Modules:PythonExplodeVolumeTransform-Documentation-3.4 - Revision history

Nicole: /* Source code & documentation */

2010-01-15T22:24:38Z

Source code & documentation

Marianna at 20:22, 26 May 2009

2009-05-26T20:22:26Z

Lantiga at 15:39, 6 April 2009

2009-04-06T15:39:29Z

Lantiga at 15:37, 6 April 2009

2009-04-06T15:37:46Z

Lantiga at 15:37, 6 April 2009

2009-04-06T15:37:07Z

Lantiga: /* Quick Tour of Features and Use */

2009-04-06T12:23:57Z

Quick Tour of Features and Use

Lantiga: /* Examples, Use Cases & Tutorials */

2009-04-06T12:20:18Z

Examples, Use Cases & Tutorials

Lantiga: /* Module Description */

2009-04-06T12:18:17Z

Module Description

Kikinis: /* Examples, Use Cases & Tutorials */

2009-04-06T11:19:23Z

Examples, Use Cases & Tutorials

Lantiga at 10:42, 11 February 2009

2009-02-11T10:42:09Z

@@ Line 68: / Line 68: @@
 Follow this [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Python/ link] to the module.
-[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.
+[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Links] to documentation generated by doxygen.
 == More Information ==

@@ Line 1: / Line 1: @@
 [[Documentation-3.4|Return to Slicer 3.4 Documentation]]
 __NOTOC__
 ===Module Name===

@@ Line 9: / Line 9: @@
 |}
 {|
-|[[Image:ExplodeVolumeTransform3.png|thumb|320px|Figure 3: Exploded RAS orientation volume: ijkToRAS transform + IJK volume]]
+|[[Image:ExplodeVolumeTransform3.png|thumb|320px|Figure 3: Exploded RAS volume: ijkToRAS transform + IJK volume (see MRML tree widget on the left)]]
-|[[Image:ExplodeVolumeTransform4.png|thumb|320px|Figure 4: IJK volume in Figure 2 moved under the output transform assumes RAS orientation]]
+|[[Image:ExplodeVolumeTransform4.png|thumb|320px|Figure 4: The volume loaded with IJK orientation (from Figure 2) moved under the output transform assumes RAS orientation]]
 |}

@@ Line 5: / Line 5: @@
 {|
-|[[Image:ExplodeVolumeTransform1.png|thumb|280px|Figure 1: Volume loaded with RAS orientation (orientation "From file")]]
+|[[Image:ExplodeVolumeTransform1.png|thumb|320px|Figure 1: Volume loaded with RAS orientation (orientation "From file")]]
-|[[Image:ExplodeVolumeTransform2.png|thumb|280px|Figure 2: Same volume loaded with IJK orientation]]
+|[[Image:ExplodeVolumeTransform2.png|thumb|320px|Figure 2: Same volume loaded with IJK orientation]]
 |}
 {|
-|[[Image:ExplodeVolumeTransform3.png|thumb|280px|Figure 3: Exploded RAS orientation volume: ijkToRAS transform + IJK volume]]
+|[[Image:ExplodeVolumeTransform3.png|thumb|320px|Figure 3: Exploded RAS orientation volume: ijkToRAS transform + IJK volume]]
-|[[Image:ExplodeVolumeTransform4.png|thumb|280px|Figure 4: IJK volume in Figure 2 moved under the output transform assumes RAS orientation]]
+|[[Image:ExplodeVolumeTransform4.png|thumb|320px|Figure 4: IJK volume in Figure 2 moved under the output transform assumes RAS orientation]]
 |}

@@ Line 3: / Line 3: @@
 ===Module Name===
 Python Explode Volume Transform
 == General Information ==

@@ Line 29: / Line 29: @@
 ===Quick Tour of Features and Use===
 List all the panels in your interface, their features, what they mean, and how to use them. For instance:
 * '''IO:'''
 ** ''Input Volume'': the input volume
-** ''Output Volume'': the output volume, the input volume with its IJKToRAS transform aligned with the XYZ axes, set as the child of the corresponding XYZToRAS transform.
+** ''Output Volume'': the output volume, the input volume aligned with the XYZ axes (IJK orientation), set as the child of the corresponding IJKToRAS transform.
 == Development ==

