From a12b19b5331af2f2e3d6efabc0192f2d5b31ac66 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Mon, 20 Mar 2023 14:43:40 +0000
Subject: [PATCH] tweak(pipeline): show clogging only after 30%
---
src/aliby/pipeline.py | 13 +++++++------
1 file changed, 7 insertions(+), 6 deletions(-)
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index 81fe543d..dcb807cd 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -508,11 +508,12 @@ class Pipeline(ProcessABC):
frac_clogged_traps = self.check_earlystop(
filename, earlystop, steps["tiler"].tile_size
)
- self._log(
- f"{name}:Clogged_traps:{frac_clogged_traps}"
- )
- frac = np.round(frac_clogged_traps * 100)
- pbar.set_postfix_str(f"{frac} Clogged")
+ if frac_clogged_traps > 0.3:
+ self._log(
+ f"{name}:Clogged_traps:{frac_clogged_traps}"
+ )
+ frac = np.round(frac_clogged_traps * 100)
+ pbar.set_postfix_str(f"{frac} Clogged")
else:
# stop if too many traps are clogged
self._log(
@@ -567,7 +568,7 @@ class Pipeline(ProcessABC):
"""
# get the area of the cells organised by trap and cell number
s = Signal(filename)
- df = s["/extraction/general/None/area"]
+ df = s.get_raw("/extraction/general/None/area")
# check the latest time points only
cells_used = df[
df.columns[-1 - es_parameters["ntps_to_eval"] : -1]
--
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