From 251c23bc654b7801de7864275bfd985d6553c4e3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Mon, 23 Jan 2023 12:48:51 +0000
Subject: [PATCH] fix(imagedummy): fix #62, make dimorder a prop
- Change the order to match tczyx where appropriate
- Make name and dimorder properties for Imagedummy
---
src/aliby/io/image.py | 6 ++++--
src/aliby/pipeline.py | 6 ++++--
2 files changed, 8 insertions(+), 4 deletions(-)
diff --git a/src/aliby/io/image.py b/src/aliby/io/image.py
index 57283dc4..7e021fcd 100644
--- a/src/aliby/io/image.py
+++ b/src/aliby/io/image.py
@@ -5,7 +5,7 @@ Image: Loads images and registers them.
Image instances loads images from a specified directory into an object that
also contains image properties such as name and metadata. Pixels from images
are stored in dask arrays; the standard way is to store them in 5-dimensional
-arrays: T(ime point), C(channel), Z(-stack), X, Y.
+arrays: T(ime point), C(channel), Z(-stack), Y, X.
This module consists of a base Image class (BaseLocalImage). ImageLocalOME
handles local OMERO images. ImageDir handles cases in which images are split
@@ -81,8 +81,8 @@ class BaseLocalImage(ABC):
1,
1,
1,
- self._meta["size_x"],
self._meta["size_y"],
+ self._meta["size_x"],
),
)
return self._rechunked_img
@@ -212,9 +212,11 @@ class ImageDummy(BaseLocalImage):
) # 5 z-stacks
return img
+ @property
def name(self):
pass
+ @property
def dimorder(self):
pass
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index 0d26f678..0062c61a 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -112,7 +112,7 @@ class PipelineParameters(ParametersABC):
ntps_to_eval=5,
),
logfile_level="INFO",
- logstream_level="WARNING",
+ use_explog=True,
)
}
@@ -691,7 +691,9 @@ class Pipeline(ProcessABC):
except Exception:
pass
- meta.run()
+ if config["general"]["use_explog"]:
+ meta.run()
+
meta.add_fields( # Add non-logfile metadata
{
"aliby_version": version("aliby"),
--
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