View source for Handling deformable transforms in Slicer meeting minutes

=== Operations ===
* Harden transform
*: 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.
* Clone and harden
*: Clone and harden* differs from the current *Harden transform* capability in two ways:
*# Instead of the data being moved outside of all transforms, a "copy" of the data will be moved outside of all transforms.
*# All transform types, linear and deformable, will be part of the hardening.

=== Proposed data type support ===
* Scalar volumes
* Vector volumes
** RGB
** Vector
** Displacement field
* Tensor volumes
* Models
* Fiducials and annotations
* Multivolume

=== Questions ===
* Should we maintain a link between the original and hardened data?
* Should only the hardened version be available for visualization?
** Probably yes, but display a warning on hardening
* Can you clone and harden part of the transform hierarchy?
*: Harden just the non-linear portions
* Which tools do we use for each type of data to harden/warp the data?
* When hardening applied, the user would be presented with a list of modules that can harden each type of data?
* What happens to
** pixel lattice - stays the "same"
*** create an axis-aligned bounding box in the world space, the number of pixels along each dimension will change
** spacing - affected by the transform
** orientation - affected by the transform

=== Design ===
* Level of performing the hardening
** Application level: module can register itself as the capable of hardening certain types of data.
*** For now the modules containing the algorithms (BRAINSResample, Resample Scalar/Vector/DWI Volume) will be known by the class performing the hardening
** Logic level
* Need to know the inverse of each transform
** to transform the models and fiducials
** to figure out how to define an appropriate lattice
*** 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 (still cloned)
** Resample into lattice that bounds the warping of the edge/face voxels
** Resample into a target volume
* Where?
** 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
** Subject Hierarchy right-click -> apply transform to branch
* Look at the logic of handling transforms in DICOM

=== Subject hierarchy ===

* Transforms resulting from registration point back to the fixed and moving images.  This information is stored in the *attributes* of the hierarchy node.
* Should we use the DICOM frame of reference concepts (frame of reference UID).
* Transform map between two frames of references.
* Currently, Slicer combines two concepts:
** Frame of reference
*** Everything "under" a transform is in the same frame of reference
** Transform that maps between two frames of references
*** The two frames of reference are implicitly defined by the transform hierarchy