From 5737918701130d8ca8d4bbcfc81630dca61ffd06 Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Thu, 25 Apr 2024 16:47:52 +0100
Subject: [PATCH] change(pipeline): added OMERO_channels as input
When processing zarr files with no access to OMERO, OMERO_channels
specifies the correct channels in the correct order, which may
differ from position to position and be incorrect in the meta data,
which is for all positions.
---
src/aliby/pipeline.py | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index 183b6d2..56ab553 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -169,13 +169,17 @@ class PipelineParameters(ParametersABC):
class Pipeline(ProcessABC):
"""Initialise and run tiling, segmentation, extraction and post-processing."""
- def __init__(self, parameters: PipelineParameters, store=None):
+ def __init__(
+ self, parameters: PipelineParameters, store=None, OMERO_channels=None
+ ):
"""Initialise using Pipeline parameters."""
super().__init__(parameters)
if store is not None:
store = Path(store)
# h5 file
self.store = store
+ if OMERO_channels is not None:
+ self.OMERO_channels = OMERO_channels
config = self.parameters.to_dict()
self.server_info = {
k: config["general"].get(k)
--
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