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PhenoBase and RoiSet upgrade

Merged Christopher Randolph Rhodes requested to merge dev-phenobase into master

Modified RoiSet and PhenoBase API:

  • added test coverage of PhenoBase client
  • simplified handling pipelines that return RoiSets
  • removed need to work around accessor and model validation when running pipelines outside of call_pipeline wrapper functions
  • PhenoBase now maintains a registry of RoiSets indexed by coordinate dicts
  • PhenoBase calls a single add_roiset method when populating both interactively and with batch read method
  • a PhenoBase can be empty, in which case it defers setting coordinate keys and patch series until a first RoiSet is added
  • RoiSet serializes and deserializes its source image accessor (by reference to pre-existing file, if relevant)
  • RoiSet maintains label keys of its classification model(s); PhenoBase makes no assumptions about what these are named
  • PhenoBase can output patches by classification class
  • refactored how split, sampled PhenoBase subsets are implemented; removed filtering method except in specific case of filtering by classification

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