From 59efa7ebfdb8221d6d5b5c40ea06baf8a826eb89 Mon Sep 17 00:00:00 2001
From: Peter Swain <pswain@Home-iMac.local>
Date: Wed, 22 May 2024 16:09:19 +0100
Subject: [PATCH] change(omero): get_images -> get_position_ids
More docs added too.
---
src/aliby/io/dataset.py | 4 ++--
src/aliby/io/omero.py | 45 +++++++++++++++++++++--------------------
src/aliby/pipeline.py | 2 +-
3 files changed, 26 insertions(+), 25 deletions(-)
diff --git a/src/aliby/io/dataset.py b/src/aliby/io/dataset.py
index 28ba59d1..0ec31852 100644
--- a/src/aliby/io/dataset.py
+++ b/src/aliby/io/dataset.py
@@ -146,13 +146,13 @@ class DatasetLocalOME(DatasetLocalABC):
def __init__(self, dpath: t.Union[str, Path], *args, **kwargs):
super().__init__(dpath)
assert len(
- self.get_images()
+ self.get_position_ids()
), f"No valid files found. Formats are {self._valid_suffixes}"
@property
def date(self):
"""Get the date from the metadata of the first position."""
- return ImageLocalOME(list(self.get_images().values())[0]).date
+ return ImageLocalOME(list(self.get_position_ids().values())[0]).date
def get_images(self):
"""Return a dictionary with the names of the image files."""
diff --git a/src/aliby/io/omero.py b/src/aliby/io/omero.py
index d4c11a41..b1af704c 100644
--- a/src/aliby/io/omero.py
+++ b/src/aliby/io/omero.py
@@ -83,20 +83,21 @@ class BridgeOmero:
def ome_class(self):
"""Initialise Omero Object Wrapper for instances when applicable."""
if not hasattr(self, "_ome_class"):
- assert (
- self.conn.isConnected() and self.ome_id is not None
- ), "No Blitz connection or valid omero id"
- ome_type = [
- valid_name
- for valid_name in ("Dataset", "Image")
- if re.match(
- f".*{ valid_name }.*",
- self.__class__.__name__,
- re.IGNORECASE,
- )
- ][0]
- self._ome_class = self.conn.getObject(ome_type, self.ome_id)
- assert self._ome_class, f"{ome_type} {self.ome_id} not found."
+ if self.conn.isConnected() and self.ome_id is not None:
+ ome_type = [
+ valid_name
+ for valid_name in ("Dataset", "Image")
+ if re.match(
+ f".*{ valid_name }.*",
+ self.__class__.__name__,
+ re.IGNORECASE,
+ )
+ ][0]
+ # load data
+ self._ome_class = self.conn.getObject(ome_type, self.ome_id)
+ assert self._ome_class, f"{ome_type} {self.ome_id} not found."
+ else:
+ raise Exception("No Blitz connection or valid omero id.")
return self._ome_class
def create_gate(self) -> bool:
@@ -181,17 +182,17 @@ class Dataset(BridgeOmero):
@property
def name(self):
- """Get name."""
+ """Get name of experiment."""
return self.ome_class.getName()
@property
def date(self):
- """Get date."""
+ """Get date of experiment."""
return self.ome_class.getDate()
@property
def unique_name(self):
- """Create unique name."""
+ """Get full name of experiment including its date."""
return "_".join(
(
str(self.ome_id),
@@ -200,7 +201,7 @@ class Dataset(BridgeOmero):
)
)
- def get_images(self):
+ def get_position_ids(self):
"""Get dict of image names and IDs from OMERO."""
return {
im.getName(): im.getId() for im in self.ome_class.listChildren()
@@ -215,7 +216,7 @@ class Dataset(BridgeOmero):
@property
def files(self):
- """Get files from OMERO."""
+ """Get a dict of FileAnnotationWrappers, typically for log files."""
if not hasattr(self, "_files"):
self._files = {
x.getFileName(): x
@@ -232,10 +233,10 @@ class Dataset(BridgeOmero):
@property
def tags(self):
- """Get tags from OMERO."""
- if self._tags is None:
+ """Get a dict of TagAnnotationWrapper from OMERO for each position."""
+ if not hasattr(self, "_tags"):
self._tags = {
- x.getname(): x
+ x.getId(): x
for x in self.ome_class.listAnnotations()
if isinstance(x, omero.gateway.TagAnnotationWrapper)
}
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index 0608c66f..73966332 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -239,7 +239,7 @@ class Pipeline(ProcessABC):
)
# get log files, either locally or via OMERO
with dispatcher as conn:
- position_ids = conn.get_images()
+ position_ids = conn.get_position_ids()
directory = self.store or root_dir / conn.unique_name
if not directory.exists():
directory.mkdir(parents=True)
--
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