From 14aa8bcd90e7e98235f1654e33fa4ae45863570a Mon Sep 17 00:00:00 2001
From: Peter Swain <pswain@Home-iMac.local>
Date: Wed, 22 May 2024 13:23:45 +0100
Subject: [PATCH] docs(omero): cosmetic changes
---
src/aliby/io/omero.py | 145 ++++++++++++++++++++----------------------
1 file changed, 69 insertions(+), 76 deletions(-)
diff --git a/src/aliby/io/omero.py b/src/aliby/io/omero.py
index 8d453f5..d4c11a4 100644
--- a/src/aliby/io/omero.py
+++ b/src/aliby/io/omero.py
@@ -1,6 +1,4 @@
-"""
-Tools to manage I/O using a remote OMERO server.
-"""
+"""Tools to manage I/O using a remote OMERO server."""
import re
import typing as t
@@ -31,7 +29,8 @@ PIXEL_TYPES = {
class BridgeOmero:
"""
- Core to interact with OMERO, using credentials or fetching them from h5 file (temporary trick).
+ Interact with OMERO.
+
See
https://docs.openmicroscopy.org/omero/5.6.0/developers/Python.html
"""
@@ -44,6 +43,8 @@ class BridgeOmero:
ome_id: int = None,
):
"""
+ Initialise with OMERO login details.
+
Parameters
----------
host : string
@@ -51,33 +52,40 @@ class BridgeOmero:
username: string
password : string
ome_id: Optional int
- Unique identifier on Omero database. Used to fetch specific objects.
+ Unique identifier on Omero database.
+ Used to fetch specific objects.
"""
- # assert all((host, username, password)), str(f"Invalid credentials host:{host}, user:{username}, pass:{pass}")
- assert all(
- (host, username, password)
- ), f"Invalid credentials. host: {host}, user: {username}, pwd: {password}"
-
+ if host is None or username is None or password is None:
+ raise Exception(
+ f"Invalid credentials. host: {host}, user: {username},"
+ f" pwd: {password}"
+ )
self.conn = None
self.host = host
self.username = username
self.password = password
self.ome_id = ome_id
- # standard method required for Python's with statement
def __enter__(self):
+ """For Python's with statement."""
self.create_gate()
-
return self
+ def __exit__(self, *exc) -> bool:
+ """For Python's with statement."""
+ for e in exc:
+ if e is not None:
+ print(e)
+ self.conn.close()
+ return False
+
@property
def ome_class(self):
- # Initialise Omero Object Wrapper for instances when applicable.
+ """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")
@@ -88,35 +96,22 @@ class BridgeOmero:
)
][0]
self._ome_class = self.conn.getObject(ome_type, self.ome_id)
-
assert self._ome_class, f"{ome_type} {self.ome_id} not found."
-
return self._ome_class
def create_gate(self) -> bool:
+ """Connect to OMERO."""
self.conn = BlitzGateway(
host=self.host, username=self.username, passwd=self.password
)
self.conn.connect()
self.conn.c.enableKeepAlive(60)
-
self.conn.isConnected()
- # standard method required for Python's with statement
- def __exit__(self, *exc) -> bool:
- for e in exc:
- if e is not None:
- print(e)
-
- self.conn.close()
- return False
-
@classmethod
- def server_info_from_h5(
- cls,
- filepath: t.Union[str, Path],
- ):
- """Return server info from hdf5 file.
+ def server_info_from_h5(cls, filepath: t.Union[str, Path]):
+ """
+ Return server info from hdf5 file.
Parameters
----------
@@ -124,11 +119,6 @@ class BridgeOmero:
BridgeOmero class
filepath : t.Union[str, Path]
Location of hdf5 file.
-
- Examples
- --------
- FIXME: Add docs.
-
"""
bridge = BridgeH5(filepath)
meta = safe_load(bridge.meta_h5["parameters"])["general"]
@@ -136,10 +126,12 @@ class BridgeOmero:
return server_info
def set_id(self, ome_id: int):
+ """Set ome_id attribute."""
self.ome_id = ome_id
@property
def file_annotations(self):
+ """Get file annotations."""
valid_annotations = [
ann.getFileName()
for ann in self.ome_class.listAnnotations()
@@ -150,7 +142,10 @@ class BridgeOmero:
def add_file_as_annotation(
self, file_to_upload: t.Union[str, Path], **kwargs
):
- """Upload annotation to object on OMERO server. Only valid in subclasses.
+ """
+ Upload annotation to object on OMERO server.
+
+ Only valid in subclasses.
Parameters
----------
@@ -158,7 +153,6 @@ class BridgeOmero:
**kwargs: Additional keyword arguments passed on
to BlitzGateway.createFileAnnfromLocalFile
"""
-
file_annotation = self.conn.createFileAnnfromLocalFile(
file_to_upload,
mimetype="text/plain",
@@ -169,30 +163,35 @@ class BridgeOmero:
class Dataset(BridgeOmero):
"""
- Tool to interact with Omero Datasets remotely, access their
- metadata and associated files and images.
+ Interact with Omero Datasets remotely.
+ Access their metadata and associated files and images.
