Write composite transforms from antsApplyTransforms #1839
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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).
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Some tests |
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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