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spacetx / starfish

starfish: unified pipelines for image-based transcriptomics
https://spacetx-starfish.readthedocs.io/en/latest/
MIT License
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ApplyTransform.Warp.run() alters the TransformsList such that it can't be used again #1866

Open mattcai opened 4 years ago

mattcai commented 4 years ago

Description

Sometimes, starfish users may want to apply a TransformsList to multiple ImageStacks with ApplyTransform.Warp. For example, applying the same transforms to both dapi and primary ImageStacks. The issue is that TransformsList gets modified when used by ApplyTransform.Warp such that the next time it is used by ApplyTransform.Warp it can return erroneous results or throws an error.

A quick workaround is to only use each TransformsList once, and re-LearnTransform if needed.

Steps/Code to Reproduce

transforms bug gist

Expected Results

The transforms printed before and after Warp.run() are the same. No error is thrown on the second Warp.run().

Actual Results

Before: tile indices: {<Axes.ROUND: 'r'>: 0} translation: y=0.0, x=0.0, rotation: 0.0, scale: 1.0 tile indices: {<Axes.ROUND: 'r'>: 1} translation: y=-102.126, x=194.721, rotation: 0.0, scale: 1.0 tile indices: {<Axes.ROUND: 'r'>: 2} translation: y=-190.79, x=120.938, rotation: 0.0, scale: 1.0

After: tile indices: {<Axes.ROUND: 'r'>: 0, <Axes.CH: 'c'>: 2, <Axes.ZPLANE: 'z'>: 0} translation: y=0.0, x=0.0, rotation: 0.0, scale: 1.0 tile indices: {<Axes.ROUND: 'r'>: 1, <Axes.CH: 'c'>: 2, <Axes.ZPLANE: 'z'>: 0} translation: y=-102.126, x=194.721, rotation: 0.0, scale: 1.0 tile indices: {<Axes.ROUND: 'r'>: 2, <Axes.CH: 'c'>: 2, <Axes.ZPLANE: 'z'>: 0} translation: y=-190.79, x=120.938, rotation: 0.0, scale: 1.0

KeyError thrown.

davidhbrann commented 8 months ago

It looks like this issue is still present, and due to how the Axes of the selector gets updated. I had to make a deepcopy of TransformsList to warp both a dots fiducial image and an image stack.