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Migrate to datajoint v2 - #74

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thomasZen wants to merge 53 commits into
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migration/datajointv2
Open

thomasZen wants to merge 53 commits into
masterfrom
migration/datajointv2

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@thomasZen

@thomasZen thomasZen commented Aug 5, 2026

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This branch already has changes from #72 integrated.

When testing the tutorial schema, make sure to create a new config based on https://github.com/eulerlab/djimaging/blob/migration/datajointv2/djimaging/djconfig/djconf_template.json, adapt the path for processed files, and run the make_user.py script to have access to the updated example notebook, and the mentioned folders for the processed files have to exists already.

The example notebook then partially works already, I have to rerun it and will check it again, though.

Other notes

  • Rewrote classifier to make it compatible with scikit-learn-1.7: /gpfs01/euler/data/Resources/Classifier_v2/rgc_classifier_v2_sklearn_1_7.pkl
  • Most files will be written as blobs into the database, only big files will be written as files (for the tutorial notebook the only file was stim_trace_vAsiIasY.npy with 3.4 MB)

To check

Moving Bar Stimulus warning

Stimulus().add_movingbar(
    ntrigger_rep=1,
    trial_info=[0, 180, 45, 225, 90, 270, 135, 315],
    bardx=300,
    bardy=1000,
    velumsec=1000,
    tmovedurs=4.0,
    skip_duplicates=True,
)
[djimaging/tables/core/stimulus.py:66](http://localhost:4444/lab/workspaces/auto-R/tree/GitRepos/djimaging/djimaging/user/dj_v2_try3_tz/notebooks/GitRepos/djimaging/djimaging/tables/core/stimulus.py#line=65): UserWarning: Number of triggers in trial_info=8 must match ntrigger_rep=1.
  warnings.warn(msg)

To test

  • CellAssignment
  • AutoRoi (the example data already had roi masks for all cells)

@thomasZen thomasZen changed the title WIP: Migrate to datajoint v2 Migrate to datajoint v2 Sep 10, 2026
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3 participants