From c361e0045c08b2ab0f3fafbf56cf405c7f7a1da3 Mon Sep 17 00:00:00 2001
From: Arin Wongprommoon <arin.wongprommoon@ed.ac.uk>
Date: Tue, 11 Oct 2022 18:15:57 +0100
Subject: [PATCH] fix(postproc/chainer): group signals apart from GFP
WHY IS THIS CHANGE NEEDED?:
- grouper (which usues chainer) breaks if it accesses a channel that is
not GFP
HOW DOES THE CHANGE SOLVE THE PROBLEM?:
- chainer assumes all experiments have a GFP channel; this was
hard-coded in line 29 in chainer.py
WHAT SIDE EFFECTS DOES THIS CHANGE HAVE?:
- yet to test
EVIDENCE THAT COMMIT WORKS:
- pipelines pending
REFERENCES:
- ...
---
src/postprocessor/chainer.py | 66 ++++++++++++++++++++----------------
1 file changed, 37 insertions(+), 29 deletions(-)
diff --git a/src/postprocessor/chainer.py b/src/postprocessor/chainer.py
index 25dabb1d..9400e765 100644
--- a/src/postprocessor/chainer.py
+++ b/src/postprocessor/chainer.py
@@ -22,38 +22,46 @@ class Chainer(Signal):
"""
process_types = ("multisignal", "processes", "reshapers")
+ common_chains = {}
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
- channel = [ch for ch in self.channels if re.match("GFP", ch)][0]
- if (
- channel == "GFPFast" and "mCherry" in self.channels
- ): # Use mCherry for Batman if available
- channel = "mCherry"
-
- equivalences = {
- "m5m": (
- f"extraction/{channel}/max/max5px",
- f"extraction/{channel}/max/median",
- )
- }
-
- def replace_url(url: str, bgsub: str = ""):
- # return pattern with bgsub
- channel = url.split("/")[1]
- if "bgsub" in bgsub:
- url = re.sub(channel, f"{channel}_bgsub", url)
- return url
-
- self.common_chains = {
- alias
- + bgsub: lambda **kwargs: self.get(
- replace_url(denominator, alias + bgsub), **kwargs
- )
- / self.get(replace_url(numerator, alias + bgsub), **kwargs)
- for alias, (denominator, numerator) in equivalences.items()
- for bgsub in ("", "_bgsub")
- }
+ for channel in self.candidate_channels:
+ try:
+ channel = [
+ ch for ch in self.channels if re.match("channel", ch)
+ ][0]
+ break
+ except:
+ pass
+
+ try:
+ equivalences = {
+ "m5m": (
+ f"extraction/{channel}/max/max5px",
+ f"extraction/{channel}/max/median",
+ ),
+ }
+
+ def replace_url(url: str, bgsub: str = ""):
+ # return pattern with bgsub
+ channel = url.split("/")[1]
+ if "bgsub" in bgsub:
+ url = re.sub(channel, f"{channel}_bgsub", url)
+ return url
+
+ self.common_chains = {
+ alias
+ + bgsub: lambda **kwargs: self.get(
+ replace_url(denominator, alias + bgsub), **kwargs
+ )
+ / self.get(replace_url(numerator, alias + bgsub), **kwargs)
+ for alias, (denominator, numerator) in equivalences.items()
+ for bgsub in ("", "_bgsub")
+ }
+
+ except:
+ pass
def get(
self,
--
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