Difference between revisions of "Modules:DataModule-3.4"

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* '''MRML''' (pronounced '''mur'''-muhl) stands for the "Medical Reality Markup Language". It is an XML-based representation of a a MRML Scene.
 
* '''MRML''' (pronounced '''mur'''-muhl) stands for the "Medical Reality Markup Language". It is an XML-based representation of a a MRML Scene.
* '''MRML Scene''' is the collection of datasets and their current state, viewing parameters, semantic descriptions, and possibly also algorithm parameterization. A MRML Scene may also contain a set of alternate state configurations (scene snapshots) of interest.
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* '''MRML Scene''' is the collection of datasets and their current state, viewing parameters, semantic descriptions, and also algorithm parameterization. A MRML Scene may also contain a set of alternate state configurations (scene snapshots) of interest.
 +
 
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* '''MRML Scene description''' is the XML-based file (with extension .mrml) that contains the complete MRML Scene specification, and which '''references''' all datasets present in the MRML Scene. Slicer loads and saves MRML Scene description files. In order to load a MRML Scene from a description file, Slicer requires that all the datasets it references must be present in their referenced directory or file path.
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* '''MRML Tree''' is the hierarchical description of how data in a MRML Scene is represented. For instance, a Transformation Matrix may apply to multiple datasets, so these datasets are represented as '''children''' of the transform in a tree-view.
 
* '''MRML Tree''' is the hierarchical description of how data in a MRML Scene is represented. For instance, a Transformation Matrix may apply to multiple datasets, so these datasets are represented as '''children''' of the transform in a tree-view.
* '''MRML Nodes''' are data and parameter containers in the MRML Scene. Nodes may contain volumetric data (''e.g.'' ScalarVolumeNodes or ScalarVolumeStorageNodes) or polygonal data (''e.g'' ModelNodes or ModelStorageNodes) or the state of a particular Slicer software module (''e.g.'' EMSSegmenterNode). MRML Nodes that describe/represent data have names, and are displayed in the Data Module's MRML Scene Tree panel. All nodes are saved into the MRML Scene description file that Slicer reads and writes.
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* '''MRML Nodes''' are data and parameter containers in the MRML Scene. Nodes may contain volumetric data (''e.g.'' ScalarVolumeNodes or ScalarVolumeStorageNodes) or polygonal data (''e.g'' ModelNodes or ModelStorageNodes) or the state of a particular Slicer software module (''e.g.'' EMSSegmenterNode). MRML Nodes that describe/represent data have names, and are displayed in the Data Module's MRML Scene Tree panel. All nodes are saved into the MRML Scene description.
  
 
= Loading Scenes & Datasets, and Viewing the MRML Scene Hierarchy using the Data Module =
 
= Loading Scenes & Datasets, and Viewing the MRML Scene Hierarchy using the Data Module =

Revision as of 15:15, 6 May 2009

Home < Modules:DataModule-3.4

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Overview

This module allows you to load scenes and individual datasets of many types, and to view the scene's data hierarchy. The Data Module's "Load Panel" is first shown and described below, option by option. Then the panel that displays the MRML Scene hierarchy is described, along with functionality to modify that hierarchy and the visibility of each dataset (represented by a "Node") in the scene.

Terminology: MRML, MRML Scene Description, MRML Tree, MRML Nodes

  • MRML (pronounced mur-muhl) stands for the "Medical Reality Markup Language". It is an XML-based representation of a a MRML Scene.
  • MRML Scene is the collection of datasets and their current state, viewing parameters, semantic descriptions, and also algorithm parameterization. A MRML Scene may also contain a set of alternate state configurations (scene snapshots) of interest.
  • MRML Scene description is the XML-based file (with extension .mrml) that contains the complete MRML Scene specification, and which references all datasets present in the MRML Scene. Slicer loads and saves MRML Scene description files. In order to load a MRML Scene from a description file, Slicer requires that all the datasets it references must be present in their referenced directory or file path.
  • MRML Tree is the hierarchical description of how data in a MRML Scene is represented. For instance, a Transformation Matrix may apply to multiple datasets, so these datasets are represented as children of the transform in a tree-view.
  • MRML Nodes are data and parameter containers in the MRML Scene. Nodes may contain volumetric data (e.g. ScalarVolumeNodes or ScalarVolumeStorageNodes) or polygonal data (e.g ModelNodes or ModelStorageNodes) or the state of a particular Slicer software module (e.g. EMSSegmenterNode). MRML Nodes that describe/represent data have names, and are displayed in the Data Module's MRML Scene Tree panel. All nodes are saved into the MRML Scene description.

Loading Scenes & Datasets, and Viewing the MRML Scene Hierarchy using the Data Module

Note that this collection of load options is a temporary placeholder for a more generalized scene & data loading interface, which we are working on for future versions of the Slicer software. The load panel is shown below:

Load Data Panel

The options it contains duplicate load options currently exposed in other parts of the Slicer software. Here, we'll briefly describe each option and mention where else in Slicer the functionality can be found.

Loading New Scenes

Data-3.4-LoadScene.png

Adding a Scene

Data-3.4-AddScene.png

Adding Individual Datasets, or a Directory of Data

Data-3.4-AddData.png

Adding Scalar and Tensor Volumes

Data-3.4-AddVolume.png

Adding 3D Models, or a Directory of Models

Data-3.4-AddModel.png

Adding a Scalar Overlay to a Model

Data-3.4-AddOverlay.png

Adding a Transformation Matrix

Data-3.4-AddMatrix.png

Adding a Fiducial List

Data-3.4-AddFiducialList.png

Adding a Custom Color Table

Data-3.4-AddColorTable.png

Adding a DTI Fiber Bundle

Data-3.4-AddFiberBundle.png

Displaying and Modifying the MRML Scene Hierarchy

Load Data GUI

Show all loaded data