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

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

.. _sphx_glr_auto_examples_sample_microscope.py:

Sample microscope
=======================
This script simulates a microscopic imaging system, generating a random noise image as a mock source and capturing it
through a microscope with adjustable magnification, numerical aperture, and wavelength. It visualizes the original and
processed images dynamically, demonstrating how changes in optical parameters affect image quality and resolution.

.. GENERATED FROM PYTHON SOURCE LINES 7-64

.. code-block:: Python


    import astropy.units as u
    import numpy as np

    import set_path  # noqa - needed for setting the module search path to find openwfs
    from openwfs.plot_utilities import grab_and_show, imshow
    from openwfs.simulation import Microscope, StaticSource, Camera

    specimen_resolution = (1024, 1024)  # height × width in pixels of the specimen image
    specimen_pixel_size = 60 * u.nm  # resolution (pixel size) of the specimen image
    magnification = 40  # magnification from object plane to camera.
    numerical_aperture = 0.85  # numerical aperture of the microscope objective
    wavelength = 532.8 * u.nm  # wavelength of the light, for computing diffraction.
    camera_resolution = (256, 256)  # number of pixels on the camera
    camera_pixel_size = 6.45 * u.um  # Size of the pixels on the camera
    p_limit = 100  # Number steps in the animation

    # Create a random noise image with a few bright spots
    src = StaticSource(
        data=np.maximum(np.random.randint(-10000, 100, specimen_resolution, dtype=np.int16), 0),
        pixel_size=specimen_pixel_size,
    )

    # Create a microscope with the given parameters
    mic = Microscope(
        src,
        magnification=magnification,
        numerical_aperture=numerical_aperture,
        wavelength=wavelength,
    )

    # simulate shot noise in an 8-bit camera with auto-exposure:
    cam = Camera(
        mic,
        analog_max=None,
        shot_noise=True,
        digital_max=255,
        data_shape=camera_resolution,
        pixel_size=camera_pixel_size,
    )
    devices = {"camera": cam, "stage": mic.xy_stage}

    if __name__ == "__main__":
        import matplotlib.pyplot as plt

        plt.subplot(1, 2, 1)
        imshow(src.data)
        plt.title("Original image")
        plt.subplot(1, 2, 2)
        plt.title("Scanned image")
        ax = None
        for p in range(p_limit):
            mic.xy_stage.x = p * 1 * u.um
            mic.numerical_aperture = 1.0 * (p + 1) / p_limit  # NA increases to 1.0
            ax = grab_and_show(cam, ax)
            plt.title(f"NA: {mic.numerical_aperture}, δ: {mic.abbe_limit.to_value(u.um):2.2} μm")
            plt.pause(0.2)


.. _sphx_glr_download_auto_examples_sample_microscope.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_