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Updates for TREC pipelines

Christopher Randolph Rhodes requested to merge int_trec into staging

Changes supporting use of pipelines in trec-adaptive-feedback project:

  • generally, accessors' and models' IDs can be set with respective argument
  • test client methods now handle response success check and variable parsing
  • implemented functional threshold segmentation and (in base.roiset) classification models; threshold is relative to dataset full range (0.0 to 1.0)
  • consequently, more tests cover base package without dependency on ilastik
  • RoiSet returned by pipelines get IDs and are registered in server session, accesible at respective endpoints
  • Pydantic models only used by FastAPI now; underlying model, accessor, and pipeline functions should interact with python objects and parameter dictionaries only
  • RoiSet filters also include minimal and diagonal height, width dimension; are applied before time-intensity pixel array operations to increase performance
  • performance improvement when passing patch stacks to ilastik pixel classifier
  • RoiSet.classify_by can optionally filter by additional classification columns, e.g. to implement intensity gating
Edited by Christopher Randolph Rhodes

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