Documentation/Nightly/Developers/MRML - Revision history

Lasso: Moved to readthedocs

2020-06-04T20:35:16Z

Moved to readthedocs

Show changes

JChris.FillionR: /* MRML Nodes */

2016-06-08T15:54:27Z

MRML Nodes

Gregsharp at 17:57, 29 October 2015

2015-10-29T17:57:48Z

JChris.FillionR at 22:33, 3 April 2015

2015-04-03T22:33:11Z

JChris.FillionR: /* MRML Scene */

2015-04-03T22:30:13Z

MRML Scene

JChris.FillionR: /* Slicer MRML Overview */

2015-04-03T22:29:01Z

Slicer MRML Overview

JChris.FillionR: /* Relationship between nodes */

2015-04-03T22:23:45Z

Relationship between nodes

JChris.FillionR: /* Relationship between nodes */

2015-04-03T21:48:11Z

Relationship between nodes

JChris.FillionR: /* MRML Nodes */

2015-04-03T21:47:48Z

MRML Nodes

JChris.FillionR at 18:04, 3 April 2015

2015-04-03T18:04:37Z

@@ Line 25: / Line 25: @@
 * MRML nodes are designed to store the state of the Slicer application, both raw data and visualization, and storage parameters. A set of core MRML nodes that store the state of core Slicer modules is listed [{{doxygen-class-url|vtkMRMLNode}} here].
-* MRML nodes are organized into C++ class hierarchies, all derived from [http://slicer.org/doc/html/classvtkMRMLNode.html#details vtkMRMLNode] class. For example, [{{doxygen-class-url|vtkMRMLTransformableNode}}#details vtkMRMLTransformableNode] is the parent class of Volume, Model, Fiducial, and Transformation nodes; [{{doxygen-class-url|vtkMRMLVolumeNode}}#details vtkMRMLVolumeNode] is a parent of [{{doxygen-class-url|vtkMRMLScalarVolumeNode}}#details vtkMRMLScalarVolumeNode] and [{{doxygen-class-url|vtkMRMLVectorVolumeNode}}#details vtkMRMLVectorVolumeNode].
+* MRML nodes are organized into C++ class hierarchies, all derived from  [{{doxygen-class-url|vtkMRMLNode}}#details vtkMRMLNode] class. For example, [{{doxygen-class-url|vtkMRMLTransformableNode}}#details vtkMRMLTransformableNode] is the parent class of Volume, Model, Fiducial, and Transformation nodes; [{{doxygen-class-url|vtkMRMLVolumeNode}}#details vtkMRMLVolumeNode] is a parent of [{{doxygen-class-url|vtkMRMLScalarVolumeNode}}#details vtkMRMLScalarVolumeNode] and [{{doxygen-class-url|vtkMRMLVectorVolumeNode}}#details vtkMRMLVectorVolumeNode].
 * All MRML nodes have to implement certain standard API: ReadAttributes, WriteAttributes, Copy, etc.

@@ Line 42: / Line 42: @@
 To avoid name clashes custom modules that adds attributes to nodes should prefix the attribute name with the module's name and the '.' character. Example: the DoseVolumeHistogram module can use attribute names such as <code>DoseVolumeHistogram.StructureSetName</code>, <code>DoseVolumeHistogram.Unit</code>, <code>DoseVolumeHistogram.LineStyle</code>.
-= Relationship between nodes =
+= MRML Node References =
-Data node can optionally implement interfaces like [{{doxygen-class-url|vtkMRMLDisplayableNode}} Displayable], [{{doxygen-class-url|vtkMRMLStorableNode}} Storable] and [{{doxygen-class-url|vtkMRMLTransformableNode}} Transformable].
+There are two mechanism for specifying that nodes are related: hierarchy nodes and node references.  The node reference is the simpler of the two methods.  MRML nodes can reference and observe other MRML nodes using the node reference API.  The framework will automatically take care of (1) read/write/copy of node references, (2) updating references on scene import, and (3) adding and deleting nodes.  A node may reference multiple nodes, each performing a distinct role, and each addressed by a unique string.
-Each one of these interfaces have its own requirements. For example, a transformable node will expected to be associated with a transform node. Such association are done by creating [[Documentation/{{documentation/version}}/Developers/MRML/NodeReferences|MRML References]].
+Data node can optionally implement interfaces like [{{doxygen-class-url|vtkMRMLDisplayableNode}} Displayable], [{{doxygen-class-url|vtkMRMLStorableNode}} Storable] and [{{doxygen-class-url|vtkMRMLTransformableNode}} Transformable]. Each one of these interfaces have its own requirements. For example, a transformable node will expected to be associated with a transform node. Such association are done by creating [[Documentation/{{documentation/version}}/Developers/MRML/NodeReferences|MRML References]].
 For more details, see [[Documentation/{{documentation/version}}/Developers/MRML/NodeReferences|here]].

