Write composite transforms from antsApplyTransforms#1839
Merged
Conversation
Previously, we only allowed writing a composite displacement field or affine, ie all transforms had to be collapsed into one output transform. See new output options for antsApplyTransforms. We preserve the option -o [compositeDisplacement.nii.gz, 1] for backwards compatibility. DOC: Change log message for imageio checks - this confused some antspy users. DOC: Document new functionality in CompositeTransformUtil
To avoid confusion, use Composite in output to mean composite transforms. Use "collapsed" to mean things composed into a single transform. Composite means a reversible process (ie, you can separate the components again).
Member
Author
|
Some tests |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
antsApplyTransforms only allowed users to collapse linear transforms into a single .mat file, or composite transforms into a single displacement field.
Now allow users to write the full composite transform. This enables users familiar with
antsApplyTransformsto write out composite transforms by specifying the components in the order they are applied when warping images. That is, one can callantsApplyTransforms -o warpedImageand thenantsApplyTransforms -o CompositeTransform[composite.h5]without changing the-toptions.The motivation is to make it easier to write composite transforms, since CompositeTransformUtil requires users to use the internal "reverse queue order" of itkCompositeTransform.
The changes are backwards compatible, but I have noted in the usage that we prefer
-o DisplacementField[ field.ext ]to
-o [ field.ext, 1 ]Thus the output options are