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ImageArray Initialization #261

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ImageArray Initialization #261

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b7b8adc
init ImageArray with kwargs
ieivanov Nov 25, 2024
0877598
add documentation on ImageArray.__init__
ieivanov Nov 27, 2024
40ac524
expand on documentation
ieivanov Nov 27, 2024
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36 changes: 22 additions & 14 deletions iohub/ngff/nodes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -310,20 +310,28 @@ def close(self):
class ImageArray(zarr.Array):
"""Container object for image stored as a zarr array (up to 5D)"""

def __init__(self, zarray: zarr.Array):
super().__init__(
store=zarray._store,
path=zarray._path,
read_only=zarray._read_only,
chunk_store=zarray._chunk_store,
synchronizer=zarray._synchronizer,
cache_metadata=zarray._cache_metadata,
cache_attrs=zarray._attrs.cache,
partial_decompress=zarray._partial_decompress,
write_empty_chunks=zarray._write_empty_chunks,
zarr_version=zarray._version,
meta_array=zarray._meta_array,
)
def __init__(self, zarray: zarr.Array = None, **kwargs):
"""Keyword arguments are passed to the zarr.Array constructor.
If a zarr.Array is provided, the constructor will use its attributes
to initialize the ImageArray.
"""
if zarray is not None:
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Can you explain when this method should be called without a argument? It is an internal wrapper, and if you don't need the wrapper, just doing Position.zgroup["0"] would give you the plain zarr.Array object.

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Dask may expect exactly zarr.Array and not a wrapped subclass for some of their internal logic. I think it's safer to match their advertised API than hacking our own wrapper.

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I added an example use case at the top and a short docstring to the __init__ function:

    def __init__(self, zarray: zarr.Array = None, **kwargs):
        """Keyword arguments are passed to the zarr.Array constructor.
        If a zarr.Array is provided, the constructor will use its attributes
        to initialize the ImageArray.
        """

I think this is a common enough use case, such that we should make iohub arrays work with the dask arrays in multiprocessing applications

kwargs.update(
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Suggested change
kwargs.update(
# Dynamically prepare kwargs for the base class to support Dask
kwargs.update(

{
"store": zarray._store,
"path": zarray._path,
"read_only": zarray._read_only,
"chunk_store": zarray._chunk_store,
"synchronizer": zarray._synchronizer,
"cache_metadata": zarray._cache_metadata,
"cache_attrs": zarray._attrs.cache,
"partial_decompress": zarray._partial_decompress,
"write_empty_chunks": zarray._write_empty_chunks,
"zarr_version": zarray._version,
"meta_array": zarray._meta_array,
}
)
super().__init__(**kwargs)
self._get_dims()

def _get_dims(self):
Expand Down