changed load_attributes to load_meta

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

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):

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

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))

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,