Documentation/Labs/Segmentations - Revision history

Grundlett: Text replacement - "\[https:\/\/www\.slicer\.org\/slicerWiki\/index.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:42:20Z

Text replacement - "\[https:\/\/www\.slicer\.org\/slicerWiki\/index.php\/([^ ]+) ([^]]+)]" to "$2"

Grundlett: Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:34:03Z

Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

Pinter at 15:24, 24 June 2016

2016-06-24T15:24:14Z

Pinter: Moved Segment Editor from future to features

2016-03-15T19:29:57Z

Moved Segment Editor from future to features

Pinter: Added info about master representation and conversion graph

2016-02-09T16:55:38Z

Added info about master representation and conversion graph

JChris.FillionR: /* Switch between scalar/labelmap volume */

2015-11-13T00:52:39Z

Switch between scalar/labelmap volume

Pinter at 17:17, 21 October 2015

2015-10-21T17:17:36Z

Pinter: Added descriptions

2015-10-21T17:16:29Z

Added descriptions

Pinter at 17:10, 21 October 2015

2015-10-21T17:10:57Z

JChris.FillionR: /* Switch between scalar/labelmap volume */

2015-07-15T19:48:42Z

Switch between scalar/labelmap volume

@@ Line 1: / Line 1: @@
 = Motivation =
-* See '''[https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx these slides]''' for motivation, features, and details of the infrastructure.
+* See '''[[File:20160526_Segmentations.pptx|these slides]]''' for motivation, features, and details of the infrastructure.
 * For further details see [https://www.assembla.com/spaces/slicerrt/wiki/Segmentation original project page], [http://www.na-mic.org/Wiki/index.php/2014_Project_Week_Breakout_Session:_Contours 2014 NA-MIC week contours breakout session page], [http://www.na-mic.org/Wiki/index.php/2015_Winter_Project_Week_Segmentations_Breakout 2015 NA-MIC week segmentations breakout session page]
 * Main issues to solve

@@ Line 14: / Line 14: @@
 * Copy/move segments between segmentations
 * Import/export representations into labelmap ormodel nodes
-* Drastic improvement in memory usage compared to labelmaps and conversion speed compared to [http://www.slicer.org/slicerWiki/index.php/Documentation/4.4/Modules/Contours Contours] (the previous SlicerRT mechanism for the same purpose, predecessor of Segmentations) due to only allocating the effective extent
+* Drastic improvement in memory usage compared to labelmaps and conversion speed compared to [[Documentation/4.4/Modules/Contours|Contours]] (the previous SlicerRT mechanism for the same purpose, predecessor of Segmentations) due to only allocating the effective extent
 * Segment Editor module that can edit segmentation labelmap representations the same way as Editor module currently can [https://www.assembla.com/spaces/slicerrt/tickets/757-create-editor-module-to-edit-segmentations/details Assembla ticket #757]
@@ Line 67: / Line 67: @@
 = Notes =
-* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Segmentations Module page]
+* [[Documentation/Nightly/Modules/Segmentations|Module page]]
 = vtkMRMLLabelMapVolumeNode integration =

@@ Line 1: / Line 1: @@
 = Motivation =
-See
+* See '''[https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx these slides]''' for motivation, features, and details of the infrastructure.
-* https://www.assembla.com/spaces/slicerrt/wiki/Segmentation
+* For further details see [https://www.assembla.com/spaces/slicerrt/wiki/Segmentation original project page], [http://www.na-mic.org/Wiki/index.php/2014_Project_Week_Breakout_Session:_Contours 2014 NA-MIC week contours breakout session page], [http://www.na-mic.org/Wiki/index.php/2015_Winter_Project_Week_Segmentations_Breakout 2015 NA-MIC week segmentations breakout session page]
 * Main issues to solve
 ** The structures (referred to as segments) that belong together must be converted together to preserve coherence
 = Features =

