.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/run_coordinate_transform.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_coordinate_transform.py>`
        to download the full example code.

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

.. _sphx_glr_auto_examples_run_coordinate_transform.py:


Coordinate Transform
====================

This script writes two positions using the high content screening (HCS)
OME-Zarr dataset with two FOV in a single well with different
coordinate transformations (i.e translation and scaling)

.. GENERATED FROM PYTHON SOURCE LINES 11-18

.. code-block:: Python

    import os
    from tempfile import TemporaryDirectory

    import numpy as np

    from iohub.ngff import TransformationMeta, open_ome_zarr








.. GENERATED FROM PYTHON SOURCE LINES 19-20

Set storage path

.. GENERATED FROM PYTHON SOURCE LINES 20-25

.. code-block:: Python


    tmp_dir = TemporaryDirectory()
    store_path = os.path.join(tmp_dir.name, "transformed.zarr")
    print("Zarr store path", store_path)





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Zarr store path /tmp/tmpkcacpph0/transformed.zarr




.. GENERATED FROM PYTHON SOURCE LINES 26-27

Create two random sample images

.. GENERATED FROM PYTHON SOURCE LINES 27-34

.. code-block:: Python

    tczyx_1 = np.random.randint(
        0, np.iinfo(np.uint16).max, size=(1, 3, 3, 32, 32), dtype=np.uint16
    )
    tczyx_2 = np.random.randint(
        0, np.iinfo(np.uint16).max, size=(1, 3, 3, 32, 32), dtype=np.uint16
    )








.. GENERATED FROM PYTHON SOURCE LINES 35-37

Coordinate Transformations (T,C,Z,Y,X)
By default the translation is the identity matrix

.. GENERATED FROM PYTHON SOURCE LINES 37-40

.. code-block:: Python

    coords_shift = [[1.0, 1.0, 1.0, 10.0, 10.0], [1.0, 1.0, 0.0, -10.0, -10.0]]
    img_scaling = [[1.0, 1.0, 1.0, 0.5, 0.5]]








.. GENERATED FROM PYTHON SOURCE LINES 41-42

Generate Transformation Metadata

.. GENERATED FROM PYTHON SOURCE LINES 42-51

.. code-block:: Python

    translation = []
    for shift in coords_shift:
        translation.append(
            TransformationMeta(type="translation", translation=shift)
        )
    scaling = []
    for scale in img_scaling:
        scaling.append(TransformationMeta(type="scale", scale=scale))








.. GENERATED FROM PYTHON SOURCE LINES 52-53

Write 5D data to a new Zarr store

.. GENERATED FROM PYTHON SOURCE LINES 53-68

.. code-block:: Python

    with open_ome_zarr(
        store_path,
        layout="hcs",
        mode="w-",
        channel_names=["DAPI", "GFP", "Brightfield"],
    ) as dataset:
        # Create and write to positions
        # This affects the tile arrangement in visualization
        position = dataset.create_position(0, 0, 0)
        position.create_image("0", tczyx_1, transform=[translation[0]])
        position = dataset.create_position(0, 0, 1)
        position.create_image("0", tczyx_2, transform=[translation[1], scaling[0]])
        # Print dataset summary
        dataset.print_tree()





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    /
     └── 0
         └── 0
             ├── 0
             │   └── 0 (1, 3, 3, 32, 32) uint16
             └── 1
                 └── 0 (1, 3, 3, 32, 32) uint16




.. GENERATED FROM PYTHON SOURCE LINES 69-72

.. note:: To see the coordinate transforms,
    open the positions individually using napari-ome-zarr.
    This will duplicate the layers (channels).

.. GENERATED FROM PYTHON SOURCE LINES 74-75

Clean up

.. GENERATED FROM PYTHON SOURCE LINES 75-75

.. code-block:: Python

    tmp_dir.cleanup()







.. _sphx_glr_download_auto_examples_run_coordinate_transform.py:

.. only:: html

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

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

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

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

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