Advanced Topics

Memory Management

Pointers to VTK object

If you are not familiar with VTK’s memory management read this general introduction and this page describing usage of smart pointers. See Slicer-specific use cases and recommendations below.

Calling the plain New() method of VTK objects and storing the returned pointer in a plain pointer should be avoided, as this very often causes memory leaks.

Bad, should be avoided:

vtkMRMLScalarVolumeNode* vol = vtkMRMLScalarVolumeNode::New();
// ... do something, such as vol->GetImageData(), someObject->SetVolume(vol)...
vol->Delete();
vol=NULL;

Recommended:

vtkNew<MRMLScalarVolumeNode> vol;
//... do something, such as vol->GetImageData(), someObject->SetVolume(vol.GetPointer())...

Also good:

vtkSmartPointer<MRMLScalarVolumeNode> vol=vtkSmartPointer<MRMLScalarVolumeNode>::New();
///... do something, such as vol->GetImageData(), someObject->SetVolume(vol)...

vtkNew is preferred in general for new object creation, as it has a simpler syntax and used almost exclusively in the Slicer core source code. A slight inconvenience is that when we need use the GetPointer() method to get the actual pointer value.

A vtkSmartPointer pointer can be created without actually creating an object, so vtkSmartPointer should be used when:

  • we don’t know the exact object type that we want to create at the time of the pointer creation (e.g., we create a vtkSmartPointer<vtkMRMLVolumeNode> and later set it to point to a vtkMRMLScalarVolumeNode or vtkMRMLVectorVolumeNode), or

  • we need to take the ownership of an already created object (using vtkSmartPointer::Take(...); see examples below)

Factory methods

Similarly to VTK, Slicer contains some “factory” methods:

  • vtkMRMLScene::CreateNodeByClass()

  • vtkMRMLScene::GetNodesByClass()

  • …

Factory methods return a pointer to a VTK object (with a reference count of 1) that the caller “owns”, so the caller must take care of releasing the object to avoid memory leak.

In C++, it is recommended to make a smart pointer take the ownership of the returned raw pointer. For example:

// GetNodesByClass is a factory method, therefore a smart pointer is used to take the ownership of the returned object
vtkSmartPointer<vtkCollection> nodes = vtkSmartPointer<vtkCollection>::Take(scene->GetNodesByClass("vtkMRMLModelNode"));

In Python, the returned Python object maintains a reference to the underlying VTK object, therefore an extra reference is no longer needed and it is recommended to be immediately removed using the UnRegister method:

nodes = scene.GetNodesByClass("vtkMRMLModelNode")
nodes.UnRegister(None) # GetNodesByClass method is NOT marked with VTK_NEWINSTANCE, manual unregistration is needed

Here are the different naming conventions for such “factory” methods:

  • GetXXX: Return an existing object, reference count is not changed, the caller is not responsible for the object.

  • NewXXX: Solely instantiate an object (typically a factory method). The caller is responsible to decrement the reference count.

  • CreateXXX: Instantiate and configure an object. The caller is responsible to decrement the reference count. If XXX is a MRML node, it is NOT added into the scene.

  • CreateAndAddXXX: Instantiate, configure and add into the scene a MRML node. The caller is not responsible to decrement the reference count.

VTK_NEWINSTANCE wrapper hint

If a factory method is marked with the VTK_NEWINSTANCE hint then the ownership is transferred to Python where garbage collection takes care of deleting the object when it is no longer needed. Calling object.UnRegister(None) is prohibited, as it would prematurely delete the object and may crash the application. In C++, the VTK_NEWINSTANCE hint has no effect, the caller of the factory method must still take the ownership of the returned object the same way as without the hint.

box = roiNode.CreateROIBoxPolyDataWorld()
# no need to call UnRegister, as CreateROIBoxPolyDataWorld method is marked with VTK_NEWINSTANCE

Loadable modules (C++)

If storing in a new variable:

vtkSmartPointer<vtkCollection> nodes = vtkSmartPointer<vtkCollection>::Take(mrmlScene->GetNodesByClass("vtkMRMLLinearTransformNode"));

If the variable is created already:

vtkSmartPointer<vtkCollection> nodes;
nodes.TakeReference(mrmlScene->GetNodesByClass("vtkMRMLLinearTransformNode"));

Unsafe, legacy method without using smart pointers (not recommended, because the Delete() method may be forgotten or skipped due to an early return from the function):

vtkCollection* nodes = mrmlScene->GetNodesByClass("vtkMRMLLinearTransformNode");
// ...
nodes->Delete();

