix_isinstance
lib2to3.fixes.fix_itertools
lib2to3.fixes.fix_itertools_imports
lib2to3.fixes.fix_long
lib2to3.fixes.fix_map
lib2to3.fixes.fix_methodattrs
lib2to3.fixes.fix_ne
lib2to3.fixes.fix_next
lib2to3.fixes.fix_nonzero
lib2to3.fixes.fix_numliterals
lib2to3.fixes.fix_operator
lib2to3.fixes.fix_paren
lib2to3.fixes.fix_raw_input
lib2to3.fixes.fix_reduce
lib2to3.fixes.fix_renamesSlicer migration guide describes how to update the code. See https://www.slicer.org/wiki/Documentation/Nightly/Developers/Tutorials/MigrationGuide/SlicerExtension#Slicer_5.0:_Python2_to_Python3
lib2to3.fixes.fix_repr
lib2to3.fixes.fix_standarderror
lib2to3.fixes.fix_sys_exc
lib2to3.fixes.fix_throw
lib2to3.fixes.fix_tuple_params
lib2to3.fixes.fix_types
lib2to3.fixes.fix_xreadlines
lib2to3.fixes.fix_zip
libfuturize.fixes.fix_absolute_import
libfuturize.fixes.fix_basestring
libfuturize.fixes.fix_cmp
libfuturize.fixes.fix_division_safe
libfuturize.fixes.fix_execfile
libfuturize.fixes.fix_future_builtins
libfuturize.fixes.fix_future_standard_library
libfuturize.fixes.fix_future_standard_library_urllib
libfuturize.fixes.fix_metaclass
libfuturize.fixes.fix_next_call
libfuturize.fixes.fix_object
libfuturize.fixes.fix_print_with_import
libfuturize.fixes.fix_raise
libfuturize.fixes.fix_unicode_keep_u
libfuturize.fixes.fix_xrange_with_import
libpasteurize.fixes.fix_newstyle

expect these two:

lib2to3.fixes.fix_idioms
lib2to3.fixes.fix_ws_comma

Note If the number of changes is large, you should consider applying each fixes independently.


Step 2

Not all changes applied automatically should be integrated. Most of the changes introducing imports from the future python package can simply be removed or removed after making use of try/except or check of sys.version_info[0].

  • Systematic conversion of keys, values or items from dictionaries do not need to be systematically converted from dict_keys/dict_values/dict_items to list. For example, this Slicer r28077 reverted some of the automatic changes applied by the future CLI.
  • Unless python classes implement the object functions next and __unicode__ specific to Python 2, nothing specific should be done and from builtins import object can be removed. Automatic removal of imports can also be automated doing:
 for f in `find ./ -name "*.py"`; do \
   sed -i '/from builtins import object/ d' $f; \
 done
  • Unless there are performances issue associated with using range in Python 2, the from builtins import range can be removed:
 for f in `find ./ -name "*.py"`; do \
   sed -i '/from builtins import range/ d' $f; \
 done
  • If there are performance issue with using range in Python 2, the following could also be done:
 import sys
 if sys.version_info[0] == 2:
   range = xrange
  • Use of aliases can also be avoided by removing
 from future import standard_library
 standard_library.install_aliases()

and instead doing something like this:

 try:
   import queue
 except ImportError:
   import Queue as queue

For a complete list aliases, see https://python-future.org/reference.html#module-future.standard_library

  • Use of old_div() function can generally be avoided by using int()

Step 3

The lib2to3.fixes.fix_idioms transformation should explicitly be applied:

  for f in `find ./ -name "*.py"`; do \
    ${Slicer_DIR}/../python-install/bin/PythonSlicer \
      --launch futurize -f lib2to3.fixes.fix_idioms --nobackups --write $f; \
  done

Slicer 5.0: Python2 to Python3 (EditorEffect imports)

Import of Editor classes should be updated. For example, see r28122.


Before:

import EditorLib
from EditorLib.EditOptions import HelpButton
from EditorLib.EditOptions import EditOptions
from EditorLib import EditUtil
class TemplateKeyEffectOptions(EditorLib.LabelEffectOptions):
  [...]


After:

import EditorLib
from EditorLib import EditOptions, HelpButton
from EditorLib import EditUtil
from EditorLib import LabelEffectOptions, LabelEffectTool, LabelEffectLogic, LabelEffect
class TemplateKeyEffectOptions(LabelEffectOptions):
  [...]


Slicer 4.9: Explicit include of ExternalProject module not needed anymore

Following r26984, calling find_package(Slicer REQUIRED) and include(${Slicer_USE_FILE}) ensure the ExternalProject CMake module is included.

Note that ExternalProjectDependency CMake module is also included.

Slicer 4.9: Explicit passing of CMAKE_OSX_* variables not needed anymore

Following r26983, calling find_package(Slicer REQUIRED) and include(${Slicer_USE_FILE}) initializes CMAKE_OSX_* variables and ensures the variables CMAKE_OSX_ARCHITECTURES, CMAKE_OSX_SYSROOT and CMAKE_OSX_DEPLOYMENT_TARGET are passed to all external projects when configuring SuperBuild based extension.

Slicer 4.9: Explicit initialization of CMAKE_BUILD_TYPE not needed anymore

Following r26978, calling find_package(Slicer REQUIRED) and include(${Slicer_USE_FILE}) initializes CMAKE_BUILD_TYPE and ensures the variables CMAKE_BUILD_TYPE and CMAKE_CONFIGURATION_TYPES are passed to all external projects when configuring SuperBuild based extension.

The module SlicerInitializeBuildType is automatically included in UseSlicer CMake module.

Slicer 4.9: Subversion not required anymore

Following r27060, Subversion is not required anymore.

Slicer 4.9: Support EP_GIT_PROTOCOL and use of ExternalProject_SetIfNotDefined for setting GIT_REPOSITORY, GIT_TAG and alike

Following r26957, extension may use the following convention to define GIT_REPOSITORY and GIT_TAG, this allows developer to override the value before the first configuration by setting the corresponding environment variable, or by explicitly configuring the project with that variable.

The option EP_GIT_PROTOCOL is also already set in ExternalProjectDependency module included by Slicer and its value is updated based on the <SUPERBUILD_TOPLEVEL_PROJECT>_USE_GIT_PROTOCOL option.

