From 822b6b95bb84e37f8f6429543a725035f2f395c9 Mon Sep 17 00:00:00 2001
From: Peter Swain <peter.swain@ed.ac.uk>
Date: Sat, 28 Jan 2023 13:39:34 +0000
Subject: [PATCH] Minimal changes in docs for pipeline
---
src/aliby/pipeline.py | 11 ++++++++---
1 file changed, 8 insertions(+), 3 deletions(-)
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index 2977cada..b31fcb4e 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -37,7 +37,9 @@ from postprocessor.core.processor import PostProcessor, PostProcessorParameters
class PipelineParameters(ParametersABC):
"""
- Parameters that host what is run and how. It takes a list of dictionaries, one for
+ Define parameters for what processes are run and how.
+
+ Input is a a list of dictionaries, one for
general in collection:
pass dictionary for each step
--------------------
@@ -53,6 +55,7 @@ class PipelineParameters(ParametersABC):
def __init__(
self, general, tiler, baby, extraction, postprocessing, reporting
):
+ """Initialise with general parameters and those for tiler, baby, extraction, postprocessing, and reporting."""
self.general = general
self.tiler = tiler
self.baby = baby
@@ -69,6 +72,7 @@ class PipelineParameters(ParametersABC):
extraction={},
postprocessing={},
):
+ # Alan: 19993 should be updated?
expt_id = general.get("expt_id", 19993)
if isinstance(expt_id, PosixPath):
expt_id = str(expt_id)
@@ -76,6 +80,7 @@ class PipelineParameters(ParametersABC):
directory = Path(general.get("directory", "../data"))
+ # connect to OMERO
with dispatch_dataset(
expt_id,
**{k: general.get(k) for k in ("host", "username", "password")},
@@ -83,7 +88,7 @@ class PipelineParameters(ParametersABC):
directory = directory / conn.unique_name
if not directory.exists():
directory.mkdir(parents=True)
- # Download logs to use for metadata
+ # download logs for metadata
conn.cache_logs(directory)
try:
meta_d = MetaData(directory, None).load_logs()
@@ -95,7 +100,7 @@ class PipelineParameters(ParametersABC):
"channels": ["Brightfield"],
"ntps": [2000],
}
- # Set minimal metadata
+ # set minimal metadata
meta_d = minimal_default_meta
tps = meta_d.get("ntps", 2000)
--
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