Python scripts and scripted modules

Factory methods return an object that the caller owns (and thus the caller has to delete, with reference count >0) and Python adds an additional reference to this object when stored in a Python variable, resulting in a reference count of >1. To make sure that the object is deleted when the Python variable is deleted, we have to remove the additional reference that the factory method added. There is currently no automatic mechanism to remove that additional reference, so it has to be done manually by calling UnRegister (the reference count shouldn’t be explicitly set to any specific value, it is only allowed to increment/decrement it using Register/UnRegister):

nodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLLinearTransformNode')
nodes.UnRegister(slicer.mrmlScene) # reference count is increased by both the factory method and the python reference; unregister to keep only the python reference
# ...

To avoid forgetting the UnRegister call, it is better to avoid factory methods whenever it is possible.

For example, instead of using the CreateNodeByClass factory method and call UnRegister manually:

n = slicer.mrmlScene.CreateNodeByClass('vtkMRMLLinearTransformNode')
slicer.mrmlScene.AddNode(n)
n.UnRegister(slicer.mrmlScene)

this should be used:

n = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLinearTransformNode')

Note: MRML scene’s CreateNodeByClass creates a node with the default settings set in the scene for that node type (using vtkMRMLScene::AddDefaultNode).

Working directory

Similarly to other software, the current directory associated with Slicer corresponds to the folder the application executable is started from.

Since the current working directory can be changed anytime by any module or Python package (e.g., to more conveniently write files in a specific directory) and it is not possible to enforce that the directory is restored to the original.

Slicer provides a way to reliably access the working directory at startup time, through the startupWorkingPath application property:

In Python:

slicer.app.startupWorkingPath

In C++:

qSlicerCoreApplication::startupWorkingPath()

View layout definition

View layout definition describes what views (3D, slice, plot, table, etc.) should be displayed and where. It is specified by an XML string.

A layout may contain multiple viewports, each viewport is a separate window, which may be displayed in the main application window or separately, for example on a second screen.

XML elements and their attributes:

  • viewports: optional, if specified then it must be the root element. It can be used for specifying multiple viewports. It contains nested layout elements.

  • layout: The layout elements describe widget containers that embed one or multiple items. Arrangement of items are specified by type attribute of the layout element. It may be root element or it may be nested in viewports or item element.

    • type: vertical, horizontal, grid, tab.

    • split: true or false (default), if true then the user can resize the views in it by dragging the splitter between the views. Default size can be set using splitSize attribute of child items. Only for vertical and horizontal layout type.

    • name: unique name of the layout, required if there are multiple viewports. If name is not specified then the empty string will be used as name. The empty string is a valid name, which refers to the default viewport, i.e., that is displayed in the application’s main window.

    • label: optional, if specified then this will be used as

    • dockable: true (default) or false display the viewport as a dockable widget.

    • dockPosition: If dockable, this can make the widget be docked by default. Valid choices are floating (default), top, bottom, left, right, bottom-left, bottom-right, top-left, top-right.

  • item: container for view(s) or layouts, nested in layout element.

    • splitSize: default size if split is enabled in the layout

  • view: view widget, nested in item element.

    • name: this name is displayed in the view’s title bar

    • horizontalStretch or verticalStretch: Relative size of views can be adjusted by specifying these stretch factors. The stretch factor must be an integer in the range of [0, 255].

    • row and column: row and column index. Only for grid layout type.

    • class: class of the view node, such as vtkMRMLSliceNode, vtkMRMLViewNode, vtkMRMLTableViewNode, vtkMRMLPlotViewNode.

    • singletontag: layout name of the view node (1, 2, … for 3D views; Red, Yellow, … for slice views)

  • property: contains view properties

    • name: property name, such as viewlabel (displayed in the view’s title bar), orientation (for slice views),

    • element text: property value

Example: Simple 4-up view layout

<layout type="vertical" split="true">
  <item>
  <view class="vtkMRMLViewNode" singletontag="1">
    <property name="viewlabel" action="default">1</property>
  </view>
  </item>
  <item>
  <view class="vtkMRMLSliceNode" singletontag="Red">
    <property name="orientation" action="default">Axial</property>
    <property name="viewlabel" action="default">R</property>
    <property name="viewcolor" action="default">#F34A33</property>
  </view>
  </item>
</layout>