  ExternalProject_SetIfNotDefined(
    ${CMAKE_PROJECT_NAME}_${proj}_GIT_REPOSITORY
    "${EP_GIT_PROTOCOL}://github.com/jcfr/shape4D.git"
    QUIET
    )

  ExternalProject_SetIfNotDefined(
    ${CMAKE_PROJECT_NAME}_${proj}_GIT_TAG
    "12fef84ca2a56feffc59d8159bdadd2ce4a4138e" # slicersalt-2018-01-22-c74c766a4c
    QUIET
    )

See:

Slicer 4.9: Use ExternalProject_AlwaysConfigure to force reconfigure of inner project

Following r26551, the function ExternalProject_AlwaysConfigure may be used to ensure the inner project is always reconfigured.

Using the `BUILD_ALWAYS` option supported by ExternalProject_Add will not have the intended effect.

See https://cmake-artichoke.readthedocs.io/en/latest/ExternalProjectDependency.html#function:ExternalProject_AlwaysConfigure

Slicer 4.9: Specifying external projects to install in SuperBuild extension

Following r27267 and r27232, the following should be used to ensure the extension can also be bundled into a Slicer custom application. When bundled, the variable ${EXTENSION_NAME}_CPACK_INSTALL_CMAKE_PROJECTS is then used to update the application's list of project to install.

#-----------------------------------------------------------------------------
set(EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS)
#list(APPEND EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS "${Foo_DIR};Foo;RuntimeLibraries;/")
set(${EXTENSION_NAME}_CPACK_INSTALL_CMAKE_PROJECTS "${EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS}" CACHE STRING "List of external projects to install" FORCE)

#-----------------------------------------------------------------------------
list(APPEND CPACK_INSTALL_CMAKE_PROJECTS "${CMAKE_BINARY_DIR};${EXTENSION_NAME};ALL;/")
list(APPEND CPACK_INSTALL_CMAKE_PROJECTS "${${EXTENSION_NAME}_CPACK_INSTALL_CMAKE_PROJECTS}")
include(${Slicer_EXTENSION_GENERATE_CONFIG})
include(${Slicer_EXTENSION_CPACK})

Slicer 4.9: Generating (Extension)Config.cmake

Initially introduced in r25944, and later improved in r25991, including ${Slicer_EXTENSION_GENERATE_CONFIG} ensure a config is generated and allow an extension to import targets from another extension by using find_package(ExtensionName REQUIRED).

[...]

include(${Slicer_EXTENSION_GENERATE_CONFIG})
include(${Slicer_EXTENSION_CPACK})

Slicer 4.9: Initializing <projectName>_BUILD_SLICER_EXTENSION option: Standalone vs Slicer extension build

The following snippet allows to automatically initialize <projectName>_BUILD_SLICER_EXTENSION to ON if Slicer_DIR is defined.

#-----------------------------------------------------------------------------
# Standalone vs Slicer extension option
#-----------------------------------------------------------------------------

# This option should be named after the project name, it corresponds to the
# option set to ON when the project is build by the Slicer Extension build
# system.

set(_default OFF)
set(_reason "${PROJECT_NAME}_BUILD_SLICER_EXTENSION is ON")
if(NOT DEFINED ${PROJECT_NAME}_BUILD_SLICER_EXTENSION AND DEFINED Slicer_DIR)
  set(_default ON)
  set(_reason "Slicer_DIR is SET")
endif()

option(${PROJECT_NAME}_BUILD_SLICER_EXTENSION "Build as a Slicer Extension" ${_default})

set(_msg "Checking if building as a Slicer extension")
message(STATUS ${_msg})
if(${PROJECT_NAME}_BUILD_SLICER_EXTENSION)
  message(STATUS "${_msg} - yes (${_reason})")
else()
  message(STATUS "${_msg} - no (${PROJECT_NAME}_BUILD_SLICER_EXTENSION is OFF)")
endif()
mark_as_superbuild(${PROJECT_NAME}_BUILD_SLICER_EXTENSION:BOOL)

Obsolete Code Removal

This section documents suggested code changes after removing support for a particular features. Each category has a short description, code snippets, a suggested upgrade path, and references to relevant commits.

Qt>=5.0.0: Remove obsolete code supporting Qt4 plugin infrastructure (C++)

These changes apply to Qt loadable modules and designer plugins

qSlicerNAMEModuleWidgetsPlugin.h

Before:

#include "vtkSlicerConfigure.h" // For Slicer_HAVE_QT5

// Qt includes
#ifdef Slicer_HAVE_QT5
#include <QtUiPlugin/QDesignerCustomWidgetCollectionInterface>
#else
#include <QDesignerCustomWidgetCollectionInterface>
#endif

[...]

class Q_SLICER_MODULE_SUBJECTHIERARCHY_WIDGETS_PLUGINS_EXPORT qSlicerSubjectHierarchyModuleWidgetsPlugin
  : public QObject
  , public QDesignerCustomWidgetCollectionInterface
{
  Q_OBJECT
#ifdef Slicer_HAVE_QT5
  Q_PLUGIN_METADATA(IID "org.qt-project.Qt.QDesignerCustomWidgetCollectionInterface")
#endif
  Q_INTERFACES(QDesignerCustomWidgetCollectionInterface);

After:

// Qt includes
#include <QtUiPlugin/QDesignerCustomWidgetCollectionInterface>

[...]

class Q_SLICER_MODULE_SUBJECTHIERARCHY_WIDGETS_PLUGINS_EXPORT qSlicerSubjectHierarchyModuleWidgetsPlugin
  : public QObject
  , public QDesignerCustomWidgetCollectionInterface
{
  Q_OBJECT
  Q_PLUGIN_METADATA(IID "org.qt-project.Qt.QDesignerCustomWidgetCollectionInterface")
  Q_INTERFACES(QDesignerCustomWidgetCollectionInterface);

qSlicerNAMEModule.h

Before:

class Q_SLICER_QTMODULES_SUBJECTHIERARCHY_EXPORT qSlicerSubjectHierarchyModule :
  public qSlicerLoadableModule
{
  Q_OBJECT
#ifdef Slicer_HAVE_QT5
  Q_PLUGIN_METADATA(IID "org.slicer.modules.loadable.qSlicerLoadableModule/1.0");
#endif

