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

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

.. _sphx_glr_auto_examples_micro_manager_scanning_microscope.py:

Micro-Manager simulated scanning microscope
======================================================================
This script simulates a scanning microscope with a pre-set image as a mock specimen.

To use it:

  * make sure  you have the PyDevice adapter installed in Micro-Manager (install the nightly build if you don't have it).
  * load the micro_manager_scanning_microscope.cfg hardware configuration in Micro-Manager,
  * locate the micro_manager_scanning_microscope.py in the file open dialog box that popps up.
  * take a snapshot or turn on live preview, you may need to auto-adjust the color scale
  * experiment with the scanning microscope parameters such as zoom in the script to see how they affect the image

.. GENERATED FROM PYTHON SOURCE LINES 13-75

.. code-block:: Python


    import astropy.units as u
    import skimage

    from openwfs.devices import ScanningMicroscope, Axis
    from openwfs.devices.galvo_scanner import InputChannel

    # parameters for Thorlabs SS30X-AG
    scale = Axis.compute_scale(
        optical_deflection=1.0 / (0.22 * u.V / u.deg),
        galvo_to_pupil_magnification=2,
        objective_magnification=16,
        reference_tube_lens=200 * u.mm,
    )

    acceleration = Axis.compute_acceleration(
        optical_deflection=1.0 / (0.22 * u.V / u.deg),
        torque_constant=2.8e5 * u.dyne * u.cm / u.A,
        rotor_inertia=8.25 * u.g * u.cm**2,
        maximum_current=4 * u.A,
    )

    # scale = 440 * u.um / u.V (calibrated)
    sample_rate = 0.5 * u.MHz
    reference_zoom = 1.2
    y_axis = Axis(
        channel="Dev4/ao0",
        v_min=-2.0 * u.V,
        v_max=2.0 * u.V,
        maximum_acceleration=acceleration,
        scale=scale,
    )
    x_axis = Axis(
        channel="Dev4/ao1",
        v_min=-2.0 * u.V,
        v_max=2.0 * u.V,
        maximum_acceleration=acceleration,
        scale=scale,
    )
    input_channel = InputChannel("Dev4/ai0", -1.0 * u.V, 1.0 * u.V)
    test_image = skimage.data.hubble_deep_field() * 256

    scanner = ScanningMicroscope(
        sample_rate=sample_rate,
        input=input_channel,
        y_axis=y_axis,
        x_axis=x_axis,
        test_pattern="image",
        reference_zoom=reference_zoom,
        resolution=1024,
        test_image=test_image,
    )

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

        scanner.binning = 4
        plt.imshow(scanner.read(), cmap="gray")
        plt.colorbar()
        plt.show()
    else:
        devices = {"microscope": scanner}


.. _sphx_glr_download_auto_examples_micro_manager_scanning_microscope.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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