.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "wo_examples/models/inplane_oriented_thick_pol3d.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_wo_examples_models_inplane_oriented_thick_pol3d.py>`
        to download the full example code.

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

.. _sphx_glr_wo_examples_models_inplane_oriented_thick_pol3d.py:


In plane oriented thick pol3d
=============================

In plane oriented thick pol3d summary

.. GENERATED FROM PYTHON SOURCE LINES 7-69

.. code-block:: Python

    import napari

    from waveorder.models import inplane_oriented_thick_pol3d

    # Parameters
    # all lengths must use consistent units e.g. um
    simulation_arguments = {"yx_shape": (256, 256)}
    transfer_function_arguments = {"swing": 0.1, "scheme": "5-State"}

    # Create a phantom
    inplane_oriented_parameters = (
        inplane_oriented_thick_pol3d.generate_test_phantom(**simulation_arguments)
    )

    # Calculate transfer function
    intensity_to_stokes_matrix = (
        inplane_oriented_thick_pol3d.calculate_transfer_function(
            **transfer_function_arguments
        )
    )

    # Display transfer function
    viewer = napari.Viewer()
    inplane_oriented_thick_pol3d.visualize_transfer_function(
        viewer, intensity_to_stokes_matrix
    )
    input("Showing transfer functions. Press <enter> to continue...")
    viewer.layers.select_all()
    viewer.layers.remove_selected()

    # Simulate
    czyx_data = inplane_oriented_thick_pol3d.apply_transfer_function(
        *inplane_oriented_parameters,
        intensity_to_stokes_matrix,
    )

    # Reconstruct
    inplane_oriented_parameters_recon = (
        inplane_oriented_thick_pol3d.apply_inverse_transfer_function(
            czyx_data, intensity_to_stokes_matrix
        )
    )

    # Display
    arrays = [
        (inplane_oriented_parameters_recon[3], "Depolarization - recon"),
        (inplane_oriented_parameters_recon[2], "Transmittance - recon"),
        (inplane_oriented_parameters_recon[1], "Orientation (rad) - recon"),
        (inplane_oriented_parameters_recon[0], "Retardance (rad) - recon"),
        (czyx_data, "Data"),
        (inplane_oriented_parameters[3], "Depolarization"),
        (inplane_oriented_parameters[2], "Transmittance"),
        (inplane_oriented_parameters[1], "Orientation (rad)"),
        (inplane_oriented_parameters[0], "Retardance (rad)"),
    ]

    for array in arrays:
        viewer.add_image(array[0].cpu().numpy(), name=array[1])

    viewer.grid.enabled = True
    viewer.grid.shape = (2, 5)
    input("Showing object, data, and recon. Press <enter> to quit...")


.. _sphx_glr_download_wo_examples_models_inplane_oriented_thick_pol3d.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: inplane_oriented_thick_pol3d.ipynb <inplane_oriented_thick_pol3d.ipynb>`

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

      :download:`Download Python source code: inplane_oriented_thick_pol3d.py <inplane_oriented_thick_pol3d.py>`

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

      :download:`Download zipped: inplane_oriented_thick_pol3d.zip <inplane_oriented_thick_pol3d.zip>`