After:

class Q_SLICER_QTMODULES_SUBJECTHIERARCHY_EXPORT qSlicerSubjectHierarchyModule :
  public qSlicerLoadableModule
{
  Q_OBJECT
  Q_PLUGIN_METADATA(IID "org.slicer.modules.loadable.qSlicerLoadableModule/1.0");

qSlicerNAMEModuleWidgetsAbstractPlugin.h

Before:

  #include <QtGlobal>
  #if(QT_VERSION < QT_VERSION_CHECKS(5, 0, 0))
  #include <QDesignerCustomWidgetInterface>
  #else
  #include <QtUiPlugin/QDesignerCustomWidgetInterface>
  #endif

  [...]

  class Q_SLICER_MODULE_SEGMENTATIONS_WIDGETS_PLUGINS_EXPORT qSlicerSegmentationsModuleWidgetsAbstractPlugin
      : public QDesignerCustomWidgetInterface
  {
  #if (QT_VERSION >= QT_VERSION_CHECK(5, 0, 0))
    Q_PLUGIN_METADATA(IID "org.qt-project.Qt.QDesignerCustomWidgetInterface")
  #endif
    Q_INTERFACES(QDesignerCustomWidgetInterface);
  }

After:

  #include <QtUiPlugin/QDesignerCustomWidgetInterface>

  [...]

  class Q_SLICER_MODULE_SEGMENTATIONS_WIDGETS_PLUGINS_EXPORT qSlicerSegmentationsModuleWidgetsAbstractPlugin
      : public QDesignerCustomWidgetInterface
  {
    Q_PLUGIN_METADATA(IID "org.qt-project.Qt.QDesignerCustomWidgetInterface")
    Q_INTERFACES(QDesignerCustomWidgetInterface);
  }


qSlicerNAMEModule.cxx and qSlicerNAMEModuleWidgetsAbstractPlugin.cxx

Remove:

 #if (QT_VERSION < QT_VERSION_CHECK(5, 0, 0))
 #include <QtPlugin>
 Q_EXPORT_PLUGIN2(customwidgetplugin, qSlicerSegmentationsModuleWidgetsPlugin);
 #endif

Qt>=5.0.0: Simpler use of QHeaderView::setSectionResizeMode

This migration guide entry is obsolete: Documentation/Nightly/Developers/Tutorials/MigrationGuide#Qt5:_Fix_error:_.E2.80.98class_QHeaderView.E2.80.99_has_no_member_named_.E2.80.98setResizeMode.E2.80.99

Solution for Cpp

Before:

 #if (QT_VERSION < QT_VERSION_CHECK(5, 0, 0))
   this->SceneViewTableWidget->horizontalHeader()->setResizeMode(QHeaderView::Stretch);
   this->SceneViewTableWidget->horizontalHeader()->setResizeMode(QHeaderView::ResizeToContents);
   this->SceneViewTableWidget->horizontalHeader()->setResizeMode(SCENE_VIEW_DESCRIPTION_COLUMN, QHeaderView::Stretch);
 #else
   this->SceneViewTableWidget->horizontalHeader()->setSectionResizeMode(QHeaderView::Stretch);
   this->SceneViewTableWidget->horizontalHeader()->setSectionResizeMode(QHeaderView::ResizeToContents);
   this->SceneViewTableWidget->horizontalHeader()->setSectionResizeMode(SCENE_VIEW_DESCRIPTION_COLUMN, QHeaderView::Stretch);
 #endif

After:

 this->SceneViewTableWidget->horizontalHeader()->setSectionResizeMode(QHeaderView::Stretch);
 this->SceneViewTableWidget->horizontalHeader()->setSectionResizeMode(QHeaderView::ResizeToContents);
 this->SceneViewTableWidget->horizontalHeader()->setSectionResizeMode(SCENE_VIEW_DESCRIPTION_COLUMN, QHeaderView::Stretch);


Solution for Python

Before:

  def _setSectionResizeMode(header, *args, **kwargs):
    if version.parse(qt.Qt.qVersion()) < version.parse("5.0.0"):
      header.setResizeMode(*args, **kwargs)
    else:
      header.setSectionResizeMode(*args, **kwargs)

    [...]
   
  _setSectionResizeMode(self.horizontalHeader(), 0, qt.QHeaderView.Stretch)

After:

 self.horizontalHeader().setSectionResizeMode(0, qt.QHeaderView.Stretch)

C++11: Update source code to use nullptr

C++11 introduced the keyword nullptr allowing to explicitly identify a pointer of type std::nullptr_t. It avoids ambiguous function overloads. See also https://stackoverflow.com/questions/20509734/null-vs-nullptr-why-was-it-replaced

Prior to supporting only C++11, 0 and NULL integral type were used to check for pointer value, and macro like Q_NULLPTR and ITK_NULLPTR macros were used to ensure usage of nullptr when C++11 support was enabled.

Updating the code base to use nullptr is done applying these methods:

  • clang-tidy for updating source code being explicitly compiled in the project.
  • regular expression for replacing occurrences of NULL in source code not being compiled (e.g conditionally compiled code, templated headers, comments)
  • replacement of occurences of VTK_NULLPTR, ITK_NULLPTR, Q_NULLPTR with nullptr

Using clang-tidy

This will iteratively check files for updates. It takes a while. The sources are only modified at the end of the process, so you could cancel anytime before with no consequences.

  1. Compile Slicer with the CMake option -DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=ON to generate the file compile_commands.json at configuration time.
  2. Run clang-tidy on the generated compile_commands.json (in the build folder: Slicer-build)
 run-clang-tidy.py -header-filter='.*' -checks='-*,modernize-use-nullptr' -fix

clang-tidy is a tool from clang. In Archlinux: sudo pacman -S clang, in other distros might be clang-extra-tools or similar.

clang-tidy will substitute NULL and 0 for nullptr when appropriate. It is an iterative process, so it may take time. Also, it replaces all the compiled code, including external dependencies. It is recommended to do a fresh build with the modified code, for testing it without modifications in any external repo.

Using regex for replacing NULL in comments and not-compiled code

After clang-tidy has modified the compiled code with the help of compile_commands.json, there will still be ignored instances of NULL and 0 in some headers, and comments.

