.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "wo_examples/models/isotropic_thin_3d.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_isotropic_thin_3d.py>`
        to download the full example code.

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

.. _sphx_glr_wo_examples_models_isotropic_thin_3d.py:


Isotropic thin 3d
=====================

# 3D partially coherent optical diffraction tomography (ODT) simulation
# J. M. Soto, J. A. Rodrigo, and T. Alieva, "Label-free quantitative
# 3D tomographic imaging for partially coherent light microscopy," Opt. Express
# 25, 15699-15712 (2017)

.. GENERATED FROM PYTHON SOURCE LINES 10-114

.. code-block:: Python


    import napari
    import numpy as np

    from waveorder.models import isotropic_thin_3d

    # Parameters
    # all lengths must use consistent units e.g. um
    simulation_arguments = {
        "yx_shape": (256, 256),
        "yx_pixel_size": 6.5 / 63,
        "wavelength_illumination": 0.532,
        "index_of_refraction_media": 1.3,
    }
    phantom_arguments = {"index_of_refraction_sample": 1.33, "sphere_radius": 5}
    z_shape = 100
    z_pixel_size = 0.25
    zyx_scale = np.array(
        [
            z_pixel_size,
            simulation_arguments["yx_pixel_size"],
            simulation_arguments["yx_pixel_size"],
        ]
    )
    transfer_function_arguments = {
        "z_position_list": (np.arange(z_shape) - z_shape // 2) * z_pixel_size,
        "numerical_aperture_illumination": 0.9,
        "numerical_aperture_detection": 1.2,
    }

    # Create a disk phantom
    yx_absorption, yx_phase = isotropic_thin_3d.generate_test_phantom(
        **simulation_arguments, **phantom_arguments
    )
    yx_absorption[:, 128:] = 0  # half absorbing
    yx_phase[128:] = 0  # half phase

    # Calculate transfer function
    (
        absorption_2d_to_3d_transfer_function,
        phase_2d_to_3d_transfer_function,
    ) = isotropic_thin_3d.calculate_transfer_function(
        **simulation_arguments, **transfer_function_arguments
    )

    # Calculate singular system
    singular_system = isotropic_thin_3d.calculate_singular_system(
        absorption_2d_to_3d_transfer_function,
        phase_2d_to_3d_transfer_function,
    )

    # Display transfer function
    viewer = napari.Viewer()
    zyx_scale = np.array(
        [
            z_pixel_size,
            simulation_arguments["yx_pixel_size"],
            simulation_arguments["yx_pixel_size"],
        ]
    )
    isotropic_thin_3d.visualize_transfer_function(
        viewer,
        absorption_2d_to_3d_transfer_function,
        phase_2d_to_3d_transfer_function,
    )
    input("Showing OTFs. Press <enter> to continue...")
    viewer.layers.select_all()
    viewer.layers.remove_selected()

    # Simulate
    zyx_data = isotropic_thin_3d.apply_transfer_function(
        yx_absorption,
        yx_phase,
        absorption_2d_to_3d_transfer_function,
        phase_2d_to_3d_transfer_function,
    )

    # Reconstruct
    (
        yx_absorption_recon,
        yx_phase_recon,
    ) = isotropic_thin_3d.apply_inverse_transfer_function(
        zyx_data,
        singular_system,
        regularization_strength=1e-2,
    )

    # Display
    arrays = [
        (yx_absorption, "Phantom - absorption"),
        (yx_phase, "Phantom - phase"),
        (zyx_data, "Data"),
        (yx_absorption_recon, "Reconstruction - absorption"),
        (yx_phase_recon, "Reconstruction - phase"),
    ]

    for array in arrays:
        scale = zyx_scale[1:] if array[0].ndim == 2 else zyx_scale
        viewer.add_image(array[0].cpu().numpy(), name=array[1], scale=scale)

    viewer.grid.enabled = True
    viewer.dims.current_step = (z_shape // 2, 0, 0)

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


.. _sphx_glr_download_wo_examples_models_isotropic_thin_3d.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: isotropic_thin_3d.ipynb <isotropic_thin_3d.ipynb>`

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

      :download:`Download Python source code: isotropic_thin_3d.py <isotropic_thin_3d.py>`

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

      :download:`Download zipped: isotropic_thin_3d.zip <isotropic_thin_3d.zip>`