Initialize nonzero_pixels_dict in reconstruction - Githubissues

PolarizedLightFieldMicroscopy / GeoBirT

Geometrical Birefringence Tomography

BSD 3-Clause "New" or "Revised" License

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Initialize nonzero_pixels_dict in reconstruction #79

Closed gschlafly closed 6 months ago

gschlafly commented 6 months ago

Description

The mask is not able to be indexed because it is a 1D array instead of a 2D array. https://github.com/PolarizedLightFieldMicroscopy/GeoBirT/blob/8e36b81ad4bb45202409d7e2f7fedd6f3c3f7905/VolumeRaytraceLFM/birefringence_implementations.py#L1575-L1577

The mask is also a 1D array when created from the mla_image. https://github.com/PolarizedLightFieldMicroscopy/GeoBirT/blob/8e36b81ad4bb45202409d7e2f7fedd6f3c3f7905/VolumeRaytraceLFM/abstract_classes.py#L578-L614

Files

birefringence_implementations.py
abstract_classes.py
run_recon.py

To Reproduce

Run run_recon.py.

gschlafly commented 6 months ago

Before identify_rays_from_pixels_mla() is called, self.nonzero_pixels_dict[(0,0)] is a 2D array.