.. 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_vector.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_vector.py>`
        to download the full example code.

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

.. _sphx_glr_wo_examples_models_inplane_oriented_thick_pol3d_vector.py:


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

In plane oriented thick pol3d vector summary

.. GENERATED FROM PYTHON SOURCE LINES 7-100

.. code-block:: Python


    import napari
    import torch

    from waveorder.models import inplane_oriented_thick_pol3d_vector

    # Parameters
    # all lengths must use consistent units e.g. um
    zyx_shape = (101, 256, 256)
    swing = 0.1
    scheme = "5-State"
    yx_pixel_size = 6.5 / 63
    z_pixel_size = 0.15
    wavelength_illumination = 0.532
    z_padding = 0
    index_of_refraction_media = 1.3
    numerical_aperture_illumination = 0.5
    numerical_aperture_detection = 1.2
    fourier_oversample_factor = 1

    # Create a phantom
    fzyx_object = inplane_oriented_thick_pol3d_vector.generate_test_phantom(
        zyx_shape
    )

    # Calculate transfer function
    (
        sfZYX_transfer_function,
        intensity_to_stokes_matrix,
        singular_system,
    ) = inplane_oriented_thick_pol3d_vector.calculate_transfer_function(
        swing,
        scheme,
        zyx_shape,
        yx_pixel_size,
        z_pixel_size,
        wavelength_illumination,
        z_padding,
        index_of_refraction_media,
        numerical_aperture_illumination,
        numerical_aperture_detection,
        fourier_oversample_factor=fourier_oversample_factor,
    )

    # Display transfer function
    viewer = napari.Viewer()
    inplane_oriented_thick_pol3d_vector.visualize_transfer_function(
        viewer,
        sfZYX_transfer_function,
        zyx_scale=(z_pixel_size, yx_pixel_size, yx_pixel_size),
    )

    input("Showing transfer functions. Press <enter> to continue...")
    viewer.layers.select_all()
    viewer.layers.remove_selected()

    # Simulate
    szyx_data = inplane_oriented_thick_pol3d_vector.apply_transfer_function(
        fzyx_object,
        sfZYX_transfer_function,
        intensity_to_stokes_matrix,
    )

    # Display
    arrays = [
        (szyx_data, "Data"),
        (fzyx_object, "Object"),
    ]

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


    # Reconstruct
    for reg_strength in [0.005, 0.008, 0.01, 0.05, 0.1]:
        fzyx_object_recon = (
            inplane_oriented_thick_pol3d_vector.apply_inverse_transfer_function(
                szyx_data,
                singular_system,
                intensity_to_stokes_matrix,
                regularization_strength=reg_strength,
            )
        )
        viewer.add_image(
            torch.real(fzyx_object_recon).cpu().numpy(),
            name=f"Object - recon, reg_strength={reg_strength}",
        )

    viewer.grid.enabled = True
    viewer.grid.shape = (2, 5)
    viewer.dims.axis_labels = ["COMPONENT", "Z", "Y", "X"]

    input("Showing object, data, and recon. Press <enter> to quit...")


.. _sphx_glr_download_wo_examples_models_inplane_oriented_thick_pol3d_vector.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_vector.ipynb <inplane_oriented_thick_pol3d_vector.ipynb>`

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

      :download:`Download Python source code: inplane_oriented_thick_pol3d_vector.py <inplane_oriented_thick_pol3d_vector.py>`

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

      :download:`Download zipped: inplane_oriented_thick_pol3d_vector.zip <inplane_oriented_thick_pol3d_vector.zip>`