Manually replace with the following regex to change those.

1) Change NULL to nullptr except when there is a quote or an underscore in front of it. And there is not a quote after.

 ack --type-add=cpp:ext:hxx,hpp,txx,tpp,cxx,cpp,c,cc --cpp "NULL" -l --print0 | xargs -0 -n 1 sed -i 's/\([^\"\_]\)NULL\([^\"\_]\)/\1nullptr\2/g'

2) The same than before but match end of line NULL

 ack --type-add=cpp:ext:hxx,hpp,txx,tpp,cxx,cpp,c,cc --cpp "NULL" -l --print0 | xargs -0 -n 1 sed -i 's/\([^\"\_]\)NULL$/\1nullptr/g'


Replace ITK_NULLPTR, VTK_NULLPTR, Q_NULLPTR


It was adapted from the ITK script in ReplaceITK_NULLPTRMacroNames.sh

  • ITK_NULLPTR:
git grep -l "ITK_NULLPTR" | fgrep -v CMakeLists.txt |fgrep -v .cmake | xargs sed -i '' -e "s/ITK_NULLPTR/nullptr/g"
  • VTK_NULLPTR:
git grep -l "VTK_NULLPTR" | fgrep -v CMakeLists.txt |fgrep -v .cmake | xargs sed -i '' -e "s/VTK_NULLPTR/nullptr/g"
  • Q_NULLPTR:
git grep -l "Q_NULLPTR" | fgrep -v CMakeLists.txt |fgrep -v .cmake | xargs sed -i '' -e "s/Q_NULLPTR/nullptr/g"

C++11: Update source code to use override

From: https://clang.llvm.org/extra/clang-tidy/checks/modernize-use-override.html

Adds override (introduced in C++11) to overridden virtual functions and removes virtual from those functions as it is not required.

virtual on non base class implementations was used to help indicate to the user that a function was virtual. C++ compilers did not use the presence of this to signify an overriden function.

In C++ 11 override and final keywords were introduced to allow overridden functions to be marked appropriately. Their presence allows compilers to verify that an overridden function correctly overrides a base class implementation.

This can be useful as compilers can generate a compile time error when:

  1. The base class implementation function signature changes.
  2. The user has not created the override with the correct signature.

First we replace ITK_OVERRIDE and VTK_OVERRIDE for override:

Replace ITK_OVERRIDE and VTK_OVERRIDE

For an example of commit message, see r28022

The regexp involving ITK was extracted from the ReplaceITK_OVERRIDEMacroNames.sh script in ITK.

  • ITK_OVERRIDE
git grep -l "ITK_OVERRIDE" | fgrep -v CMakeLists.txt |fgrep -v .cmake | xargs sed -i '' -e "s/ITK_OVERRIDE/override/g"
  • VTK_OVERRIDE
git grep -l "VTK_OVERRIDE" | fgrep -v CMakeLists.txt |fgrep -v .cmake | xargs sed -i '' -e "s/VTK_OVERRIDE/override/g"

Automatic update: Using clang-tidy

Note: Running clang-tidy -fix in parallel might cause problems, like appending multiple keywords to same function (override). It can be fixed with a grep to remove duplicates.

This will iteratively check files for updates. It takes a while. The sources are only modified at the end of the process, so you could cancel anytime before with no consequences.

Compile Slicer with the CMake option -DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=ON to generate the file compile_commands.json at configuration time. Run clang-tidy on the generated compile_commands.json (in the build folder: Slicer-build)

 run-clang-tidy.py -checks=-*,modernize-use-override  -header-filter=.* -fix

Manual fix

Multiple override are added to the same method. For example:

 void PrintSelf(ostream& os, vtkIndent indent) override override override;

We clean them with (15 here is just a high enough number):

 for n in `seq 1 15`;
 do
     ack "override override" -l --print0 | xargs -0 -n 1 sed -i \
     's/override override/override/g'
 done

When all of them are fixed, you should see in the terminal:

 sed: no input files

C++11: Update source code to use = delete

Instead of:

 vtkImageRectangularSource(const vtkImageRectangularSource&);  /// Not implemented.
 void operator=(const vtkImageRectangularSource&);  /// Not implemented.

Replace for:

 vtkImageRectangularSource(const vtkImageRectangularSource&) = delete;
 void operator=(const vtkImageRectangularSource&) = delete;

Same approach than before, use the compile_commands.json and clang-tidy in Slicer-build.

 run-clang-tidy.py -checks=-*,modernize-use-equals-delete -header-filter=.* -fix

Because we run it in parallel, multiple occurrences of = delete might have been added. Fix them with:

for n in `seq 1 15`;
do
  ack "= delete = delete" -l --print0 | xargs -0 -n 1 sed -i \
  's/= delete = delete/= delete/g'
done

And also delete comment /// Not implemented, as now it is clear with = delete.

 ack "delete" -l --print0 | xargs -0 -n 1 sed -E -i 's@delete;\s*\/*\s*[nN]ot [iI]mplemented\.?@delete;@g'
 ack "delete" -l --print0 | xargs -0 -n 1 sed -E -i 's@delete;\s*\/*\s*purposely [nN]ot [iI]mplemented\.?@delete;@g'
 ack "delete" -l --print0 | xargs -0 -n 1 sed -E -i 's@delete ITK\_DELETED\_FUNCTION;@delete;@g'

Next step in this area would be to move these declarations to the public interface (currently they are private).


C++11: Update source code to use = default

Instead of:

 virtual ~DataRequest(){}

Replace for:

 virtual ~DataRequest()= default;

Same approach than before, use the compile_commands.json and clang-tidy in Slicer-build.

 run-clang-tidy.py -checks=-*,modernize-use-equals-default -header-filter=.* -fix

Because we run it in parallel, multiple colons ;; might have been added. Fix them with:

for n in `seq 1 15`;
do
  ack "default" -l --print0 | xargs -0 -n 1 sed -i 's/= default;;/= default;/g' 
done

Add an empty space before = default if there is none:

 ack "default" -l --print0 | xargs -0 -n 1 sed -E -i 's/([^\s])= default;/\1 = default;/g'

Transition from ITK4 to ITK5

This section lists categories of code changes necessary to build Slicer with ITK 5. Each category has a short description, an example error message, a suggested upgrade path, and references to relevant commits.

