From 5ca4082123e444543e98a0a006345aaa1e37fb5f Mon Sep 17 00:00:00 2001
From: Peter Swain <peter.swain@ed.ac.uk>
Date: Wed, 6 Dec 2023 13:55:27 +0000
Subject: [PATCH] change(retained): default cutoff is 0
---
src/agora/io/signal.py | 4 +---
src/aliby/global_parameters.py | 3 ---
2 files changed, 1 insertion(+), 6 deletions(-)
diff --git a/src/agora/io/signal.py b/src/agora/io/signal.py
index 158d522..52b3122 100644
--- a/src/agora/io/signal.py
+++ b/src/agora/io/signal.py
@@ -101,9 +101,7 @@ class Signal(BridgeH5):
)
return 300
- def retained(
- self, signal, cutoff=global_parameters.signal_retained_cutoff
- ):
+ def retained(self, signal, cutoff=0):
"""Get retained cells for a Signal or list of Signals."""
if isinstance(signal, str):
# get data frame
diff --git a/src/aliby/global_parameters.py b/src/aliby/global_parameters.py
index 9fa29a4..92b58f8 100644
--- a/src/aliby/global_parameters.py
+++ b/src/aliby/global_parameters.py
@@ -36,6 +36,3 @@ fluorescence_functions = [
"imBackground",
"max5px_median",
]
-
-# default fraction of time a cell must be in the experiment to be kept by Signal
-signal_retained_cutoff = 0.8
--
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