@@ Line 16: / Line 16: @@
 * Import/export representations into labelmap ormodel nodes
 * Drastic improvement in memory usage compared to labelmaps and conversion speed compared to [http://www.slicer.org/slicerWiki/index.php/Documentation/4.4/Modules/Contours Contours] (the previous SlicerRT mechanism for the same purpose, predecessor of Segmentations) due to only allocating the effective extent
 = Design and implementation =
@@ Line 40: / Line 42: @@
 |[[Image:20150710_Segmentation_Design.png|thumb|right|961px|Class diagram]]
 |}
 = Code =
 Segmentation modules is part of the SlicerRT extension during development and will be moved to Slicer core when the developments are complete:
 * SlicerRT trunk modules:
@@ Line 53: / Line 55: @@
 = Future features =
 * CLI support for vtkMRMLSegmentationNode

@@ Line 4: / Line 4: @@
 * http://www.na-mic.org/Wiki/index.php/2014_Project_Week_Breakout_Session:_Contours
 * http://www.na-mic.org/Wiki/index.php/2015_Winter_Project_Week_Segmentations_Breakout
 = Features =
@@ Line 23: / Line 27: @@
 * Conversion between representations are driven by a conversion graph in which the nodes are the representations and the edges are conversion rules
 ** When converting with the default method (Create: 'Default' button), then the path with the lowest cost is used (rules have a cost field that gives a ballpark value for the conversion cost)
 {|
@@ Line 44: / Line 53: @@
 = Future features =
-* Editor module that can edit segmentation labelmap representations the same way as Editor module currently can
+* Editor module that can edit segmentation labelmap representations the same way as Editor module currently can [https://www.assembla.com/spaces/slicerrt/tickets/757-create-editor-module-to-edit-segmentations/details Assembla ticket #757]
 * CLI support for vtkMRMLSegmentationNode

← Older revision		Revision as of 00:52, 13 November 2015
Line 95:		Line 95:

	== Switch between scalar/labelmap volume ==		== Switch between scalar/labelmap volume ==
−	Previously it was possible to switch between scalar/labelmap type by changing an attribute value. Now scalar/labelmap volumes are stored in different classes, therefore a new node has to be created for the converted volume. Conversion options:
−	* Use the ''Cast Scalar Volume'' module to convert between scalar/labelmap volumes.
−	* Create a new node for the target representation and pass the image data of the source node to the target node. For example, conversion to labelmap volume:

−	~~scalarVolume = slicer~~.~~util~~.~~getNode('MRHead')~~	+	See [[Documentation/Nightly/FAQ#How_to_switch_between_scalar.2Flabelmap_volume_.3F]]
−	~~labelVolume = slicer.modules.volumes.logic().CreateAndAddLabelVolume(scalarVolume,scalarVolume.GetName()+'-label')~~
−	~~labelVolume.SetAndObserveImageData(scalarVolume.GetImageData())~~
−	~~slicer.mrmlScene.RemoveNode(scalarVolume)~~

@@ Line 6: / Line 6: @@
 = Features =
-* TODO
+* New Segmentation MRML node that can contain multiple segments and multiple representations for segments
 = Design and implementation =
-* TODO
+* New Segmentation MRML node that can contain multiple segments and multiple representations for all segments
 {|
 |[[Image:20150529_Segmentations.png|thumb|right|961px|Segmentations module, Visualizing model in 2D and 3D, also showing merged labelmap in 2D]]

@@ Line 78: / Line 78: @@
 Previously it was possible to switch between scalar/labelmap type by changing an attribute value. Now scalar/labelmap volumes are stored in different classes, therefore a new node has to be created for the converted volume. Conversion options:
 * Use the ''Cast Scalar Volume'' module to convert between scalar/labelmap volumes.
-* Conversion can be performed by creating a new node for the target representation and passing the image data of the source node to the target node. For example, conversion to labelmap volume:
+* Create a new node for the target representation and pass the image data of the source node to the target node. For example, conversion to labelmap volume:
      scalarVolume = slicer.util.getNode('MRHead')