use faster yaml loader and better delayed loading

bioio_sldy/reader.py

@@ -5,6 +5,7 @@
 import pathlib
 import typing
 
+import dask
 import dask.array as da
 import numpy as np
 import xarray as xr
@@ -149,9 +150,14 @@ def _read_delayed(self) -> xr.DataArray:
         for timepoint in timepoints:
             data_for_timepoint: typing.List[da.Array] = []
             for channel in channels:
-                data = image.get_data(
+                value = dask.delayed(image.get_data)(
                     timepoint=timepoint, channel=channel, delayed=True
                 )
+                data = da.from_delayed(
+                    value,
+                    shape=(image.sizeZ, image.sizeY, image.sizeX),
+                    dtype=image.dtype,
+                )
                 data_for_timepoint.append(data)
 
             data_as_list.append(da.stack(data_for_timepoint))

bioio_sldy/sldy_image.py

@@ -36,7 +36,9 @@ class SldyImage:
     _data_paths: typing.Set[pathlib.Path] = set()
 
     @staticmethod
-    def _yaml_mapping(loader: yaml.Loader, node: yaml.Node, deep: bool = False) -> dict:
+    def _yaml_mapping(
+        loader: yaml.CLoader, node: yaml.Node, deep: bool = False
+    ) -> dict:
         """
         Static method intended to map key-value pairs found in image
         metadata yaml files to Python dictionaries.
@@ -108,7 +110,7 @@ def _get_yaml_contents(
         """
         try:
             with fs.open(yaml_path) as f:
-                return yaml.load(f, Loader=yaml.Loader)
+                return yaml.load(f, Loader=yaml.CLoader)
         except FileNotFoundError:
             if is_required:
                 raise
@@ -171,7 +173,7 @@ def __init__(
         yaml.add_constructor(
             yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG,
             SldyImage._yaml_mapping,
-            yaml.Loader,
+            yaml.CLoader,
         )
 
         self._fs = fs
@@ -219,6 +221,14 @@ def __init__(
         self.timepoints = sorted(self._timepoint_to_data_paths.keys())
         self.channels = sorted(self._channel_to_data_paths.keys())
 
+        self.sizeT = self._image_record["CImageRecord70"]["mNumTimepoints"]
+        self.sizeC = self._image_record["CImageRecord70"]["mNumChannels"]
+        self.sizeZ = self._image_record["CImageRecord70"]["mNumPlanes"]
+        self.sizeY = self._image_record["CImageRecord70"]["mHeight"]
+        self.sizeX = self._image_record["CImageRecord70"]["mWidth"]
+        # TODO check this but are all sldys uint16?  bioformats seems to say so
+        self.dtype = np.dtype(np.uint16)
+
     @property
     def metadata(self) -> typing.Dict[str, typing.Optional[dict]]:
         """