Dimensions fix for retrieving voxel properties

gschlafly commented 3 months ago

Description

After the commit https://github.com/PolarizedLightFieldMicroscopy/GeoBirT/commit/cbda36702f2d14321b06af416b769b4f2d26579b, modifying the for-loop for matrix multiplication, the reconstruction process fails when using only the restricted set of parameters.

Screenshots

Files

https://github.com/PolarizedLightFieldMicroscopy/GeoBirT/blob/cbda36702f2d14321b06af416b769b4f2d26579b/src/VolumeRaytraceLFM/birefringence_implementations.py#L2149-L2151

To Reproduce

Run the function recon_voxel() which includes the command reconstructor.reconstruct(all_prop_elements=False).

Tasks

[ ] Inspect the dimensions of volume.optic_axis_planar. I do know why this variable is different than volume.optic_axis_active.
[ ] Add a pytest that tests this aspect of the reconstruction process. This issue currently exists even though all current tests pass.

gschlafly commented 3 months ago

I found that running reconstructor.reconstruct(all_prop_elements=True) also failed because some properties were undefined. However, setting recon_config.interation_parameters["two_optic_axis_components"] = False before creating the reconstructor allowed the reconstruction process to run properly. We still also want to be able to reconstruct from just the two optic axis components.

gschlafly commented 3 months ago

This line of code is actually causing the error first: https://github.com/PolarizedLightFieldMicroscopy/GeoBirT/blob/cbda36702f2d14321b06af416b769b4f2d26579b/src/VolumeRaytraceLFM/birefringence_implementations.py#L2146-L2148 Relevant dimensions

gschlafly commented 3 months ago

Fixed by 5c7bdabcf3f9022348e700079c8f9dbec7ec37c3

PolarizedLightFieldMicroscopy / BirTomo