Transcript Slicer 3.0 Architecure

Slicer MRML
• MRML Library provides API for managing medical image
data types (Volumes, Models, Transforms, Fiducials,
Cameras, etc) and their visualization.
• Each data type is represented by a special MRML node.
• MRML Scene is a collection of MRML nodes.
• Slicer MRML data model is implemented independent of
the visualization and algorithmic components of the system.
• Other Slicer components (Logic and GUI) observe changes
in MRML scene and individual nodes and process change
MRML events.
National Alliance for Medical Image Computing
http://na-mic.org
Slicer MRML Scene
• MRML Scene manages MRML nodes : add,
delete, find, find by type, etc.
• MRML Scene provides persistence of MRML
nodes (reading/writing to/from XML file).
• MRML Scene provides Undo/Redo mechanism
that restores a previous state of the scene and
individual nodes.
National Alliance for Medical Image Computing
http://na-mic.org
Slicer MRML Nodes
• The MRML nodes are designed to store the state of the
Slicer application, both raw data and visualization
parameters.
• All MRML nodes have to implement certain standard API:
ReadAttributes, WriteAttributes, Copy, etc.
• MRML nodes are organized into C++ class hierarchies, all
derived from vtkMRMLNode class.
• For example vtkMRMLTransformableNode is the parent
class of Volume, Model, Fiducial, and Transformation
nodes; vtkVolumeNode is a parent of
vtkMRMLScalarVolumeNode and
vtkMRMLVectorVolumeNode
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http://na-mic.org
MRML Nodes Class Hierarchy
(vtkMRML)Node
TransformableNode
VolumeNode
ModelNode
FiducialNode
TransformNode
LinearTransformNode
ScalarVolumeNode
TensorVolumeNode
VectorVolumeNode
DiffusionWeightedVolumeNode
DiffusionTensorVolumeNode
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http://na-mic.org
References to MRML Nodes
• Some MRML nodes have references to other
nodes.
• Transformable Node has a reference to a
Transformation node. Transformation node has a
reference to its parent Transformation node.
• References are stored by node ID.
• Use vtkSetReferenceStringMacro to set
reference ID (it registers reference with the
scene).
• Access methods should check if the referenced
node is still in the MRML scene using its ID.
National Alliance for Medical Image Computing
http://na-mic.org
Transform Hierarchy and Node
References
TransformNode0
TransformNodeID
=NULL
ModeNode0
TransformNodeID
= ‘TransofrmNode1’
VolumeNode0
TransformNodeID
= ‘TransofrmNode2’
TransformNode1
TransformNodeID
= TransformNode0
TransformNode2
TransformNodeID
= TransformNode1
National Alliance for Medical Image Computing
http://na-mic.org
MRML Events and Observers
• Changes in MRML scene and individual nodes
propagate to other observing nodes, GUI and
Logic objects via vtk events and commandobserver mechanism.
• Use vtk AddObserver() and InvokeEvent()
methods. vtk SetMacro generates ModifiedEvent.
• The command-observer mechanism for MRML is
implemented using helper vtkObserverManager,
class, MRML Observer macros, and
ProcessMRMLEvents method.
• Observers should store a registered pointer to a
MRML node to prevent callbacks on a deleted
object.
National Alliance for Medical Image Computing
http://na-mic.org
Events and Observers Example
ViewerWidget
observes
ProcessMRMLEvents()
callback
ModelNode
ProcessMRMLEvents()
update transforms
observes
InvokeEvent(TransformModifiedEvent)
callback
LinearTransofmNode
observes
vtkMatrix4x4
ProcessMRMLEvents()
callback
SetElement()
InvokeEvent(ModifiedEvent)
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http://na-mic.org
InvokeEvent(TransformModifiedEvent)
MRML Observer API
• Defined in Libs/MRML/vtkMRMLNode.h
• VtkSetMRMLObjectMacro - registers MRML node with
another vtk object (another MRML node, Logic or GUI). No
observers added.
• VtkSetAndObserveMRMLObjectMacro - registers MRML
node and adds an observer for vtkCommand::ModifyEvent.
• VtkSetAndObserveMRMLObjectEventsMacro - registers
MRML node and adds an observer for a specified set of
events.
• SetAndObserveMRMLScene[Events]() method is used in
GUI and Logic to observe Modify, NewScene, NodeAdded,
etc. events.
• ProcessMRMLEvents method should be implemented in
MRML nodes, Logic, and GUI classes in order to process
events from the observed nodes.
National Alliance for Medical Image Computing
http://na-mic.org
Creating Custom MRML Node
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Custom MRML nodes provide persistent storage for the
module parameters.
Custom MRML nodes should be registered with the MRML
scene using RegisterNodeClass() so they can be saved
and restored from a scene file.
Classes should implement the following methods:
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CreateNodeInstance() – similar to VTK New() method only
not static.
GetNodeTagName() – return a unique XML tag for this node.
ReadXMLAttributes() – reads node attributes from XML file
as name-value pairs.
WriteXML() – writes node attributes to output stream (as in
interpolate="1" ).
Copy() – copies node attributes.
National Alliance for Medical Image Computing
http://na-mic.org
Creating Custom MRML Node continued
• If the node has references to other nodes the following
additional methods should be implemented:
– UpdateReferenceID() - updates the stored reference to another
node.
– UpdateScene()- updates other nodes in the scene depending
on this node or updates this node if it depends on other nodes
when the scene is read in. This method is called automatically
by XML parser after all nodes are created.
• An example of a custom MRML node implementation:
vtkMRMLGradientAnisotropicDiffusionFilterNode in
Modules/GradientAnisotropicDiffusionFilter directory.
• To add node to the MRML scene:
– In the code: use standard vtk New() and add node to the scene
using vtkMRMLScene::AddNode(vtkMRMLNode *)
– By user request: use vtkSlicerNodeSelectorWidget that creates
a new node from the module’s UI.
National Alliance for Medical Image Computing
http://na-mic.org
Undo/Redo Architecture for
Slicer3
• Undo/Redo is based on saving and restoring the state of
MRML nodes in the Scene.
• MRML scene can save snapshot of all nodes into a special
Undo and Redo stacks.
• The Undo and Redo stacks store copies of nodes that have
changed from the previous snapshot. The node that have
not changes are stored by a reference (pointer).
• When an Undo is called on the scene, the current state of
Undo stack is copied into the current scene and also into
Redo stack.
• => All Undoable operations must store their data as MRML
nodes
National Alliance for Medical Image Computing
http://na-mic.org
Undo Implementation
Undo Stack
Initial Scene
Delta1 Scene
MRML Scene
Delta2 Scene
N1
N2
Saved Scene
N1
N4
N3
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N4
N5
N5
How to use Undo API
• Developer controls at what point the snapshot is saved by
calling SaveStateForUndo method on the MRML scene.
– SaveStateForUndo() - saves the state of all nodes in the
scene
– SetActiveScene(vtkMRMLScene *) - saves the state of the
specified node.
– SetActiveScene(vtkCollection*) - saves the state of the
specified collection of nodes.
• SaveStateForUndo() should be called in GUI/Logic classes
before changing the state of MRML nodes. Usually done in
the ProcessGUIEvents method that processes events from
the user interactions with GUI widgets.
• SaveStateForUndo() should not be called while processing
transient events such as continuous events sent by KW UI
while dragging a slider (for example
vtkKWScale::ScaleValueStartChangingEvent).
National Alliance for Medical Image Computing
http://na-mic.org