Referencing this list might be helpful if Slicer extensions requiring updates to be compatible with ITK 5.

Make also sure to read through the ITK 5 migration guide.

Utilities/ITKv5Preparation directory contains bash scripts which have been used to update ITK to version 5. These scripts can assist with updating external code bases to ITK 5 content and style.

Upgrading to ITKv5 or keep using ITKv4 GenerateThreadedData

If the ThreadedGenerateData does not use threadId, change the name of the function to DynamicThreadedGenerateData Replace:

  void ThreadedGenerateData( const OutputRegionType& threadRegion, ThreadIdType threadId )

with:

  void DynamicThreadedGenerateData( const OutputRegionType& threadRegion )

If you want to keep using the ITKv4 thread system (with ThreadedGenerateData), add to the constructor of your ITK class:

  this->DynamicMultiThreadingOff();

itkMultiThreader refactor

Replace lines like:

  #include <itkMultiThreader.h>

  itk::MultiThreader::Pointer ProcessingThreader;

  ITK_THREAD_RETURN_TYPE

  ITK_THREAD_RETURN_VALUE

  SetNumberOfThreads()

with:

  #include <itkPlatformMultiThreader.h>

  itk::PlatformMultiThreader::Pointer ProcessingThreader;

  itk::ITK_THREAD_RETURN_TYPE

  itk::ITK_THREAD_RETURN_DEFAULT_VALUE

  SetNumberOfWorkUnits()

SimpleFastMutexLock, FastMutexLock and MutexLock are deprecated

Instead use std::mutex available in C++11

Replace:

  #include "itkSimpleFastMutexLock.h"
  #include "itkFastMutexLock.h"
  #include "itkMutexLock.h"

  SimpleFastMutexLock
  FastMutexLock
  MutexLock

  m_Lock->Lock();
  m_Lock->Unlock();

with:

  #include <mutex>

  std::mutex

  m_Lock.lock();
  m_Lock.unlock();

Transition from VTK7-Qt4 to VTK8-Qt5

This section lists categories of code changes necessary to build and run Slicer with VTK 8.0 and Qt5. Each category has a short description, a suggested upgrade path, and references to relevant commits (TBD once merged).

Slicer SuperBuild Extension: Enable C++11 in external projects

SuperBuild extensions may have to enable C++11 for their external projects. Add the following lines to CMAKE_CACHE_ARGS in ExternalProject_Add

   -DCMAKE_CXX_STANDARD:STRING=${CMAKE_CXX_STANDARD}
   -DCMAKE_CXX_STANDARD_REQUIRED:BOOL=${CMAKE_CXX_STANDARD_REQUIRED}
   -DCMAKE_CXX_EXTENSIONS:BOOL=${CMAKE_CXX_EXTENSIONS}

Suggested commit message:

COMP: Enable C++11 in external projects

See https://www.slicer.org/wiki/Documentation/Nightly/Developers/Tutorials/MigrationGuide/VTK7-Qt4-to-VTK8-Qt5#Slicer_SuperBuild_Extension:_Enable_C.2B.2B11_in_external_projects

Error message similar to:

/path/to/Slicer-build/ITKv4-build/Modules/Core/Common/itkConfigure.h:59:6: warning: #warning "WARNING:  The current project is configured to use a C++ standard version older than the C++ standard used for this build of ITK" [-Wcpp]
     #warning "WARNING:  The current project is configured to use a C++ standard version older than the C++ standard used for this build of ITK"
      ^

Qt5: Update loadable modules to use new plugin macros

In Qt5, the Q_EXPORT_PLUGIN, Q_EXPORT_PLUGIN2 macros have been deprecated in favor of the new Q_PLUGIN_METADATA macro.

Error message similar to:

error: static assertion failed: Old plugin system used

Suggested commit message:

COMP: Qt5: Fix error: static assertion failed: Old plugin system used

See https://www.slicer.org/wiki/Documentation/Nightly/Developers/Tutorials/MigrationGuide/VTK7-Qt4-to-VTK8-Qt5#Qt5:_Update_loadable_modules_to_use_new_plugin_macros

Solution (part 1):

In qSlicer<NameOfModule>Module.h, replace lines like:

  Q_OBJECT
  Q_INTERFACES(qSlicerLoadableModule);

with:

  Q_OBJECT
#ifdef Slicer_HAVE_QT5
  Q_PLUGIN_METADATA(IID "org.slicer.modules.loadable.qSlicerLoadableModule/1.0");
#endif
  Q_INTERFACES(qSlicerLoadableModule);

Solution (part 2):


In qSlicer<NameOfModule>Module.cxx, Replace lines like:

Q_EXPORT_PLUGIN2(qSlicer<NameOfModule>Module, qSlicer<NameOfModule>Module);

with:

#if (QT_VERSION < QT_VERSION_CHECK(5, 0, 0))
#include <QtPlugin>
Q_EXPORT_PLUGIN2(qSlicer<NameOfModule>Module, qSlicer<NameOfModule>Module);
#endif

References:

Qt5: Update DesignerPlugin to use QtUiPlugin/QDesignerCustomWidgetInterface

In Qt5, the QtDesigner/QDesignerCustomWidgetInterface header have been deprecated in favor of the new QtUiPlugin/QDesignerCustomWidgetInterface header.

