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Vector-optics birefringence reconstruction prototype #170

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talonchandler and others added 8 commits April 23, 2024 14:25
* 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

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Co-authored-by: Ivan Ivanov <ivan.ivanov@czbiohub.org>
Base automatically changed from alg-dev to main July 5, 2024 20:52
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