angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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Update progress bar for helpful debugging #1028

Closed camisowers closed 1 year ago

camisowers commented 1 year ago

Is your feature request related to a problem? Please describe. It would be useful to include the FOV name in any progress bar outputs, so that when something goes wrong during processing the user can know exactly at which point the problem occurred.

Describe the solution you'd like

  1. Implement progress bars for any major processing functions that do not have them.
    • fiber segmentation
  2. Update any existing progress bars to have the FOV name in the output.
  3. For functions that already include the FOV name, make sure to update the name at the beginning of processing and not the end.
    • Currently, the FOV name and the completion status are updated once processing is complete; this results in the previous FOV name still displayed when the function errors out.

Describe alternatives you've considered An atrocious amount of print statements to let the user know which FOV is being processed.

Additional context We can also implement this progress bar structure in toffy as well (most useful for longer processing such as rosetta and normalization).