Modules:AtlasCreator - Revision history

Belhachemi: /* The Command Line Interface */

2011-07-21T17:09:17Z

The Command Line Interface

Haehn: /* Known bugs */

2011-04-27T22:06:22Z

Known bugs

Haehn: /* Notes from the Developer(s) */

2011-04-18T15:07:51Z

Notes from the Developer(s)

Haehn: /* External invocation using the Atlas Creator MRML Node */

2011-04-15T19:29:32Z

External invocation using the Atlas Creator MRML Node

Haehn: /* External invocation using the Atlas Creator MRML Node */

2011-04-15T19:29:19Z

External invocation using the Atlas Creator MRML Node

Haehn: /* Development */

2011-04-15T19:28:49Z

Development

Haehn: /* External invocation using the Atlas Creator MRML Node */

2011-04-15T19:28:06Z

External invocation using the Atlas Creator MRML Node

Haehn: /* Usage */

2011-04-15T19:26:49Z

Usage

Haehn: /* Notes from the Developer(s) */

2011-04-15T19:26:22Z

Notes from the Developer(s)

Haehn: /* Notes from the Developer(s) */

2011-04-15T19:25:19Z

Notes from the Developer(s)

@@ Line 196: / Line 196: @@
 <pre>
-$ cd Slicer3-release/lib/Slicer3/Modules/AtlasCreator/atlascreator.py
+$ cd Slicer3-release/lib/Slicer3/Modules/AtlasCreator/
 $ python atlascreator.py --help
 AtlasCreator for 3D Slicer
@@ Line 219: / Line 219: @@
 The '''full documentation of the commandline interface''' is available on [[Modules:AtlasCreator:CLI|a separate page]].
 == Development ==

← Older revision		Revision as of 22:06, 27 April 2011
Line 288:		Line 288:

	===Known bugs===		===Known bugs===
		+	The AtlasCreator is currently ''not'' supported on Windows machines.

	===Usability issues===		===Usability issues===

@@ Line 267: / Line 267: @@
 </pre>
+{|
-Separate notes on the development are available [[Modules:AtlasCreator:Development|on a separate page]].
+|[[Image:AcFlowNew.png|thumb|280px|The '''computational steps''' of the Atlas Creator]]
 ===Dependencies===

@@ Line 232: / Line 232: @@
 ===='''External invocation using the Atlas Creator MRML Node'''====
-It is easy to include the Atlas Creator in third-party 3D Slicer modules (C++,Tcl,Python are supported) or run it via the Tcl or Python consoles. To do so, one has to configure the vtkMRMLAtlasCreatorNode and fire a launch event.
+It is easy to include the Atlas Creator in third-party 3D Slicer modules (C++, Tcl and Python are supported) or run it via the Tcl or Python consoles. To do so, one has to configure the vtkMRMLAtlasCreatorNode and fire a launch event.
 The following example outlines the procedure by configuring a ''Pair fixed'' computation against a defaultCase (Python was chosen for this example):

@@ Line 232: / Line 232: @@
 ===='''External invocation using the Atlas Creator MRML Node'''====
-It is easy to include the Atlas Creator in third=party 3D Slicer modules (C++,Tcl,Python are supported) or run it via the Tcl or Python consoles. To do so, one has to configure the vtkMRMLAtlasCreatorNode and fire a launch event.
+It is easy to include the Atlas Creator in third-party 3D Slicer modules (C++,Tcl,Python are supported) or run it via the Tcl or Python consoles. To do so, one has to configure the vtkMRMLAtlasCreatorNode and fire a launch event.
 The following example outlines the procedure by configuring a ''Pair fixed'' computation against a defaultCase (Python was chosen for this example):

← Older revision		Revision as of 19:28, 15 April 2011
Line 219:		Line 219:

	The '''full documentation of the commandline interface''' is available on [[Modules:AtlasCreator:CLI\|a separate page]].		The '''full documentation of the commandline interface''' is available on [[Modules:AtlasCreator:CLI\|a separate page]].
		+
		+
		+
		+
		+

	== Development ==		== Development ==

@@ Line 41: / Line 41: @@
 # [[Modules:AtlasCreator#extended|The extended graphical user interface]]
 # [[Modules:AtlasCreator#cli|The command line interface]]
-# External invocation using the Atlas Creator MRML Node
+# [[Modules:AtlasCreator#mrml|External invocation using the Atlas Creator MRML Node]]
 ===Use Cases, Examples===
@@ Line 219: / Line 219: @@
 The '''full documentation of the commandline interface''' is available on [[Modules:AtlasCreator:CLI|a separate page]].
 == Development ==

← Older revision		Revision as of 19:26, 15 April 2011
Line 229:		Line 229:
	===Notes from the Developer(s)===		===Notes from the Developer(s)===

		+	<span id='mrml'></span>
	===='''External invocation using the Atlas Creator MRML Node'''====		===='''External invocation using the Atlas Creator MRML Node'''====

← Older revision		Revision as of 19:25, 15 April 2011
Line 228:		Line 228:

	===Notes from the Developer(s)===		===Notes from the Developer(s)===
		+
		+	===='''External invocation using the Atlas Creator MRML Node'''====
		+
		+	It is easy to include the Atlas Creator in third=party 3D Slicer modules (C++,Tcl,Python are supported) or run it via the Tcl or Python consoles. To do so, one has to configure the vtkMRMLAtlasCreatorNode and fire a launch event.
		+
		+	The following example outline the procedure (Python was chosen for this example):
		+
		+	<pre>
		+	from Slicer import slicer
		+	import os
		+
		+	# we use the testdata which is shipped with the Atlas Creator
		+	dataPath = os.path.normpath(slicer.Application.GetBinDir().. + '/../share/Slicer3/Modules/AtlasCreator/TestData/')
		+
		+	# create a new Atlas Creator MRML Node
		+	n = slicer.vtkMRMLAtlasCreatorNode()
		+
		+	# Initialize with a default configuration
		+	n.InitializeByDefault()
		+
		+	# set the original images by specifying the absolute filepaths for all cases divided by space
		+	n.SetOriginalImagesFilePathList(dataPath + '/originals/case60.nrrd ' + dataPath + '/originals/case61.nrrd ' + dataPath + '/originals/case62.nrrd')
		+	# set the segmentations by specifying the absolute filepaths for all cases divided by space
		+	n.SetSegmentationsFilePathList(dataPath + '/segmentations/case60.nrrd ' + dataPath + '/segmentations/case61.nrrd ' + dataPath + '/segmentations/case62.nrrd')
		+
		+	# configure an output directory
		+	n.SetOutputDirectory('/tmp/acout/')
		+
		+	# set the default case
		+	n.SetFixedTemplateDefaultCaseFilePath(dataPath + '/originals/case62.nrrd')
		+
		+	# add the MRML node to the scene
		+	slicer.MRMLScene.AddNode(n)
		+
		+	# start the computation by firing the launch event
		+	n.Launch()
		+	</pre>
		+
		+

	Separate notes on the development are available [[Modules:AtlasCreator:Development\|on a separate page]].		Separate notes on the development are available [[Modules:AtlasCreator:Development\|on a separate page]].