Affine registration

[jboulanger]

Description

Intensity based affine registration of image pairs.

• estimate a transform to register the moving image using ndi.affine_transform
• supports 2d and 3d images
• supports color image using channel_axis parameter (more flexible for 3d images)
• supports affine, euclidean and translation motion models using a string parameter
• supports weights/mask to use only a part of the image. Modifies the normalized_mutual_information to support weights.
• includes 2 solvers: lucas kanade [1] and studholme [2,3] parametrized as functions callback
• related to PR 3544 and 7050. The studholme solver is inspired heavily from PR 3544.
• include an quantification of alignment error (target registration error)

The API tries to take inspiration from the PR3455, however I found it not very user friendly to pass callback for handling euclidean or translation motion model. Moreover the logic is different between the two solvers and could not find a way to conciliate the previously discussed API with the added solver. PR3455 was relying on transforms in the example to handle restricted model (euclidean) which is not compatible with ndi.affine_transform, here we stick to ndi.affine_transform to ba able to handle 3D images.

Comparison bewteen the solvers and cv2.findTransformECC. The 2nd row display the registration error map.

Registration of a brain MRI volume

TODO

• euclidean is not implemented for lucas kanade solver for dimension > 2.

References

1. algo_affine
2. Studholme C, Hill DL, Hawkes DJ. Automated 3-D registration of MR and CT images of the head. Med Image Anal. 1996 Jun;1(2):163-75.
3. J. Nunez-Iglesias, S. van der Walt, and H. Dashnow, Elegant SciPy: The Art of Scientific Python. O’Reilly Media, Inc., 2017.

Checklist

• A descriptive but concise pull request title
• Docstrings for all functions
• Unit tests
• A gallery example in ./doc/examples for new features
• Contribution guide is followed (as much as possible)

Release note

For maintainers and optionally contributors, please refer to the instructions on how to document this PR for the release notes.

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