O3-autofocus-merge #207
O3-autofocus-merge #207
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Update author metadata format in CITATION.cff
* add stir_plate CLI * docs and check for empty pos list * use logging instead of click.echo * style
* check min exp time * check for demo mode after validating illumination.csv file * bugfixes and extensions * bugfix * style
* abort stalled O3 autofocus * add note on hardcoded value
* add extra logging and make sure O3 will not run outside of travel range * fix bug in galvo positioning during o3 refocus * set o3 stage position at beginning of new acquisition
mantis/acquisition/acq_engine.py
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This will be undone in a subsequent zarr-focused PR.
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Thanks, this looks good to me. The O3 autofocus currently is a fragile and evolving feature. I just merged #205 which reflects the latest use case. You're welcome to pull these changes in this PR or open a separate one. A bit more context, we've deprecated the KinesisPiezoMotor stage, and we are currently setting use_pycromanager=False in acquire_ls_defocus_stack, i.e. using mmc directly to fetch images rather than running a pycromanager acquisition. We've found that pycromanager acquisitions would stall infrequently, but often enough to break multi-day acquisitions, and getting images through mmc directly is more robust; this will probably be better with pymmcore-plus. All in all, after the mantis rebuild we discussed we won't be running O3 autofocus as it currently stands, so it's OK if you don't worry much about it at this point.
Merge Ivan's changes to O3 refocus into pymmcore-plus development branch. As a side-effect, this gets O3 working in pymmcore-plus.