.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "wo_examples/models/phase_thick_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_phase_thick_3d.py>`
        to download the full example code.

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

.. _sphx_glr_wo_examples_models_phase_thick_3d.py:


phase thick 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 10-85

.. code-block:: Python


    import napari
    import numpy as np

    from waveorder.models import phase_thick_3d

    # Parameters
    # all lengths must use consistent units e.g. um
    simulation_arguments = {
        "zyx_shape": (100, 256, 256),
        "yx_pixel_size": 6.5 / 63,
        "z_pixel_size": 0.25,
        "index_of_refraction_media": 1.3,
    }
    phantom_arguments = {"index_of_refraction_sample": 1.50, "sphere_radius": 5}
    transfer_function_arguments = {
        "z_padding": 0,
        "wavelength_illumination": 0.532,
        "numerical_aperture_illumination": 0.9,
        "numerical_aperture_detection": 1.2,
    }

    # Create a phantom
    zyx_phase = phase_thick_3d.generate_test_phantom(
        **simulation_arguments, **phantom_arguments
    )

    # Calculate transfer function
    (
        real_potential_transfer_function,
        imag_potential_transfer_function,
    ) = phase_thick_3d.calculate_transfer_function(
        **simulation_arguments, **transfer_function_arguments
    )

    # Display transfer function
    viewer = napari.Viewer()
    zyx_scale = np.array(
        [
            simulation_arguments["z_pixel_size"],
            simulation_arguments["yx_pixel_size"],
            simulation_arguments["yx_pixel_size"],
        ]
    )
    phase_thick_3d.visualize_transfer_function(
        viewer,
        real_potential_transfer_function,
        imag_potential_transfer_function,
        zyx_scale,
    )
    input("Showing OTFs. Press <enter> to continue...")
    viewer.layers.select_all()
    viewer.layers.remove_selected()

    # Simulate
    zyx_data = phase_thick_3d.apply_transfer_function(
        zyx_phase,
        real_potential_transfer_function,
        transfer_function_arguments["z_padding"],
        brightness=1e3,
    )

    # Reconstruct
    zyx_recon = phase_thick_3d.apply_inverse_transfer_function(
        zyx_data,
        real_potential_transfer_function,
        imag_potential_transfer_function,
        transfer_function_arguments["z_padding"],
    )

    # Display
    viewer.add_image(zyx_phase.numpy(), name="Phantom", scale=zyx_scale)
    viewer.add_image(zyx_data.numpy(), name="Data", scale=zyx_scale)
    viewer.add_image(zyx_recon.numpy(), name="Reconstruction", scale=zyx_scale)
    input("Showing object, data, and recon. Press <enter> to quit...")


.. _sphx_glr_download_wo_examples_models_phase_thick_3d.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: phase_thick_3d.ipynb <phase_thick_3d.ipynb>`

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

      :download:`Download Python source code: phase_thick_3d.py <phase_thick_3d.py>`

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

      :download:`Download zipped: phase_thick_3d.zip <phase_thick_3d.zip>`