minerva.data.readers.zarr_reader

Classes

`LazyPaddedPatchedZarrReader`	Reads patches from a Zarr array. This class is a subclass of
`PatchedZarrReader`	Reads patches from a Zarr array. This class is a subclass of

Module Contents

class minerva.data.readers.zarr_reader.LazyPaddedPatchedZarrReader(*args, path, **kwargs)[source]

Bases: minerva.data.readers.patched_array_reader.LazyPaddedPatchedArrayReader

Reads patches from a Zarr array. This class is a subclass of LazyPaddedPatchedArrayReader and is designed to read patches from a Zarr array, performing padding in a lazy manner (padding is done in __getitem__ call). If no padding is necessary, use PatchedZarrReader.

Reads patches from a Zarr array. This class is a subclass of LazyPaddedPatchedArrayReader. All other parameters are the same as parent class. Please refer to the documentation of LazyPaddedPatchedArrayReader for more information. This class can be used when padding is necessary and the whole dataset doesn’t fit into memory.

Parameters

pathPathLike: Path to the Zarr array.

Notes

The Zarr array is expected to be stored on disk. If the array is not stored on disk, it is recommended to use the LazyPaddedPatchedArrayReader class instead.
Padding is computed when necessary during __getitem__ calls.

Examples

```python >>> from pathlib import Path >>> data_path = Path(“data.zarr”) >>> reader = LazyPaddedPatchedZarrReader( … path=data_path, … data_shape=(5, 5), … stride=(2, 5), … pad_width=((1,1), (0,2)), … ) >>> print(len(reader)) >>> print(reader[0])

path

Parameters:: path (minerva.utils.typing.PathLike)

class minerva.data.readers.zarr_reader.PatchedZarrReader(*args, path, **kwargs)[source]

Bases: minerva.data.readers.patched_array_reader.PatchedArrayReader

Reads patches from a Zarr array. This class is a subclass of PatchedArrayReader and is designed to read patches from a Zarr array.

Reads patches from a Zarr array. This class is a subclass of PatchedArrayReader. All other parameters are the same as parent class. Please refer to the documentation of PatchedArrayReader for more information.

Parameters

pathPathLike: Path to the Zarr array.

Notes

The Zarr array is expected to be stored on disk. If the array is not stored on disk, it is recommended to use the PatchedArrayReader class instead.
When using padding, the padding is applied to the entire array. This will load the entire array into memory. If the array is too large to fit into memory, it is recommended to pad before. See LazyPaddedPatchedZarrReader for an a lazy alternative.

Examples

```python >>> from pathlib import Path >>> data_path = Path(“data.zarr”) >>> reader = PatchedZarrReader( … path=data_path, … data_shape=(5, 5), … stride=(2, 5), … ) >>> print(len(reader)) >>> print(reader[0])

path

Parameters:: path (minerva.utils.typing.PathLike)