Phase reconstruction is invariant to voxel-size #164
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ziw-liu
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Apr 16, 2024
ziw-liu
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Apr 23, 2024
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talonchandler
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Jul 5, 2024
* Phase reconstruction is invariant to voxel-size (#164) * fix bug finding focus in stack with only one slice * refactor for clarify * formatting * print -> warnings.warn * test single-slice case * fix test bugs * z-scale-invariant test object * no rescaling on output * forward simulation takes a "brightness" - simulating real microscope * fix example script * add background parameter for fluorescence forward model * test voxel-size invariance * rename I_norm -> direct_intensity * refactor to clarify discretization factor * remove comment * fix fluorescence example bug * improved docsring --------- Co-authored-by: Ivan Ivanov <[email protected]> * np.product -> np.prod --------- Co-authored-by: Ivan Ivanov <[email protected]>
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This PR is paired with a confluence page with more context.
Before: phase reconstructions varied with the square of the z step size.
After: phase density reconstructions are invariant to the z step size.
This PR:
Note: this is a PR to
alg-dev, a new branch from main that I will develop on for the next few PRs. My commit history is not clean (git accident), but this PR's diff is clean.