@@ Line 24: / Line 24: @@
 * The module is appropriate when a CLI module can only handle non-oriented images (i.e. images oriented as the XYZ axes), like pure-VTK modules.
-* The typical use is as follows: run a volume through this filter, use the output volume as input for the non-orientation-aware CLI module and place the output of this latter module under the XYZToRAS transform generated by the present module by using the MRML tree widget.
+* The typical use is as follows: run a volume through this filter, use the output volume as input for the non-orientation-aware CLI module and place the output of this latter module under the IJKToRAS transform generated by the present module by using the MRML tree widget.
-* Use case: you have data generated from a RAS-agnostic program (e.g. fiber tracts generated in Matlab) and you want to place them in your RAS oriented scene in Slicer. What you do is then to load the MR b0 volume with orientation "From file", explode its ijkToRAS Transform, load the fiber tracts and place them under the exploded transform in the MRML tree. You can then optionally right-click on the fiber tract nodes and choose "Harden transforms" in order to have the transform applied to the fiber point, so you can save them in RAS.
+* Use case: you have data generated from a RAS-agnostic program (e.g. fiber tracts generated in Matlab) and you want to place them in your RAS oriented scene in Slicer. What you do is then to load the MR b0 volume with orientation "From file", explode its ijkToRAS Transform, load the fiber tracts and place them under the exploded transform in the MRML tree (note that you may have to invert the transform beforehand if what you move under the transform is a polydata, as in this case). You can then (optionally) right-click on the fiber tract nodes and choose "Harden transforms" in order to have the transform applied to the fiber points. At this point you can save them in RAS.
 ===Quick Tour of Features and Use===

@@ Line 17: / Line 17: @@
 ===Module Description===
-This Python module takes a volume in input, computes its XYZToRAS transform by matrix manipulation, where XYZ is the local (VTK-compatible) coordinate system, and generate a XYZ-oriented volume in the MRML scene as a child of the XYZToRASTransform.
+This Python module takes a volume in input, extracts its IJKToRAS transform by matrix manipulation, where IJK is the local (VTK-compatible) coordinate system, and generates an IJK-oriented volume in the MRML scene as a child of a IJKToRAS transform node.
 == Usage ==

@@ Line 1: / Line 1: @@
- [[Documentation-3.4|Return to Slicer 3.4 Documentation]]
+[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
 __NOTOC__
 ===Module Name===
-MyModule
+Python Explode Volume Transform
 == General Information ==
 ===Module Type & Category===
-Type: Interactive or CLI
+Type: CLI
-Category: Base or (Filtering, Registration, ''etc.'')
+Category: Python Modules
 ===Authors, Collaborators & Contact===
-* Author1: Affiliation & logo, if desired
+* Luca Antiga: Mario Negri Institute
-* Contributor1: Affiliation & logo, if desired
+* Daniel Blezek: Mayo Clinic
-* Contributor2: Affiliation & logo, if desired
+* Contact: Luca Antiga, antiga@marionegri.it
 ===Module Description===
-Overview of what the module does goes here.
+This Python module takes a volume in input, computes its XYZToRAS transform by matrix manipulation, where XYZ is the local (VTK-compatible) coordinate system, and generate a XYZ-oriented volume in the MRML scene as a child of the XYZToRASTransform.
 == Usage ==
@@ Line 30: / Line 23: @@
 ===Examples, Use Cases & Tutorials===
-* Note use cases for which this module is especially appropriate, and/or link to examples.
+* The module is appropriate when a CLI module can only handle non-oriented images (i.e. images oriented as the XYZ axes), like pure-VTK modules.
-* Link to examples of the module's use
+* The typical use is as follows: run a volume through this filter, use the output volume as input for the non-orientation-aware CLI module and place the output of this latter module under the XYZToRAS transform generated by the present module by using the MRML tree widget.
 ===Quick Tour of Features and Use===
 List all the panels in your interface, their features, what they mean, and how to use them. For instance:
-* '''Input panel:'''
+* '''IO:'''
-* '''Parameters panel:'''
+** ''Input Volume'': the input volume
-* '''Output panel:'''
+** ''Output Volume'': the output volume, the input volume with its IJKToRAS transform aligned with the XYZ axes, set as the child of the corresponding XYZToRAS transform.
 == Development ==
@@ Line 46: / Line 37: @@
 ===Dependencies===
-Other modules or packages that are required for this module's use.
+Python
 ===Known bugs===
@@ Line 60: / Line 51: @@
 ===Source code & documentation===
-Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.
+Follow this [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Python/ link] to the module.
 [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.
@@ Line 68: / Line 59: @@
 ===Acknowledgment===
 ===References===