added signal's retained cutoff to global_parameters

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.
 

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