Error message similar to:

/path/to/include/QtDesigner/QDesignerCustomWidgetInterface:4:4: warning: #warning Header <QtDesigner/QDesignerCustomWidgetInterface> is deprecated. Please include <QtUiPlugin/QDesignerCustomWidgetInterface> instead. [-Wcpp]
 #  warning Header <QtDesigner/QDesignerCustomWidgetInterface> is deprecated. Please include <QtUiPlugin/QDesignerCustomWidgetInterface> instead.
    ^

Suggested commit message:

COMP: Update designer plugin to support Qt5

See https://www.slicer.org/wiki/Documentation/Nightly/Developers/Tutorials/MigrationGuide/VTK7-Qt4-to-VTK8-Qt5#Qt5:_Update_DesignerPlugin_to_use_QtUiPlugin.2FQDesignerCustomWidgetInterface

Solution (part 1):

In Widgets/DesignerPlugins/qSlicer<NameOfModule>ModuleWidgetsAbstractPlugin.h, replace lines like:

#include <QDesignerCustomWidgetInterface>

with:

#include <QtGlobal>
#if (QT_VERSION < QT_VERSION_CHECK(5, 0, 0))
#include <QDesignerCustomWidgetInterface>
#else
#include <QtUiPlugin/QDesignerCustomWidgetInterface>
#endif

Solution (part 2):

In Widgets/DesignerPlugins/qSlicer<NameOfModule>ModuleWidgetsAbstractPlugin.h, replace lines like:

Q_INTERFACES(QDesignerCustomWidgetInterface);

with:

#if (QT_VERSION >= QT_VERSION_CHECK(5, 0, 0))
  Q_PLUGIN_METADATA(IID "org.qt-project.Qt.QDesignerCustomWidgetInterface")
#endif
  Q_INTERFACES(QDesignerCustomWidgetInterface);

Qt5: Update DesignerPlugin to use QtUiPlugin/QDesignerCustomWidgetCollectionInterface

Error message similar to:

/path/to/5.9.1/gcc_64/include/QtDesigner/QDesignerCustomWidgetCollectionInterface:4:4: warning: #warning Header <QtDesigner/QDesignerCustomWidgetCollectionInterface> is deprecated. Please include <QtUiPlugin/QDesignerCustomWidgetCollectionInterface> instead. [-Wcpp]
 #  warning Header <QtDesigner/QDesignerCustomWidgetCollectionInterface> is deprecated. Please include <QtUiPlugin/QDesignerCustomWidgetCollectionInterface> instead.
    ^

Solution (part 1):

In Widgets/DesignerPlugins/qSlicer<NameOfModule>ModuleWidgetsPlugin.h, replace lines like:

#include <QDesignerCustomWidgetCollectionInterface>

with:

#include "vtkSlicerConfigure.h" // For Slicer_HAVE_QT5

 // Qt includes
#ifdef Slicer_HAVE_QT5
#include <QtUiPlugin/QDesignerCustomWidgetCollectionInterface>
#else
#include <QDesignerCustomWidgetCollectionInterface>
#endif

Solution (part 2):

In Widgets/DesignerPlugins/qSlicer<NameOfModule>ModuleWidgetsPlugin.h, replace lines like:

Q_INTERFACES(QDesignerCustomWidgetCollectionInterface);

with:

#if (QT_VERSION >= QT_VERSION_CHECK(5, 0, 0))
  Q_PLUGIN_METADATA(IID "org.qt-project.Qt.QDesignerCustomWidgetInterface")
#endif
   Q_INTERFACES(QDesignerCustomWidgetCollectionInterface);

Qt5: any use of QWebKit needs to switch to QWebEngine

TBD

Qt5: QVTKOpenGLWidget

When using Qt5, QVTKOpenGLWidget should be used in place of QVTKGLWidget.

To ensure that QVTKOpenGLWidget receives a properly configured OpenGL context it's necessary to call QSurfaceFormat::setDefaultFormat() before constructing the QApplication instance. QVTKOpenGLWidget::defaultFormat() supplies a suitable format, although it's recommended to disable multisampling for full compatibility with advanced rendering techniques. See http://doc.qt.io/qt-5/qopenglwidget.html.


Error message similar to:

 error: no matching function for call to ‘QVTKWidget::QVTKWidget(QWidget*&)’
        scalarsToColorsView = new QVTKWidget(ctkVTKDiscretizableColorTransferWidget);
                                                                                   ^

Solution (part 1):

In NameOfClass.h file, replace lines like:

 #include <QVTKWidget.h>

with:

 #if CTK_USE_QVTKOPENGLWIDGET
 #include <QVTKOpenGLWidget.h>
 #else
 #include <QVTKWidget.h>
 #endif


Solution (part 2):

In NameOfClass.h file, replace lines like:

 QVTKWidget* View;

with:

 #if CTK_USE_QVTKOPENGLWIDGET
   QVTKOpenGLWidget* View;
 #else
   QVTKWidget* View;
 #endif


Solution (part 3):

In NameOfClass.cpp file, replace lines like:

 this->View = new QVTKWidget;

with:

 #if CTK_USE_QVTKOPENGLWIDGET
   this->View = new QVTKOpenGLWidget;
 #else
   this->View = new QVTKWidget;
 #endif

Qt5: Fix error: 'class QString' has no member named 'toAscii'

Replace call to toAscii().data() with toLatin1().data()

References:

Qt5: Fix error: ‘class QHeaderView’ has no member named ‘setResizeMode’

Error message similar to:

 error: ‘class QHeaderView’ has no member named ‘setResizeMode’
    headerView->setResizeMode(FileColumn, QHeaderView::Stretch);

Solution:

Replace lines like:

 headerView->setResizeMode(FileColumn, QHeaderView::Stretch);

with:

 #if (QT_VERSION < QT_VERSION_CHECK(5, 0, 0))
   headerView->setResizeMode(FileColumn, QHeaderView::Stretch);
 #else
   headerView->setSectionResizeMode(FileColumn, QHeaderView::Stretch);
 #endif

Solution for Python:

 from packaging import version
 ...
 def _setSectionResizeMode(header, *args, **kwargs):
   """ To be compatible with Qt4 and Qt5 """
   if version.parse(qt.Qt.qVersion()) < version.parse("5.0.0"):
     header.setResizeMode(*args, **kwargs)
   else:
     header.setSectionResizeMode(*args, **kwargs)
 ...
 _setSectionResizeMode(horizontalHeader, 1, qt.QHeaderView.ResizeToContents)

VTK8: Use hierarchy files for VTK Python wrapping

In VTK8 it's necessary to generate hierarchy files for proper wrapping VTK classes in Python. Without the information provided by the hierarchy files, the Python wrapping tool lacks complete information about classes and types. In this case, the generated classes contain methods that shouldn't be wrapped and fail to compile, and include references to types such as vtkTypeBool. Once the hierarchy files are generated and provided to the Python wrapping tool, the generated classes compile and typedefs like vtkTypeBool are correctly resolved.

