Updates for TREC pipelines
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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added 4 commits
- ee2d250e - Method to test whether accessor can be used as a mask
- ef72ee95 - IntensityThresholdInstanceMaskSegmentationModel enforces a mono image but...
- be6040f3 - Int64 type was causing issues downstream in eval/query calls; Int16 is adequate
- 1819a0f6 - Removed aggregation method, instead can filter by other classification results
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