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

model_server/base/roiset.py

@@ -1130,7 +1130,7 @@ class RoiSetWithDerivedChannels(RoiSet):
         :return: None
         """
 
-        acc_in = self.get_patches_acc(channels=channels, expanded=False, pad_to=None).get_channels(channels)
+        acc_in = self.get_patches_acc(channels=channels, expanded=False, pad_to=None)
         if derived_channel_functions is not None:
             for fcn in derived_channel_functions:
                 der = fcn(acc_in) # returns patch stack