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Support falcon datasets with latest micromanager #237

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merged 13 commits into from
Nov 12, 2024

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talonchandler
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@talonchandler talonchandler commented Aug 6, 2024

This PR adds support for

Tested on:
Input: /hpc/instruments/cm.falcon/zebrafish/20240808_coro1a_mpeg_1dpf_10x/fish_with_coro1a_1/
Output: /hpc/projects/balla_group/imaging/zebrafish_infection/falcon/2024_08_08_coro1a_mpeg_1dpf_10x/0-zarr/timelapse1.zarr

@ieivanov the new Tile Creator prefix format might affect OPS in this future, so I'm requesting your review.
@dsundarraman heads up that we need to convert with this branch going forward.

TODO:

  • add tests that xy_stage = pos.get("DefaultXYStage"); stage_pos = pos.get(xy_stage) handles all previous cases

@talonchandler talonchandler marked this pull request as ready for review August 10, 2024 00:26
iohub/mm_fov.py Outdated Show resolved Hide resolved
@ziw-liu ziw-liu added enhancement New feature or request μManager Micro-Manager files and metadata labels Sep 11, 2024
@ahillsley
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Does it make sense to remove the naming convention and replace with the new? Can we just add a new try / except so that it can handle both old and new?

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ieivanov commented Nov 9, 2024

Does it make sense to remove the naming convention and replace with the new? Can we just add a new try / except so that it can handle both old and new?

We are trying to keep this code clean, so I'd prefer fixing this issue properly rather than adding switch cases. I'll make time to test this, help from @ziw-liu or @talonchandler confirming that xy_stage = pos.get("DefaultXYStage"); stage_pos = pos.get(xy_stage) handles all previous cases is welcome too.

@ieivanov ieivanov requested a review from ahillsley November 9, 2024 20:28
@ieivanov
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ieivanov commented Nov 9, 2024

Tested and ready to merge after review

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Code looks good. Thanks!

@ieivanov ieivanov merged commit 1957ea0 into main Nov 12, 2024
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@ieivanov ieivanov deleted the support-falcon-stage-positions branch November 12, 2024 19:49
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4 participants