From eee67de6812334603b674814f897293914ca40ea Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Fri, 20 Oct 2023 17:06:39 +0100
Subject: [PATCH] added signal's retained cutoff to global_parameters
---
src/agora/io/signal.py | 4 +++-
src/aliby/global_parameters.py | 3 +++
2 files changed, 6 insertions(+), 1 deletion(-)
diff --git a/src/agora/io/signal.py b/src/agora/io/signal.py
index 6b9457b..03dc98f 100644
--- a/src/agora/io/signal.py
+++ b/src/agora/io/signal.py
@@ -107,7 +107,9 @@ class Signal(BridgeH5):
with h5py.File(self.filename, "r") as f:
return list(f.attrs["channels"])
- def retained(self, signal, cutoff=0.8):
+ def retained(
+ self, signal, cutoff=global_parameters.signal_retained_cutoff
+ ):
"""
Load data (via decorator) and reduce the resulting dataframe.
diff --git a/src/aliby/global_parameters.py b/src/aliby/global_parameters.py
index 92b58f8..9fa29a4 100644
--- a/src/aliby/global_parameters.py
+++ b/src/aliby/global_parameters.py
@@ -36,3 +36,6 @@ 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
--
GitLab