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segmenter: fix EcoTaxa import errors#953

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sonnyp merged 2 commits into
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fix/ecotaxa-import-errors
May 5, 2026
Merged

segmenter: fix EcoTaxa import errors#953
sonnyp merged 2 commits into
mainfrom
fix/ecotaxa-import-errors

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@babo989

@babo989 babo989 commented May 4, 2026

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"Fixes two EcoTaxa import blockers reported by Jeremy (issues
fairscope/PlanktoScope3#270, #521):

  • `object_contour` exceeds EcoTaxa's 250-char column limit. The polygon emitted in segmenter: emit object_contour polygon for audit visualizer #940 for the audit visualizer is now excluded from
    the TSV. It stays in the per-object metadata.json so the audit visualizer keeps working.
  • `Ecotaxa_*` archive/TSV prefix uses a capital E, which EcoTaxa rejects. Lowercased to `ecotaxa_*` in both the zip filename
    (`init.py`) and the TSV filename (`ecotaxa.py`).
  • Cleanup of the filename duplication (`Ecotaxa_yotel_4501_yotel_4501_A_004`): the imager's directory layout
    already gives `acq_id = <sample_id>_`, so the redundant prefix is stripped before the ID is concatenated. Now produces
    `ecotaxa_yotel_4501_A_004.zip`.

@sonnyp sonnyp changed the title segmenter: fix EcoTaxa import errors (contour length + lowercase prefix) segmenter: fix EcoTaxa import errors May 5, 2026
@sonnyp sonnyp merged commit 7ee96c6 into main May 5, 2026
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@sonnyp sonnyp deleted the fix/ecotaxa-import-errors branch May 5, 2026 12:59
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2 participants