From fc286f9907639b6b7f7095bd006de4a13819819f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Fri, 6 Jan 2023 18:50:23 +0000
Subject: [PATCH] fix(Pipeline): incorporate new Dataset/ImageDir
---
src/aliby/io/image.py | 22 +++++++++++-----------
src/aliby/pipeline.py | 15 +++++----------
2 files changed, 16 insertions(+), 21 deletions(-)
diff --git a/src/aliby/io/image.py b/src/aliby/io/image.py
index 816c9e13..6379c909 100644
--- a/src/aliby/io/image.py
+++ b/src/aliby/io/image.py
@@ -40,7 +40,7 @@ def get_image_class(source: t.Union[str, int, t.Dict[str, str], PosixPath]):
elif isinstance(source, dict) or (
isinstance(source, (str, PosixPath)) and Path(source).is_dir()
):
- instatiator = ImageDirectory
+ instatiator = ImageDir
elif isinstance(source, str) and Path(source).is_file():
instatiator = ImageLocalOME
else:
@@ -88,6 +88,15 @@ class BaseLocalImage(ABC):
def data(self):
return self.get_data_lazy()
+ def __enter__(self):
+ return self
+
+ def __exit__(self, *exc):
+ for e in exc:
+ if e is not None:
+ print(e)
+ return False
+
class ImageLocalOME(BaseLocalImage):
"""
@@ -127,15 +136,6 @@ class ImageLocalOME(BaseLocalImage):
self._meta = meta
- def __enter__(self):
- return self
-
- def __exit__(self, *exc):
- for e in exc:
- if e is not None:
- print(e)
- return False
-
@property
def name(self):
return self._meta["name"]
@@ -211,7 +211,7 @@ class ImageDir(BaseLocalImage):
- Provides Dimorder as it is set in the filenames, or expects order during instatiation
"""
- def __init__(self, path: t.Union[str, PosixPath]):
+ def __init__(self, path: t.Union[str, PosixPath], **kwargs):
super().__init__(path)
self.image_id = str(self.path.stem)
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index 989a0e4a..ed3b608b 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -29,7 +29,7 @@ from agora.io.writer import ( # BabyWriter,
)
from aliby.baby_client import BabyParameters, BabyRunner
from aliby.haystack import initialise_tf
-from aliby.io.dataset import Dataset, DatasetLocalOME, DatasetLocalDir
+from aliby.io.dataset import dispatch_dataset
from aliby.io.image import get_image_class
from aliby.tile.tiler import Tiler, TilerParameters
from extraction.core.extractor import Extractor, ExtractorParameters
@@ -83,12 +83,8 @@ class PipelineParameters(ParametersABC):
general["expt_id"] = expt_id
directory = Path(general.get("directory", "../data"))
- dataset_wrapper = (
- lambda x: DatasetLocal(x)
- if isinstance(expt_id, str)
- else Dataset(int(x), **general.get("server_info"))
- )
- with dataset_wrapper(expt_id) as conn:
+
+ with dispatch_dataset(expt_id) as conn:
directory = directory / conn.unique_name
if not directory.exists():
directory.mkdir(parents=True)
@@ -101,7 +97,7 @@ class PipelineParameters(ParametersABC):
"channels": ["Brightfield"],
"ntps": [2000],
}
- print(f"WARNING:Metadata: error when uploading: {e}")
+ print(f"WARNING:Metadata: error when loading: {e}")
# Set minimal metadata
meta_d = minimal_default_meta
@@ -273,8 +269,7 @@ class Pipeline(ProcessABC):
print("Searching OMERO")
# Do all all initialisations
- dataset_wrapper = DatasetLocal if isinstance(expt_id, str) else Dataset
- with dataset_wrapper(
+ with dispatch_dataset(
expt_id, **self.general.get("server_info", {})
) as conn:
image_ids = conn.get_images()
--
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