Documentation/Nightly/Modules/Transforms - Revision history

Lasso: Moved to readthedocs

2021-01-03T03:18:26Z

Moved to readthedocs

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Lasso at 01:48, 13 April 2020

2020-04-13T01:48:38Z

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

2019-11-27T02:36:26Z

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

Lasso at 04:25, 1 November 2019

2019-11-01T04:25:05Z

Lasso: /* Examples */

2019-05-30T03:43:50Z

Examples

Lasso at 04:33, 5 December 2018

2018-12-05T04:33:16Z

Inorton: /* Transform files */

2018-09-25T20:04:43Z

Transform files

Inorton: /* Transform files */

2018-09-25T19:51:58Z

Transform files

JChris.FillionR at 20:51, 8 February 2018

2018-02-08T20:51:06Z

Hillarylia at 20:23, 29 June 2016

2016-06-29T20:23:03Z

← Older revision		Revision as of 01:48, 13 April 2020
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	{{documentation/{{documentation/version}}/module-parametersdescription}}		{{documentation/{{documentation/version}}/module-parametersdescription}}
		+
		+	Note: Linear transform edit sliders only show relative translation and rotation because a transformation can be achieved using many different series of transforms. To make this clear to users, only one transform slider can be non-zero at a time (all previously modified sliders are reset to 0 when a slider is moved). The only exception is translation sliders in "translate first" mode (i.e., when translation in global/local coordinate system button is not depressed): in this case there is a only one way how a specific translation can be achieved, transform sliders are not reset to 0. An rotation knob control widget would be a more appropriate visual representation of the behavior than sliders, but slider is chosen because it is a standard widget and users are already familiar with it.

	===Transform display options===		===Transform display options===

@@ Line 55: / Line 55: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Tutorials}}
-* Please use tutorial about [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Training loading and viewing data].
+* Please use tutorial about [[Documentation/4.0/Training|loading and viewing data]].
 <!-- ---------------------------- -->

@@ Line 149: / Line 149: @@
    [0.36608, 0.60599, 0.70623, -0.48185],
    [0, 0, 0, 1]])
 # Update matrix in transform node
-transformNode.SetAndObserveMatrixTransformToParent(transformMatrixVTK)
+transformNode.SetAndObserveMatrixTransformToParent(slicer.util.vtkMatrixFromArray(transformMatrixNP))
 </pre>

@@ Line 125: / Line 125: @@
 ===Examples===
-How to programmatically apply a transform to a transformable node:
+How to programmatically apply a [http://slicer.org/doc/html/classvtkMRMLTransformNode.html transform] to a transformable node:
- vtkNew<[http://slicer.org/doc/html/classvtkMRMLTransformNode.html vtkMRMLTransformNode]> transformNode;
- scene->AddNode(transformNode.GetPointer());
+<pre>
- ...
+vtkNew<vtkMRMLTransformNode> transformNode;
- vtkNew<vtkMatrix4x4> matrix;
+scene->AddNode(transformNode.GetPointer());
- ...
+...
- transform->SetMatrixTransformToParent( matrix.GetPointer() );
+vtkNew<vtkMatrix4x4> matrix;
- ...
+...
- vtkMRMLVolumeNode* transformableNode = ...; // or vtkMRMLModelNode*...
+transform->SetMatrixTransformToParent( matrix.GetPointer() );
- transformableNode->SetAndObserveTransformNodeID( transformNode->GetID() );
+...
 Example of moving a volume along a trajectory using a transform