Once the VTK8 changes are merged, generating hierarchy files is handled by https://github.com/Slicer/Slicer/blob/master/CMake/vtkMacroKitPythonWrap.cmake.

References:

VTK8: Use of vtkTypeMacro requires to use the correct base class

Error message similar to:

error: expected unqualified-id before 'protected'

This error is usually a symptom of an incorrect base class when using vtkTypeMacro.

Solution:

Assuming the class vtkIGTLToMRMLPoint derives from vtkIGTLToMRMLBase,

Replace lines like:

vtkTypeMacro(vtkIGTLToMRMLPoint,vtkObject);

with:

vtkTypeMacro(vtkIGTLToMRMLPoint,vtkIGTLToMRMLBase);

References:

VTK8: Copy constructor and equal operator should be disabled

Error message similar to:

error: use of deleted function 'vtkMyClass::vtkMyClass(const vtkMyClass&)'

This error is usually a symptom of not disabling the copy constructor and equal operator.

Solution:

Replace lines like:

protected:
  vtkMyClass();
  ~vtkMyClass();

with:

protected:
  vtkMyClass();
  ~vtkMyClass();
  vtkMyClass(const vtkMyClass&);
  void operator=(const vtkMyClass&);

VTK8: Call InitializeObjectBase() in vtkObject New() methods

In VTK8 it's necessary for vtkObject New() methods to call InitializeObjectBase() on the new object for proper tracking with vtkDebugLeaks. The standard macros (vtkStandardNewMacro, vtkObjectFactoryNewMacro) handle this. For those classes that don't use the macros, add a call to InitializeObjectBase() immediately after constructing the object by new vtkXXX().

Additionally, vtkObjectFactory::CreateInstance() now doesn't register the class name with vtkDebugLeaks if the factory fails to create the object. Therefore, it's no longer necessary to unregister the class name with vtkDebugLeaks. Remove calls to vtkDebugLeaks::DestructClass(className) following vtkObjectFactory::CreateInstance().

To support both VTK8 and earlier versions of VTK, wrap these changes in preprocessor checks for whether VTK_HAS_INITIALIZE_OBJECT_BASE is defined.

References:

VTK8: Add C++11 keywords

VTK8 requires C++11. Subclasses of VTK classes must mark overridden methods with VTK_OVERRIDE.

VTK8: vtkWindowToImageFilter::SetMagnification() is deprecated

VTK8.1 deprecated vtkWindowToImageFilter::SetMagnification() and vtkWindowToImageFilter::GetMagnification(). Replace calls to those methods with SetScale() and GetScale(). See https://github.com/Kitware/VTK/commit/af0a95fa7dd4e25ef869a0bc6077e547f18baa29.

VTK8: vtkInstantiator is deprecated

VTK8.1 deprecated vtkInstantiator. See https://github.com/Kitware/VTK/commit/11bb6a4d395e877847355a63de2e2e8f8d9e1d91

Error message similar to:

/path/to/SlicerIGT-Release/ToolWatchdog/MRMLDM/WatchdogInstantiator.cxx:10:1: error: expected constructor, destructor, or type conversion before ‘void’
 void WatchdogInstantiator::ClassInitialize()
 ^
/path/to/SlicerIGT-Release/ToolWatchdog/MRMLDM/WatchdogInstantiator.cxx: In static member function ‘static void WatchdogInstantiator::ClassFinalize()’:
/path/to/SlicerIGT-Release/ToolWatchdog/MRMLDM/WatchdogInstantiator.cxx:21:3: error: ‘vtkInstantiator’ has not been declared
	 vtkInstantiator::UnRegisterInstantiator("vtkMRMLWatchdogDisplayableManager", vtkInstantiatorvtkMRMLWatchdogDisplayableManagerNew);
	 ^
/path/to/SlicerIGT-Release/ToolWatchdog/MRMLDM/WatchdogInstantiator.cxx:21:80: error: ‘vtkInstantiatorvtkMRMLWatchdogDisplayableManagerNew’ was not declared in this scope
	 vtkInstantiator::UnRegisterInstantiator("vtkMRMLWatchdogDisplayableManager", vtkInstantiatorvtkMRMLWatchdogDisplayableManagerNew);
	                                                                              ^

Solution (part 1):

Update associated CMakeLists.txt replacing lines like:

set(VTK_USE_INSTANTIATOR_NEW 1)
if(${VTK_VERSION_MAJOR} GREATER 5)
  include(${VTK_CMAKE_DIR}/vtkMakeInstantiator.cmake)
endif()
VTK_MAKE_INSTANTIATOR3("${MODULE_NAME}Instantiator"
  displayable_manager_instantiator_SRCS
  "${displayable_manager_SRCS}"
  "${${KIT}_EXPORT_DIRECTIVE}"
  ${CMAKE_CURRENT_BINARY_DIR}
  "${KIT}Export.h"
  )

with:

SlicerConfigureDisplayableManagerObjectFactory(
  TARGET_NAME ${KIT}
  SRCS "${displayable_manager_SRCS}"
  EXPORT_MACRO "${${KIT}_EXPORT_DIRECTIVE}"
  EXPORT_HEADER "${KIT}Export.h"
  OUTPUT_SRCS_VAR displayable_manager_instantiator_SRCS
  )

Solution (part 2):

Update associated qSlicer<NameOfModule>Module.h (or any test requiring displayable manager) adding lines like:

 // DisplayableManager initialization
 #include <vtkAutoInit.h>
 VTK_MODULE_INIT(vtkSlicer<NameOfModule>ModuleMRMLDisplayableManager)


Solution (part 2 - maintaining backward compatibility with Slicer 4.8):

 #include <vtkSlicerVersionConfigure.h> // For Slicer_VERSION_MAJOR, Slicer_VERSION_MINOR
 
 
 [...]
 
