From 793ce5d7438e26e78753199c3586013e60cdac2f Mon Sep 17 00:00:00 2001
From: pswain <peter.swain@ed.ac.uk>
Date: Fri, 20 Oct 2023 11:30:59 +0100
Subject: [PATCH] changed load_attributes to load_meta
---
src/agora/abc.py | 2 +-
src/agora/io/reader.py | 4 ++--
src/agora/io/writer.py | 10 ++++++----
src/aliby/io/omero.py | 8 +++-----
src/extraction/core/extractor.py | 11 ++++-------
5 files changed, 16 insertions(+), 19 deletions(-)
diff --git a/src/agora/abc.py b/src/agora/abc.py
index 6bdb93b8..928c1709 100644
--- a/src/agora/abc.py
+++ b/src/agora/abc.py
@@ -190,8 +190,8 @@ class ProcessABC(ABC):
"""
self._parameters = parameters
# convert parameters to dictionary
- # and then define each parameter as an attribute
for k, v in parameters.to_dict().items():
+ # define each parameter as an attribute
setattr(self, k, v)
@property
diff --git a/src/agora/io/reader.py b/src/agora/io/reader.py
index b6793483..8f0410a4 100644
--- a/src/agora/io/reader.py
+++ b/src/agora/io/reader.py
@@ -5,7 +5,7 @@ import h5py
import numpy as np
from agora.io.bridge import groupsort
-from agora.io.writer import load_attributes
+from agora.io.writer import load_meta
class DynamicReader:
@@ -13,7 +13,7 @@ class DynamicReader:
def __init__(self, file: str):
self.file = file
- self.metadata = load_attributes(file)
+ self.metadata = load_meta(file)
class StateReader(DynamicReader):
diff --git a/src/agora/io/writer.py b/src/agora/io/writer.py
index 0913308f..768fcdab 100644
--- a/src/agora/io/writer.py
+++ b/src/agora/io/writer.py
@@ -15,9 +15,10 @@ from agora.io.bridge import BridgeH5
#################### Dynamic version ##################################
-def load_attributes(file: str, group="/"):
+def load_meta(file: str, group="/"):
"""
- Load the metadata from an h5 file and convert to a dictionary, including the "parameters" field which is stored as YAML.
+ Load the metadata from an h5 file and convert to a dictionary, including
+ the "parameters" field which is stored as YAML.
Parameters
----------
@@ -26,8 +27,9 @@ def load_attributes(file: str, group="/"):
group: str, optional
The group in the h5 file from which to read the data
"""
- # load the metadata, stored as attributes, from the h5 file and return as a dictionary
+ # load the metadata, stored as attributes, from the h5 file
with h5py.File(file, "r") as f:
+ # return as a dict
meta = dict(f[group].attrs.items())
if "parameters" in meta:
# convert from yaml format into dict
@@ -51,7 +53,7 @@ class DynamicWriter:
self.file = file
# the metadata is stored as attributes in the h5 file
if Path(file).exists():
- self.metadata = load_attributes(file)
+ self.metadata = load_meta(file)
def _log(self, message: str, level: str = "warn"):
# Log messages in the corresponding level
diff --git a/src/aliby/io/omero.py b/src/aliby/io/omero.py
index a56a1c0e..0ea37359 100644
--- a/src/aliby/io/omero.py
+++ b/src/aliby/io/omero.py
@@ -131,7 +131,6 @@ class BridgeOmero:
FIXME: Add docs.
"""
- # metadata = load_attributes(filepath)
bridge = BridgeH5(filepath)
meta = safe_load(bridge.meta_h5["parameters"])["general"]
server_info = {k: meta[k] for k in ("host", "username", "password")}
@@ -268,7 +267,6 @@ class Dataset(BridgeOmero):
FIXME: Add docs.
"""
- # metadata = load_attributes(filepath)
bridge = BridgeH5(filepath)
dataset_keys = ("omero_id", "omero_id,", "dataset_id")
for k in dataset_keys:
@@ -301,21 +299,21 @@ class Image(BridgeOmero):
cls,
filepath: t.Union[str, Path],
):
- """Instatiate Image from a hdf5 file.
+ """
+ Instantiate Image from a h5 file.
Parameters
----------
cls : Image
Image class
filepath : t.Union[str, Path]
- Location of hdf5 file.
+ Location of h5 file.
Examples
--------
FIXME: Add docs.
"""
- # metadata = load_attributes(filepath)
bridge = BridgeH5(filepath)
image_id = bridge.meta_h5["image_id"]
return cls(image_id, **cls.server_info_from_h5(filepath))
diff --git a/src/extraction/core/extractor.py b/src/extraction/core/extractor.py
index 6d025188..21841438 100644
--- a/src/extraction/core/extractor.py
+++ b/src/extraction/core/extractor.py
@@ -7,7 +7,7 @@ import pandas as pd
from agora.abc import ParametersABC, StepABC
from agora.io.cells import Cells
-from agora.io.writer import Writer, load_attributes
+from agora.io.writer import Writer, load_meta
from aliby.tile.tiler import Tiler
from extraction.core.functions.defaults import exparams_from_meta
from extraction.core.functions.distributors import reduce_z, trap_apply
@@ -89,7 +89,7 @@ class Extractor(StepABC):
or leaf level.
"""
- # TODO Alan: Move this to a location with the SwainLab defaults
+ # TODO Move this to a location with the SwainLab defaults
default_meta = {
"pixel_size": 0.236,
"z_size": 0.6,
@@ -119,10 +119,11 @@ class Extractor(StepABC):
self.params = parameters
if store:
self.local = store
- self.load_meta()
+ self.meta = load_meta(self.local)
else:
# if no h5 file, use the parameters directly
self.meta = {"channel": parameters.to_dict()["tree"].keys()}
+
if tiler:
self.tiler = tiler
available_channels = set((*tiler.channels, "general"))
@@ -236,10 +237,6 @@ class Extractor(StepABC):
# merge the two dicts
self._all_funs = {**self._custom_funs, **ALL_FUNS}
- def load_meta(self):
- """Load metadata from h5 file."""
- self.meta = load_attributes(self.local)
-
def get_tiles(
self,
tp: int,
--
GitLab