On-the-fly Reconstruction

[clinton-huynh]

This PR is to add the feature that will update live reconstructions onto napari during a running MDA.

NOTES:

• Can only do phase or birefringence reconstruction.
• This program only works for a custom micromanager build (currently on branch ometiff_getters of mehta-lab/micro-manager, which will be getting a PR).
• Currently hard coding the paths of the transfer function, reconstructed data, configuration settings, and a temporary zarr array (for birefrigence overlay zarr).
• Adapted only for the "Image stack file" (OME-TIFF) and "NDTiff" save formats.

How to run:

1. Calibrate the microscope for reconstruction.
2. Configure the settings of the MDA.
3. Run the command python script converted_zarr_file type_of_reconstruction.
   Example: python recOrder/recOrder/scripts/listener_and_opener.py /converted.zarr birefringence

Possible Improvements:

• Implement a way to customize the various paths in a more user friendly way.
• Refactoring the different reconstruction types and save formats so that constant if/else checks are reduced.
• Implement a thread pool design so that multiple reconstructions may go off and not have a single thread do all the reconstructions in a queue.

[ziw-liu]

Should we target the live-recon-compatibility branch instead?

[deprecated-napari-hub-preview-bot]

Preview page for your plugin is ready here:
https://preview.napari-hub.org/mehta-lab/recOrder/393
Updated: 2023-08-03T18:26:25.285979

[talonchandler]

I'm going to move this to draft, and we will almost certainly cherry pick useful snippets during the upcoming make-a-thon.