Integrate pymmcore-plus port and autotracker #186
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…into autotracker
…umes that there are shifts computed and returned.
…into autotracker
small fix on phase cross corr
printing positions in the same order
Update printing positions and logging
use t=0 as reference
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
Co-Authored-By: Taylla Milena Theodoro <[email protected]>
Co-Authored-By: Taylla Milena Theodoro <[email protected]>
Co-Authored-By: Taylla Milena Theodoro <[email protected]>
Co-Authored-By: Taylla Milena Theodoro <[email protected]>
* add autotracker stall debugging * abort stalled O3 autofocus * add phase reconstruction * update pcc removing padding * bug fix * clean gpu * keep track of gpu vars * autotracker debug Co-Authored-By: Taylla Milena Theodoro <[email protected]> * clip shift_zyx Co-Authored-By: Taylla Milena Theodoro <[email protected]> * update limits Co-Authored-By: Taylla Milena Theodoro <[email protected]> * remove log transform from PCC and adding max shift Co-Authored-By: Taylla Milena Theodoro <[email protected]> --------- Co-authored-by: Taylla Theodoro <[email protected]>
Co-Authored-By: Taylla Milena Theodoro <[email protected]>
Co-Authored-By: Taylla Milena Theodoro <[email protected]>
Co-Authored-By: Taylla Milena Theodoro <[email protected]>
Co-Authored-By: Taylla Milena Theodoro <[email protected]>
* 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
Co-Authored-By: Taylla Milena Theodoro <[email protected]>
* debug - don't use PM for O3 autofocus * add deprecation note
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This PR is meant to promote integration of 2 different development branches, so the developers of each can remain aware of each other's work and can align on design decisions.
It is not necessarily intended to be merged.