Example: Layout containing two viewports

<viewports>
 <!--default viewport-->
 <layout type="horizontal">
  <item>
   <view class="vtkMRMLSliceNode" singletontag="Red">
    <property name="orientation" action="default">Axial</property>
    <property name="viewlabel" action="default">R</property>
    <property name="viewcolor" action="default">#F34A33</property>
   </view>
  </item>
  <item>
   <view class="vtkMRMLViewNode" singletontag="1">
    <property name="viewlabel" action="default">1</property>
   </view>
  </item>
 </layout>
 <!--second dockable viewport-->
 <layout name="views+" type="horizontal" label="Views+" dockable="true" dockPosition="bottom">>
  <item>
   <view class="vtkMRMLSliceNode" singletontag="Red+">
    <property name="orientation" action="default">Axial</property>
    <property name="viewlabel" action="default">R+</property>
    <property name="viewcolor" action="default">#f9a99f</property>
    <property name="viewgroup" action="default">1</property>
   </view>
  </item>
  <item>
   <view class="vtkMRMLViewNode" singletontag="1+" type="secondary">
    <property name="viewlabel" action="default">1+</property>
    <property name="viewgroup" action="default">1</property>
   </view>
  </item>
 </layout>
</viewports>

Event broker

The basic idea of the EventBroker is to avoid the following kind of code that shows up in GUIs and other classes that depend on events generated by other classes:

node->AddObserver(vtkCommand::ModifiedEvent, callbackCommand)

Problem

The problems with this:

  • node ‘owns’ the observer, but the callbackCommand is opaque so it doesn’t know anything about what will happen when the event is invoked

  • the GUI needs to explicitly remove the observer before it is destroyed

  • node is not introspectable; you cannot get a list of observers on the node (all data and methods are private)

  • there’s no easy way to know what side effects will happen for any Set call (either a priori or experimentally).

  • there’s no way to collapse events or disable them

Solution

The EventBroker solve this by introducing a singleton that manages all observations.

The EventBroker is a singleton, available as:

vtkEventBroker *broker = vtkEventBroker::GetInstance();

with the broker, you can make a call like the following:

broker->AddObservation(node, vtkCommand::ModifiedEvent, this, callbackCommand);

where node is the subject of the observation.

Tip

The broker is also available for use from Python, but for adding observers in Python, it is recommended to use the higher-level slicer.util.VTKObservationMixin instead.

The broker does the following:

  • adds DeleteEvent observers to both node and this so it can remove the observation automatically when either side is destroyed

  • keeps an introspectable list of all observers it knows about

  • has an option to keep a log of all event invocations for debugging and performance analysis

  • has an option to turn off all event invocations

  • has an asynchronous option to queue all event invocations and invoke them later (off by default)

  • has option to collapse redundant events in the queue

Future options include:

  • add a timer to log the amount of time taken to process each event

  • specify that some observations must be handled synchronously (e.g. for progress events that shouldn’t be collapsed)

See the file vtkEventBroker API documentation for more information on logging options and introspection features.

How to work with the vtkObserverManager

Discussion of Jan 27 2012:

[…] the problem wasn’t that the Event Broker was used instead of going through vtkObserverManager, but that the vtkObject::AddObserver() was used with the callback command of the observer manager (that was later deleted which made the client data of the callback dirty when the event was fired).

We should eventually review the entire “observation” mechanism, there are currently 3 ways of observing vtkObjects:

  • via the vtkObserverManager API (please everybody use that one for now)

  • via the EventBroker directly

  • via vtkObject::AddObserver directly

All three methods are valid but inconsistent with each other. In addition, it is still not user friendly to observe MRML nodes (using static functions as callback… how to synchronize a MRML node with a VTK widget in a displayable manager? how to observe with Python…).

Bugs related to observers:

  • Volume Rendering (Slicer issue #1572, Slicer issue #1744)

    • Use AddObserver with vtkObserverManager callback that is deleted before an observed event is fired, crash when trying to dereference the deleted observer.

  • Python (Slicer issue #1656)

    • PyObject of the observer is deleted before an observed event is fired. crash in the callback

  • Current design notes

    • For logics, vtk[SetAnd]ObserveMRMLNode[Events]Macro can only observe MRML nodes (see vtkMRMLAbstractLogic::MRMLNodesCallback)

    • For QObjects listening to vtkObjects, destruction must unlink observations (modules must call setMRMLScene(0) in destructor?)

References

The following reference provided insight on requirements and design precedents.