workflow_v2 branch change log

Change log in src/ophys_etl/modules

1. allow trace extraction to work with 0 ROIs
   a. allow trace extraction to work with 0 rois · AllenInstitute/ophys_etl_pipelines@001a46e (github.com)

2. change np.int and np.float to 'int' and 'float' for compatibility with newer numpy versions where these are deprecated

3. denoising fine-tuning
   a. improve logging for debugging issues
   b. add support for downsample

4. trace extraction
   a. allow trace extraction to work with zero ROIs

5. postprocess_rois
   a. include logic to ensure any empty ROI is removed

6. event detection
   a. remove code dependent on the package FastLZero so it does not need to be imported. Reduplicate the code in the codebase. This is to fix import issues with that package.

7. modified motion border check to not flag ROIs that are touching the border. The previous logic flagged ROIs that were touching the right or bottom borders but not the top or left borders.

For deeper detail, see this PR on main. Only look at the comparisons of the code in the modules directory.

Exclusion label updates

Several exclusion labels were deprecated since they are detected by the classifier or are handled by the segmentation. Note that the proposed is_cell that's generated by the ROI classifier is not yet implemented anywhere in the pipeline. This will need to be done.

See here for a comprehensive list of exclusion labels as well as the decisions to exclude them. https://alleninstitute-brainscience.atlassian.net/browse/PSB-83?focusedCommentId=82922

Planned changes

1. parallelize neuropil subtraction main loop