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

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

.. _sphx_glr_auto_examples_plot_magnification.py:


Zooming in on a seeded specimen
===============================

One seeded specimen, gold particles on holey carbon over a copper mesh grid, seen from a
low-magnification atlas down to single particles. The images are the noiseless electron
flux the twin renders before the detector model.

.. GENERATED FROM PYTHON SOURCE LINES 9-31



.. image-sg:: /auto_examples/images/sphx_glr_plot_magnification_001.png
   :alt: 120x, field 85.3 um, 2,500x, field 4.1 um, 20,000x, field 0.512 um, 60,000x, field 0.171 um
   :srcset: /auto_examples/images/sphx_glr_plot_magnification_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


    import matplotlib.pyplot as plt

    from de_twin import DigitalTwin, ManualClock

    twin = DigitalTwin("Dense Au on holey C", camera="DESim", clock=ManualClock(), seed=3)
    feature = twin.specimen.features()[0]  # a particle cluster, in world micrometres

    fig, axes = plt.subplots(1, 4, figsize=(12, 3.4))
    for ax, (mag, intensity) in zip(axes, [(120, 0.97), (2500, 0.75), (20000, 0.5), (60000, 0.5)]):
        twin.column.set("Magnification", mag)
        twin.column.set_intensity(intensity)  # spread the beam at low magnification
        if mag >= 20000:
            twin.column.move_stage(x=-feature.center_um[0], y=-feature.center_um[1])
        flux = twin.flux(twin.request())
        optics = twin.optics(twin.request())
        ax.imshow(flux, cmap="gray")
        fov_um = optics.specimen_pixel_nm * flux.shape[1] / 1000
        ax.set_title(f"{mag:,}x, field {fov_um:.3g} um", fontsize=9)
        ax.axis("off")
    fig.tight_layout()
    plt.show()


.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 5.071 seconds)


.. _sphx_glr_download_auto_examples_plot_magnification.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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