From dd4965ab2e9c44473beb3e5d0d8a93ae03810e71 Mon Sep 17 00:00:00 2001
From: Peter Swain <peter.swain@ed.ac.uk>
Date: Fri, 23 Feb 2024 14:09:27 +0000
Subject: [PATCH] change(pipeline): works for all Baby versions
---
src/aliby/pipeline.py | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index c05bc3b..ace2816 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()
--
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