@@ Line 41: / Line 41: @@
 ** Built-in colormap editor
 * MetaImage (mha), NIFTI (nii) vector volumes can be loaded as displacement field (grid) transform
 <!-- ---------------------------- -->
@@ Line 50: / Line 51: @@
 * Visualize the displacement that transforms specify: Transforms can be visualized in both 2D and 3D views, as glyphs representing the displacement vectors as arrows, cones, or spheres; regular grids that are deformed by the transform; or contours that represent lines or surfaces where the displacement magnitude has a specific value.
-* Apply transforms: You can dynamically transform a node by selecting them in the ''Transformable'' list and clicking the ''right arrow'' button. Whenever the transform changes, the transformed nodes are updated accordingly. The ''Harden Transform'' (its button is below the ''left arrow'' button) can be used for applying the transform to nodes permanently. Transforms themselves can be transformed, therefore chain of transforms can be constructed. Non-linear transforms can be concatenated too, but to to the lack of standard file format for storing concatenated inverted transforms, such composite non-linear transforms cannot be saved to file.
+* Apply transforms: You can dynamically transform a node by selecting them in the ''Transformable'' list and clicking the ''right arrow'' button. Whenever the transform changes, the transformed nodes are updated accordingly. The ''Harden Transform'' (its button is below the ''left arrow'' button) can be used for applying the transform to nodes permanently. Transforms themselves can be transformed, therefore chain of transforms can be constructed. Non-linear transforms can be concatenated, too. If non-linear transform is hardened on a volume then the volume is resampled using the same spacing and axis directions as the original volume (using linear interpolation). Extents are updated to fully contain the transformed volume. If image resampling modules are used then output image geometry and interpolator can be chosen.
 <!-- ---------------------------- -->

@@ Line 191: / Line 191: @@
 ===Transform files===
-* Slicer stores tansform in VTK classes in memory but uses ITK transform IO classes to read/write transforms to files. ITK's convention is to use LPS coordinate system as opposed to RAS coordinate system in Slicer (see [[Coordinate systems]] page for details). Conversion between VTK and ITK transform classes are implemented in [https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Core/vtkITKTransformConverter.h vtkITKTransformConverter].
+* Slicer stores transforms in VTK classes in memory, but uses ITK transform IO classes to read/write transforms to files. ITK's convention is to use LPS coordinate system as opposed to RAS coordinate system in Slicer (see [[Coordinate systems]] page for details). Conversion between VTK and ITK transform classes are implemented in [https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Core/vtkITKTransformConverter.h vtkITKTransformConverter].
 * ITK stores the transform in resampling (a.k.a., image processing) convention, i.e., that transforms points from fixed to moving coordinate system. This transform is usable as is for resampling a moving image in the coordinate system of a fixed image. For transforming points and surface models to the fixed coordinate system, one needs the transform in the modeling (a.k.a. computer graphics) convention, i.e., transform from moving to fixed coordinate system (which is the inverse of the "image processing" convention).
 * Transform nodes in Slicer can store transforms in both modeling (when ToParent transform is set) and resampling way (when FromParent transform is set). When writing transform to ITK files, linear transforms are inverted as needed and written as an AffineTransform. Non-linear transforms cannot be inverted without losing information (in general), therefore if a non-linear transform is defined in resampling convention in Slicer then it is written to ITK file using special "Inverse" transform types (e.g., InverseDisplacementFieldTransform instead of DisplacementFieldTransform). Definition of the inverse classes are available in [https://github.com/Slicer/Slicer/blob/master/Libs/MRML/Core/vtkITKTransformInverse.h vtkITKTransformInverse]. The inverse classes are only usable for file IO, because currently ITK does not provide a generic inverse transform computation method. Options to manage inverse transforms in applications:

@@ Line 199: / Line 199: @@
 * Transforms module in Slicer shows linear transform matrix values in RAS coordinate system, according to resampling convention. Therefore to retrieve the same values from an ITK transforms as shown in Slicer GUI, one has switch between RAS/LPS and modeling/resampling:
 <pre>
 // Convert from LPS (ITK) to RAS (Slicer)
@@ Line 214: / Line 215: @@
 // Convert the sense of the transform (from ITK resampling to Slicer modeling transform)
 vtkMatrix4x4::Invert(transformVtk_RAS);
 </pre>

@@ Line 27: / Line 27: @@
 Features:
-* Short video demonstrating the main features: http://screencast.com/t/Z6dQVjK3m
+* '''Short video demonstrating the main features:''' http://screencast.com/t/Z6dQVjK3m
 * Support non-linear transforms in the Transforms module: allow Apply, Harden, Invert transform
 * Transform information displayed in the Transforms module (type of transform, basic properties)