.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/run_update_ome_zarr.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_run_update_ome_zarr.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_run_update_ome_zarr.py:


Update OME-Zarr Version
=======================

This script shows how to write the same OME-Zarr image
using a new version.

.. GENERATED FROM PYTHON SOURCE LINES 10-17

.. code-block:: Python

    from pathlib import Path
    from tempfile import TemporaryDirectory

    import numpy as np

    from iohub.ngff import TransformationMeta, open_ome_zarr








.. GENERATED FROM PYTHON SOURCE LINES 18-19

Set storage path

.. GENERATED FROM PYTHON SOURCE LINES 19-23

.. code-block:: Python

    tmp_dir = TemporaryDirectory()
    old_store_path = Path(tmp_dir.name) / "old.zarr"
    new_store_path = Path(tmp_dir.name) / "new.zarr"








.. GENERATED FROM PYTHON SOURCE LINES 24-25

Create a version 0.4 OME-Zarr dataset

.. GENERATED FROM PYTHON SOURCE LINES 25-46

.. code-block:: Python

    random_image = np.random.randint(
        0, np.iinfo(np.uint16).max, size=(10, 2, 32, 128, 128), dtype=np.uint16
    )
    scale = [2.0, 3.0, 4.0, 5.0, 6.0]


    with open_ome_zarr(
        old_store_path,
        layout="hcs",
        mode="w-",
        channel_names=["DAPI", "GFP"],
        version="0.4",
    ) as old_dataset:
        position = old_dataset.create_position("A", "1", "0")
        image = position.create_image(
            "0",
            random_image,
            chunks=(1, 1, 4, 32, 32),
            transform=[TransformationMeta(type="scale", scale=scale)],
        )








.. GENERATED FROM PYTHON SOURCE LINES 47-48

Write the same image with version 0.5 and sharding

.. GENERATED FROM PYTHON SOURCE LINES 48-71

.. code-block:: Python


    with open_ome_zarr(old_store_path, mode="r", layout="hcs") as old_dataset:
        with open_ome_zarr(
            new_store_path,
            layout="hcs",
            mode="w",
            channel_names=old_dataset.channel_names,
            version="0.5",
        ) as new_dataset:
            for name, old_position in old_dataset.positions():
                row, col, fov = name.split("/")
                new_position = new_dataset.create_position(row, col, fov)
                old_image = old_position["0"]
                new_image = new_position.create_image(
                    "0",
                    data=old_image.numpy(),
                    chunks=(1, 1, 4, 32, 32),
                    shards_ratio=(2, 1, 8, 4, 4),
                    transform=old_position.metadata.multiscales[0]
                    .datasets[0]
                    .coordinate_transformations,
                )








.. GENERATED FROM PYTHON SOURCE LINES 72-73

Read the new FOV to verify it was written correctly

.. GENERATED FROM PYTHON SOURCE LINES 73-79

.. code-block:: Python

    with open_ome_zarr(new_store_path / "A/1/0", mode="r") as dataset:
        assert dataset.scale == scale
        image = dataset["0"]
        assert image.shards == (2, 1, 32, 128, 128)
        assert np.array_equal(image.numpy(), random_image)








.. GENERATED FROM PYTHON SOURCE LINES 80-81

Clean up

.. GENERATED FROM PYTHON SOURCE LINES 81-82

.. code-block:: Python

    tmp_dir.cleanup()








.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 6.408 seconds)


.. _sphx_glr_download_auto_examples_run_update_ome_zarr.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: run_update_ome_zarr.ipynb <run_update_ome_zarr.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: run_update_ome_zarr.py <run_update_ome_zarr.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: run_update_ome_zarr.zip <run_update_ome_zarr.zip>`