Omp checkpointing + duplicate spot removal - Githubissues

reillytilbury / coppafish

Python version of iss software

MIT License

4 stars 2 forks source link

Omp checkpointing + duplicate spot removal #344

Closed paulshuker closed 1 month ago

paulshuker commented 1 month ago

OMP now checkpoints itself after each tile is completed (except for the first tile which must always be computed when re-running since the OMP mean spot must be found using it for reproducibility).
OMP duplicate spots are now not saved to the notebook.
The notebook's numpy array variables can no longer be changed once already saved as it now returns a copy of the numpy array.
Better unit testing.
Unit test code coverage now logged.

Checklist

[x] I have updated the changelog.txt, if applicable.
[ ] I have bumped the software version in _version.py, if applicable.
[x] I have checked that the unit tests passed.
[x] I have checked that Minnie and/or RoboMinnie passed.
[x] I have resolved merge conflicts.

paulshuker commented 1 month ago

OMP already does prepare the zarr group "results.zarr" externally in the output directory, then it is moved by the notebook page itself when it is complete. This means I can use the semi-complete results in the output directory when re-running. I had to add a "omp_last_config.pkl" to ensure that the OMP config did not change between runs. If it does, then it does not use the semi-complete results saved to disk as a safety measure.