Parameters
----------
- expt_id: int Dataset id on server
- server_info: dict host, username and password
-
+ expt_id: int
+ Dataset id on server
+ server_info: dict
+ Host, username and password
"""
def __init__(self, expt_id: int, **server_info):
+ """Initialise with experiment OMERO ID and server details."""
super().__init__(ome_id=expt_id, **server_info)
@property
def name(self):
+ """Get name."""
return self.ome_class.getName()
@property
def date(self):
+ """Get date."""
return self.ome_class.getDate()
@property
def unique_name(self):
+ """Create unique name."""
return "_".join(
(
str(self.ome_id),
@@ -202,12 +201,13 @@ class Dataset(BridgeOmero):
)
def get_images(self):
+ """Get dict of image names and IDs from OMERO."""
return {
im.getName(): im.getId() for im in self.ome_class.listChildren()
}
def get_channels(self):
- """Get channels from OMERO."""
+ """Get list of channels from OMERO."""
for im in self.ome_class.listChildren():
channels = [ch.getLabel() for ch in im.getChannels()]
break
@@ -215,6 +215,7 @@ class Dataset(BridgeOmero):
@property
def files(self):
+ """Get files from OMERO."""
if not hasattr(self, "_files"):
self._files = {
x.getFileName(): x
@@ -227,11 +228,11 @@ class Dataset(BridgeOmero):
)
elif len(self.file_annotations) != len(self._files):
raise Exception("Number of files and annotations do not match")
-
return self._files
@property
def tags(self):
+ """Get tags from OMERO."""
if self._tags is None:
self._tags = {
x.getname(): x
@@ -241,6 +242,7 @@ class Dataset(BridgeOmero):
return self._tags
def cache_logs(self, root_dir):
+ """Save the log files for an experiment."""
valid_suffixes = ("txt", "log")
for _, annotation in self.files.items():
filepath = root_dir / annotation.getFileName().replace("/", "_")
@@ -268,11 +270,6 @@ class Dataset(BridgeOmero):
Image class
filepath : t.Union[str, Path]
Location of hdf5 file.
-
- Examples
- --------
- FIXME: Add docs.
-
"""
bridge = BridgeH5(filepath)
dataset_keys = ("omero_id", "omero_id,", "dataset_id")
@@ -284,14 +281,11 @@ class Dataset(BridgeOmero):
class Image(BridgeOmero):
- """
- Loads images from OMERO and gives access to the data and metadata.
- """
+ """Load images from OMERO and their data and metadata."""
def __init__(self, image_id: int, **server_info):
"""
- Establishes the connection to the OMERO server via the Argo
- base class.
+ Connect to the OMERO server.
Parameters
----------
@@ -315,11 +309,6 @@ class Image(BridgeOmero):
Image class
filepath : t.Union[str, Path]
Location of h5 file.
-
- Examples
- --------
- FIXME: Add docs.
-
"""
bridge = BridgeH5(filepath)
image_id = bridge.meta_h5["image_id"]
@@ -327,17 +316,21 @@ class Image(BridgeOmero):
@property
def name(self):
+ """Get name."""
return self.ome_class.getName()
@property
def data(self):
+ """Get image data as a 5D dask array - TCXYZ."""
return get_data_lazy(self.ome_class)
@property
def metadata(self):
"""
- Store metadata saved in OMERO: image size, number of time points,
- labels of channels, and image name.
+ Get metadata from OMERO as a dict.
+
+ Get image size, number of time points, labels of channels,
+ and image name.
"""
meta = dict()
meta["size_x"] = self.ome_class.getSizeX()
@@ -352,17 +345,16 @@ class Image(BridgeOmero):
class UnsafeImage(Image):
"""
- Loads images from OMERO and gives access to the data and metadata.
- This class is a temporary solution while we find a way to use
- context managers inside napari. It risks resulting in zombie connections
- and producing freezes in an OMERO server.
+ Load images from OMERO and gives access to the data and metadata.
+ This class is a temporary solution while we find a way to use
+ context managers inside napari. It risks resulting in zombie
+ connections and producing freezes in an OMERO server.
"""
def __init__(self, image_id, **server_info):
"""
- Establishes the connection to the OMERO server via the Argo
- base class.
+ Connect to the OMERO server.
Parameters
----------
@@ -375,6 +367,7 @@ class UnsafeImage(Image):
@property
def data(self):
+ """Get image data as a 5D dask array - TCXYZ."""
try:
return get_data_lazy(self.ome_class)
except Exception as e:
@@ -384,26 +377,26 @@ class UnsafeImage(Image):
def get_data_lazy(image) -> da.Array:
"""
- Get 5D dask array, with delayed reading from OMERO image.
+ Get 5D dask array - TCXYZ.
+
+ Use delayed reading from OMERO image.
"""
nt, nc, nz, ny, nx = [getattr(image, f"getSize{x}")() for x in "TCZYX"]
pixels = image.getPrimaryPixels()
dtype = PIXEL_TYPES.get(pixels.getPixelsType().value, None)
# using dask
get_plane = delayed(lambda idx: pixels.getPlane(*idx))
-
- def get_lazy_plane(zct):
- return da.from_delayed(get_plane(zct), shape=(ny, nx), dtype=dtype)
-
# 5D stack: TCZXY
t_stacks = []
- for t in range(nt):
+ for tpt in range(nt):
c_stacks = []
for c in range(nc):
z_stack = []
for z in range(nz):
- z_stack.append(get_lazy_plane((z, c, t)))
+ plane = da.from_delayed(
+ get_plane((z, c, tpt)), shape=(ny, nx), dtype=dtype
+ )
+ z_stack.append(plane)
c_stacks.append(da.stack(z_stack))
t_stacks.append(da.stack(c_stacks))
-
return da.stack(t_stacks)
--
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