From 0d3bb03f77c23b3a63789498a6f12abeb0dd58d4 Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Thu, 22 Feb 2024 16:56:18 +0000
Subject: [PATCH] fix(pipeline): baby.errors.BadOutput caught
---
src/aliby/pipeline.py | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index 24a19d7..ab287da 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -386,7 +386,11 @@ class Pipeline(ProcessABC):
result = babyrunner.run_tp(i)
except baby.errors.Clogging:
self.log(
- "WARNING:Clogging threshold exceeded in BABY."
+ "WARNING: Clogging threshold exceeded in BABY."
+ )
+ except baby.errors.BadOutput:
+ self.log(
+ "WARNING: Bud has been assigned as its own mother."
)
baby_writer.write(
data=result,
@@ -471,7 +475,8 @@ 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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