minerva.data.readers.mdio_reader

Classes

LazyPaddedPatchedMDIOReader

Reads patches from a MDIO array. This class is a subclass of

PatchedMDIOReader

Reads patches from a MDIO array. This class is a subclass of

Module Contents

class minerva.data.readers.mdio_reader.LazyPaddedPatchedMDIOReader(*args, path, mdio_data='data/chunked_012', **kwargs)[source]

Bases: minerva.data.readers.zarr_reader.LazyPaddedPatchedZarrReader

Reads patches from a MDIO array. This class is a subclass of LazyPaddedPatchedZarrReader and is designed to read patches from the the data Zarr array inside thre MDIO array subdirectory, performing padding in a lazy manner (padding is done in __getitem__ call). If no padding is necessary, use PatchedMDIOReader.

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

Parameters

pathPathLike

Path to the MDIO array.

mdio_data: str

Name of data array inside MDIO subdirectory. Defaults to ‘data/chunked_012’

Notes

  1. The MDIO 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.

  2. Padding is computed when necessary during __getitem__ calls.

Examples

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

mdio_path
Parameters:

  • path (minerva.utils.typing.PathLike)

  • mdio_data (str)

class minerva.data.readers.mdio_reader.PatchedMDIOReader(*args, path, mdio_data='data/chunked_012', **kwargs)[source]

Bases: minerva.data.readers.zarr_reader.PatchedZarrReader

Reads patches from a MDIO array. This class is a subclass of PatchedZarrReader and is designed to read patches from the the data Zarr array inside thre MDIO array subdirectory.

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

Parameters

pathPathLike

Path to the MDIO array.

mdio_data: str

Name of data array inside MDIO subdirectory. Defaults to ‘data/chunked_012’

Notes

  1. The MDIO 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.

  2. 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 LazyPaddedPatchedMDIOReader for an a lazy alternative.

Examples

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

mdio_path
Parameters:

  • path (minerva.utils.typing.PathLike)

  • mdio_data (str)