diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py index c05bc3b12b4f2944e7f6a482a26c1559a10a6e62..ace28169afcb5f6cd2163c6ce702c4169403e7f9 100644 --- a/src/aliby/pipeline.py +++ b/src/aliby/pipeline.py @@ -19,7 +19,7 @@ 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 @@ -420,6 +420,7 @@ class Pipeline(ProcessABC): "state": loaded_writers["state"].datatypes.keys(), "baby": ["mother_assign"], } + breakpoint() # START PIPELINE frac_clogged_traps = 0.0 @@ -730,7 +731,8 @@ 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()