From 572b1787a3f78ef023976a0568d93d0ac20a116a Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Mon, 2 Oct 2023 14:31:48 +0100
Subject: [PATCH] removed duplicate line for ref_channel in tiler
---
src/aliby/pipeline.py | 4 ++++
src/aliby/tile/tiler.py | 3 ---
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index e5d5bc66..d80f441c 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -340,6 +340,10 @@ class Pipeline(ProcessABC):
position_ids = self.apply_filter(position_ids, position_filter)
if not len(position_ids):
raise Exception("No images to segment.")
+ else:
+ print("Positions:")
+ for pos in position_ids:
+ print("\t" + pos.split(".")[0])
# create and run pipelines
if distributed != 0:
# multiple cores
diff --git a/src/aliby/tile/tiler.py b/src/aliby/tile/tiler.py
index 5a60609a..4ca3f5e1 100644
--- a/src/aliby/tile/tiler.py
+++ b/src/aliby/tile/tiler.py
@@ -246,12 +246,9 @@ class Tiler(StepABC):
"channels",
list(range(metadata.get("size_c", 0))),
)
-
self.ref_channel = self.get_channel_index(parameters.ref_channel)
if self.ref_channel is None:
self.ref_channel = self.backup_ref_channel
-
- self.ref_channel = self.get_channel_index(parameters.ref_channel)
self.tile_locs = tile_locs
try:
self.z_perchannel = {
--
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