From 252915c649dddc91dae3a36b8428f3940baf094c Mon Sep 17 00:00:00 2001
From: Arin Wongprommoon <arin.wongprommoon@ed.ac.uk>
Date: Tue, 11 Oct 2022 18:31:55 +0100
Subject: [PATCH] fix(extraction): define candidate channels
WHY IS THIS CHANGE NEEDED?:
- invoked grouper (which used chainer, which in turn is based on
Signal), encountered AttributeError: 'Chainer' object has no
attributes 'candidate_channels'
HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- chainer used to rely on av_channels in
extraction/core/functions/defaults.py, so renamed that to
candidate_channels
- added a candidate_channels attribute to Signal object to fulfil references
---
src/agora/io/signal.py | 11 +++++++++++
src/extraction/core/functions/defaults.py | 8 ++++----
2 files changed, 15 insertions(+), 4 deletions(-)
diff --git a/src/agora/io/signal.py b/src/agora/io/signal.py
index 489a5256..4f90df92 100644
--- a/src/agora/io/signal.py
+++ b/src/agora/io/signal.py
@@ -33,6 +33,17 @@ class Signal(BridgeH5):
"mother_label",
)
+ self.candidate_channels = (
+ "GFP",
+ "GFPFast",
+ "mCherry",
+ "Flavin",
+ "Citrine",
+ "mKO2",
+ "Cy5",
+ "pHluorin405",
+ )
+
equivalences = {
"m5m": ("extraction/GFP/max/max5px", "extraction/GFP/max/median")
}
diff --git a/src/extraction/core/functions/defaults.py b/src/extraction/core/functions/defaults.py
index 2d715c80..c5b520f1 100644
--- a/src/extraction/core/functions/defaults.py
+++ b/src/extraction/core/functions/defaults.py
@@ -17,7 +17,7 @@ def exparams_from_meta(
"multichannel_ops": {},
}
- av_channels = {
+ candidate_channels = {
"Citrine",
"GFP",
"GFPFast",
@@ -41,9 +41,9 @@ def exparams_from_meta(
default_rm = {r: default_metrics for r in default_reductions}
# default_rm["None"] = ["nuc_conv_3d"] # Uncomment this to add nuc_conv_3d (slow)
- av_flch = av_channels.intersection(meta["channels/channel"]).difference(
- {"Brightfield", "DIC", "BrightfieldGFP"}
- )
+ av_flch = candidate_channels.intersection(
+ meta["channels/channel"]
+ ).difference({"Brightfield", "DIC", "BrightfieldGFP"})
for ch in av_flch:
base["tree"][ch] = default_rm
--
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