@@ Line 1: / Line 1: @@
 <noinclude>{{documentation/versioncheck}}</noinclude>
 = Slicer MRML Overview =
@@ Line 34: / Line 35: @@
 * When a data node is created, it is also necessary to create the corresponding display and storage nodes to allow proper visualization and saving to file. This is where [[Documentation/Nightly/Developers/Logics|MRMLLogic]] can be helpful in providing function allowing to create a node and is associated display and data node if needed. Note also that in some cases, Slicer detects if the display and storage node is missing and tries to create a default nodes, but the developers should not rely on this error-recovery mechanism.
 = Relationship between nodes =
@@ Line 40: / Line 47: @@
 Each one of these interfaces have its own requirements. For example, a transformable node will expected to be associated with a transform node. Such association are done by creating [[Documentation/{{documentation/version}}/Developers/MRML/NodeReferences|MRML References]].
 = References to MRML Nodes =
@@ Line 100: / Line 91: @@
   –By user request: use vtkSlicerNodeSelectorWidget that creates a new node from the module’s UI.
+<!--
 = Undo/Redo Mechanism =
@@ Line 128: / Line 119: @@
 * vtkMRMLScene::ClearUndoStack() – clears the undo history.
 * vtkMRMLScene::ClearRedoStack() – clears the redo history.
 = Other Useful References =

@@ Line 13: / Line 13: @@
 = MRML Scene =
-*MRML Scene manages MRML nodes : add, delete, find, find by type, etc.
+* 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 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.
 = MRML Nodes =

@@ Line 2: / Line 2: @@
 = Slicer MRML Overview =
-*MRML Library provides API for managing medical image data types (Volumes, Models, Transforms, Fiducials, Cameras, etc) and their visualization.
+* 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.
+* Each data type is represented by a special MRML node.
-*MRML Scene is a collection of MRML nodes.
+* MRML Scene is a collection of MRML nodes.
-*Slicer MRML data model is implemented independent of the visualization and algorithmic components of the system.
+* Slicer MRML data model is implemented independent of the visualization and algorithmic components of the system.
-*Other Slicer components ([[Documentation/Nightly/Developers/Logics|Logic]] and Qt Widget) observe changes in MRML scene and individual nodes and process change MRML events.
+* Other Slicer components ([[Documentation/{{documentation/version}}/Developers/Logics|Logic]] and Qt Widget) observe changes in MRML scene and individual nodes and process change MRML events.
-For more details on MRML architecture see [http://www.na-mic.org/Wiki/images/e/e3/Slicer_3-alpha-2006-04-03.ppt Architecture Slides].
 = MRML Scene =

@@ Line 35: / Line 35: @@
 Data node can optionally implement interfaces like [{{doxygen-class-url|vtkMRMLDisplayableNode}} Displayable], [{{doxygen-class-url|vtkMRMLStorableNode}} Storable] and [{{doxygen-class-url|vtkMRMLTransformableNode}} Transformable].
-Each one of these interfaces have its own requirements. For example, a transformable node will expected to be associated with a transform node. Such association are done by creating MRML Reference.
+Each one of these interfaces have its own requirements. For example, a transformable node will expected to be associated with a transform node. Such association are done by creating [[Documentation/{{documentation/version}}/Developers/MRML/NodeReferences|MRML References]].
 = MRML Hierarchy Node =

@@ Line 6: / Line 6: @@
 *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.
+*Other Slicer components ([[Documentation/Nightly/Developers/Logics|Logic]] and Qt Widget) observe changes in MRML scene and individual nodes and process change MRML events.
 For more details on MRML architecture see [http://www.na-mic.org/Wiki/images/e/e3/Slicer_3-alpha-2006-04-03.ppt Architecture Slides].
@@ Line 14: / Line 14: @@
 *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.
+*MRML Scene provides Undo/Redo mechanism that restores a previous state of the scene and individual nodes.
 = MRML Nodes =
@@ Line 39: / Line 39: @@
 **Storage node: describes how the data should be stored persistently on disk (file format, file name)
 *When a data node is created, it is also necessary to create the corresponding display and storage nodes to allow proper visualization and saving to file. In some cases Slicer detects if the display and storage node is missing and tries to create a default nodes, but the developers should not rely on this error-recovery mechanism.
 {|
-|[[Image: Slicer3_MRML_Node_Hier.jpg|thumb|400px]]
+|[[File:ClassvtkMRMLNode_inherit_graph.png|thumb|400px]]
 |}
-= MRML Hierarchy =
+= MRML Hierarchy Node =
 [[File:HierarchyNodesDiagram.jpg|400px]]
@@ Line 53: / Line 59: @@
 MRML nodes can store custom attributes as (attribute name; attribute value) pairs.
-To avoid name clashes custom modules that adds attributes to nodes should prefix the attribute name with the module's name and the '.' character. Example: the DoseVolumeHistogram module can use attribute names such as DoseVolumeHistogram.StructureSetName, DoseVolumeHistogram.Unit, DoseVolumeHistogram.LineStyle.
+To avoid name clashes custom modules that adds attributes to nodes should prefix the attribute name with the module's name and the '.' character. Example: the DoseVolumeHistogram module can use attribute names such as <code>DoseVolumeHistogram.StructureSetName</code>, <code>DoseVolumeHistogram.Unit</code>, <code>DoseVolumeHistogram.LineStyle</code>.
 = References to MRML Nodes =