fix(baby_sitter): bug in getdata

Data now passed with x and y in the correct order;
References to session removed from BabyParameters

src/aliby/baby_sitter.py

@@ -10,7 +10,7 @@ from agora.abc import ParametersABC, StepABC
 
 
 class BabyParameters(ParametersABC):
-    """Parameters used for analysing the results from BABY."""
+    """Parameters used for running BABY."""
 
     def __init__(
         self,
@@ -18,7 +18,6 @@ class BabyParameters(ParametersABC):
         clogging_thresh,
         min_bud_tps,
         isbud_thresh,
-        session,
     ):
         """Initialise parameters for BABY."""
         # pixel_size is specified in BABY's model sets
@@ -26,7 +25,6 @@ class BabyParameters(ParametersABC):
         self.clogging_thresh = clogging_thresh
         self.min_bud_tps = min_bud_tps
         self.isbud_thresh = isbud_thresh
-        self.session = session
 
     @classmethod
     def default(cls, **kwargs):
@@ -36,7 +34,6 @@ class BabyParameters(ParametersABC):
             clogging_thresh=1,
             min_bud_tps=3,
             isbud_thresh=0.5,
-            session=None,
         )
 
     def update_baby_modelset(self, path: t.Union[str, Path, t.Dict[str, str]]):
@@ -85,7 +82,6 @@ class BabyRunner(StepABC):
                 clogging_thresh=parameters.clogging_thresh,
                 min_bud_tps=parameters.min_bud_tps,
                 isbud_thresh=parameters.isbud_thresh,
-                session=parameters.session,
             )
         self.crawler = BabyCrawler(brain)
         self.brightfield_channel = self.tiler.ref_channel_index
@@ -98,10 +94,8 @@ class BabyRunner(StepABC):
     def get_data(self, tp):
         """Get image and re-arrange axes."""
         img_from_tiler = self.tiler.get_tp_data(tp, self.brightfield_channel)
-        # move z axis to the last axis
-        img_z_at_end = np.moveaxis(img_from_tiler, 1, destination=-1)
-        # move y axis before the x axis
-        img = np.moveaxis(img_z_at_end, 2, destination=1)
+        # move z axis to the last axis; Baby expects (n, x, y, z)
+        img = np.moveaxis(img_from_tiler, 1, destination=-1)
         return img
 
     def _run_tp(

src/aliby/pipeline.py

 """Set up and run pipelines: tiling, segmentation, extraction, and then post-processing."""
+
 import logging
 import os
 import re
@@ -15,7 +16,7 @@ from pathos.multiprocessing import Pool
 from tqdm import tqdm
 
 try:
-    if baby.__version__ == "v0.30.1":
+    if baby.__version__:
         from aliby.baby_sitter import BabyParameters, BabyRunner
 except AttributeError:
     from aliby.baby_client import BabyParameters, BabyRunner
@@ -178,6 +179,7 @@ class Pipeline(ProcessABC):
             for k in ("host", "username", "password")
         }
         self.expt_id = config["general"]["id"]
+        self.setLogger(config["general"]["directory"])
 
     @staticmethod
     def setLogger(
@@ -233,7 +235,6 @@ class Pipeline(ProcessABC):
             print("\t" + f"{i}: " + pos.split(".")[0])
         # add directory to configuration
         self.parameters.general["directory"] = str(directory)
-        self.setLogger(directory)
         return position_ids
 
     def channels_from_OMERO(self):
@@ -464,8 +465,7 @@ def check_earlystop(filename: str, es_parameters: dict, tile_size: int):
     )
     # find tiles with cells covering too great a fraction of the tiles' area
     traps_above_athresh = (
-        cells_used.groupby("trap").sum().apply(np.mean, axis=1)
-        / tile_size**2
+        cells_used.groupby("trap").sum().apply(np.mean, axis=1) / tile_size**2
         > es_parameters["thresh_trap_area"]
     )
     return (traps_above_nthresh & traps_above_athresh).mean()