minerva.data.readers.zarr_reader
================================

.. py:module:: minerva.data.readers.zarr_reader


Classes
-------

.. autoapisummary::

   minerva.data.readers.zarr_reader.LazyPaddedPatchedZarrReader
   minerva.data.readers.zarr_reader.PatchedZarrReader


Module Contents
---------------

.. py:class:: LazyPaddedPatchedZarrReader(*args, path, **kwargs)

   Bases: :py:obj:`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
   ----------
   path : PathLike
       Path to the Zarr array.
   Notes
   -----
   1.  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.

   2.  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])



   .. py:attribute:: path


.. py:class:: PatchedZarrReader(*args, path, **kwargs)

   Bases: :py:obj:`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
   ----------
   path : PathLike
       Path to the Zarr array.
   Notes
   -----
   1.  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.

   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 `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])



   .. py:attribute:: path