 // DisplayableManager initialization
 #if Slicer_VERSION_MAJOR == 4 && Slicer_VERSION_MINOR >= 9
 #include <vtkAutoInit.h>
 VTK_MODULE_INIT(vtkSlicer<NameOfModule>ModuleMRMLDisplayableManager)
 #endif

For example, see https://github.com/SlicerIGT/SlicerIGT/pull/155/commits/2f866ea8872435b9a3a7382dd0549231da00406f

VTK 8.2: Signature of vtkFSLookupTable::MapValue updated

The signature of the function was updated in Kitware/VTK@43f6ee3

Error message similar to:

 error: invalid conversion from ‘const unsigned char*’ to ‘unsigned char*’ [-fpermissive]
 overriding virtual function return type differs and is not covariant from 'vtkLookupTable::MapValue'

Solution:

Update code to use `const` keyword. For example, see r26708

Slicer scripted module initialization steps after application startup

In Slicer 4.8 and earlier versions, those module initialization steps that required application startup completed, often were called using a singleshot timer, because timer events were only processed after the application startup was completed. In Slicer 4.9, some event processing is performed before the application startup is completed, therefore instead of relying on a timer, the application's startupCompleted() signal must be used.

Replace line like:

   qt.QTimer.singleShot(0, self.myAdditionalInitializationSteps)

with:

   slicer.app.connect("startupCompleted()", self.myAdditionalInitializationSteps)

Transition from VTK6 to VTK7

This section lists categories of code changes necessary to build Slicer with VTK 7.1. Each category has a short description, an example error message, a suggested upgrade path, and references to relevant commits.

Referencing this list might be helpful if Slicer extensions require updates to be compatible with VTK 7.1.

Deprecated the vtkStreamer class hierarchy

VTK has deprecated the vtkStreamer class hierarchy.

Error message similar to:

'VTK_INTEGRATE_FORWARD' : undeclared identifier

Solution:

Replace lines like:

#include "vtkStreamer.h"

with:

#include "vtkHyperStreamline.h"

References:

Deprecated vtkMatrix4x4::operator[] method

VTK has deprecated the vtkMatrix4x4::operator[] method.

Error message similar to:

binary '[' : 'vtkMatrix4x4' does not define this operator or a conversion to a type acceptable to the predefined operator

Solution:

Replace lines like:

(*mat)[i][j] = val;
val = (*mat)[i][j];

with:

mat->SetElement(i, j, val);
val = mat->GetElement(i, j);

References:

Removed vtksys/ios, vtksys/stl compatibility layers

VTK has removed the vtksys/ios and vtksys/stl compatibility layers.

Error message similar to:

Cannot open include file: 'vtksys/ios/iostream': No such file or directory

Solution:

Replace lines like:

#include <vtksys/ios/iostream>
#include <vtksys/ios/sstream>

vtksys_ios::ofstream ofs;

with:

#include <iostream>
#include <sstream>

std::ofstream ofs;

Replace lines like:

#include <vtksys/stl/string>
#include <vtksys/stl/vector>

vtksys_stl::string str;
vtksys_stl::vector<double> vec;

with:

#include <string>
#include <vector>

std::string str;
std::vector<double> vec;

References:

vtkDataArray refactored

VTK has refactored the vtkDataArray class hierarchy.

Error message similar to:

'class XXX’ has no member named ‘SetTupleValue’

Solution:

Replace lines like:

array->GetTupleValue(0, val);
array->SetTupleValue(0, val);
array->InsertTupleValue(i, val);
array->InsertNextTupleValue(val);

with:

array->GetTypedTuple(0, val);
array->SetTypedTuple(0, val);
array->InsertTypedTuple(i, val);
array->InsertNextTypedTuple(val);

Replace lines like:

#include <vtkDataArrayTemplate.h>

<any reference to "vtkDataArrayTemplate">

with:

#include <vtkAOSDataArrayTemplate.h>

<reference to "vtkAOSDataArrayTemplate">

References:

Deprecated pipeline update methods

VTK has deprecated and replaced certain pipeline update methods.

Error message similar to:

'class XXX’ has no member named ‘SetUpdateExtent’

Solution:

Follow suggestions in VTK changelog: https://github.com/Kitware/VTK/blob/master/Documentation/Doxygen/ChangesVTK-7-1.md#pipeline-update-methods

References:

Updated Python wrapping

VTK has updated its Python wrapping to support Python 3 and to wrap more code by default.

Symptoms:

Compile or link error while building a Python-wrapped class or library.

Solution 1:

In CMakeLists.txt, add the WRAP_EXCLUDE_PYTHON property anywhere that the WRAP_EXCLUDE property is defined on source files.

Solution 2:

Replace lines of code like:

//BTX
...
//ETX

with:

#ifndef __VTK_WRAP__
...
#endif // __VTK_WRAP__

References:

vtkMTimeType

VTK introduced a specific type—vtkMTimeType—to be used for vtkObject modified time (MTime).

Error message similar to:

vtkDiffusionTensorGlyph::GetMTime': overriding virtual function return type differs and is not covariant from 'vtkObject::GetMTime'

Solution:

Update code that uses unsigned long or unsigned long int for modified times to use vtkMTimeType.

References:

vtkStandardNewMacro expects vtkObjectFactory.h

Error message similar to:

 expected constructor, destructor, or type conversion before ‘;’ token
   vtkStandardNewMacro(vtkSlicerModelClipLogic);

Solution:

Add:

 #include <vtkObjectFactory.h>

Transition from VTK5 to VTK6

This section documents required change to make Slicer code work with VTK6.


Use SetInputPolyDataConnection and GetPolyDataConnection

Starting with Slicer r24801, support for VTK5 API was removed and VTK6 API should be used.

Error message similar to:

error: ‘class vtkMRMLModelDisplayNode’ has no member named ‘SetInputPolyData’
 resultDisplay->SetInputPolyData(resultModel->GetPolyData());
                ^

Solution:

Replace occurrences of SetInputPolyData/GetPolyData with SetInputPolyDataConnection/GetPolyDataConnection.

Use AllocateScalars

Starting with Slicer r24801, support for VTK5 API was removed and VTK6 API should be used.

Error message similar to:

  error: no matching function for call to ‘vtkImageData::SetNumberOfScalarComponents(int)’
    mp_phi->SetNumberOfScalarComponents(1);
                                         ^

Solution:

Replace lines like:

 imageData->SetScalarTypeToUnsignedShort();		
 imageData->SetNumberOfScalarComponents(1); // image holds one value intensities		
 imageData->AllocateScalars(); // allocate storage for image data

with:

 imageData->AllocateScalars(VTK_UNSIGNED_SHORT, 1); // allocate storage for image data