Handling deformable transforms in Slicer meeting minutes - Revision history

Pinter at 15:31, 18 June 2013

2013-06-18T15:31:29Z

Pinter at 15:25, 18 June 2013

2013-06-18T15:25:59Z

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2013-06-18T13:55:15Z

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* Should it be handled on what level?
** MRML level (Transformable, VolumesLogic?)
** '''Using modules (BRAINSResample, Resample Scalar/Vector/DWI Volume)''' - Subject Hierarchy would know what module can transform what objects using what transforms and use them
* Invertability / reversibility
** '''Should it create clones of the 'hardened' objects?''' - in Subject Hierarchy
** Should we maintain a history in the hardened nodes?
** '''Harden option on drop (I can't display but can resample)''' - in Data and Transforms modules
* Plugin mechanism for registering non-linear transforms
** Modules register themselves in the fashion "I can apply X type of transform to Y type objects"
*** The application could call these algorithms (instead of registering from outside)
** GUI decision if hardened
* Where?
** Data module
** Transforms module (display tree, and add a 'Harden' button to the panels)
** Subject Hierarchy right-click -> apply transform to branch
* Harden all the way up or until all the parents are linear or just one level a time?
* Extend to contain bounding box
** In case of non-linear transforms, go down the edges to specify the output bounding box
** Options: resample in source lattice (still cloned), the one above, rsample in target volume

Ideas
* Look at the DICOM transform logic
** Make frame of reference concept explicit in Slicer?

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 * Should we maintain a link between the original and hardened data?
 * Should only the hardened version be available for visualization?
 * Can you clone and harden part of the transform hierarchy?
 *: Harden just the non-linear portions
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 === Design ===
-* Module can register itself as the capable of hardening certain types of data.
+* Level of performing the hardening
-** For now the modules containing the algorithms (BRAINSResample, Resample Scalar/Vector/DWI Volume) will be known by the class performing the hardening
+** Application level: module can register itself as the capable of hardening certain types of data.
 * Need to know the inverse of each transform
 ** to transform the models and fiducials
@@ Line 39: / Line 42: @@
 *** need to back transform all the edge/face voxels to find the bounding box in the world space
 * Three options presented to the user
-** Resample in source lattice
+** Resample in source lattice (still cloned)
 ** Resample into lattice that bounds the warping of the edge/face voxels
 ** Resample into a target volume
@@ Line 46: / Line 49: @@
 ** Transforms module: display tree, and add a 'Harden' button to the panels
 ** Subject Hierarchy right-click -> apply transform to branch
 === Subject hierarchy ===

@@ Line 1: / Line 1: @@
-* Should it be handled on what level?
+=== Operations ===
-** MRML level (Transformable, VolumesLogic?)
+* Harden transform
-** '''Using modules (BRAINSResample, Resample Scalar/Vector/DWI Volume)''' - Subject Hierarchy would know what module can transform what objects using what transforms and use them
+*: Harden transform* is an existing capability that collapses linear transforms in a transform hierarchty.  Hardening is available as a context menu on a (data) node in the Data module. When hardened, the data object is moved in the Data module to be outside all transformations with the effect of the transform hierarchy applied. *Harden transform* is only available for transform hierarchies involving linear transforms.
-* Invertability / reversibility
+* Clone and harden
-** '''Should it create clones of the 'hardened' objects?''' - in Subject Hierarchy
+*: Clone and harden* differs from the current *Harden transform* capability in two ways:
-** Should we maintain a history in the hardened nodes?
+*# Instead of the data being moved outside of all transforms, a "copy" of the data will be moved outside of all transforms.
-** '''Harden option on drop (I can't display but can resample)''' - in Data and Transforms modules
+*# All transform types, linear and deformable, will be part of the hardening.
-* Plugin mechanism for registering non-linear transforms
-** Modules register themselves in the fashion "I can apply X type of transform to Y type objects"
+=== Proposed data type support ===
-*** The application could call these algorithms (instead of registering from outside)
+* Scalar volumes
-** GUI decision if hardened
+* Vector volumes
 * Where?
-** Data module
+** Tie into the drag and drop of the Data module and prompt the user to harden the transform.
-** Transforms module (display tree, and add a 'Harden' button to the panels)
+** Transforms module: display tree, and add a 'Harden' button to the panels
 ** Subject Hierarchy right-click -> apply transform to branch
-Ideas
+=== Subject hierarchy ===
-* Look at the DICOM transform logic
-** Make frame of reference concept explicit in Slicer?
+* Transforms resulting from registration point back to the fixed and moving images.  This information is stored in the *attributes* of the hierarchy node.