.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples/standards/pixel_coodinates.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_examples_standards_pixel_coodinates.py>`
        to download the full example code.

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

.. _sphx_glr_examples_standards_pixel_coodinates.py:


====================
Coordinates in Pyxem
====================

Pyxem is flexible in how it handles coordinates for a diffraction pattern.

There are three main ways to handle coordinates in Pyxem:

1. Pixel coordinates
2. Calibrated Coordinates with evenly spaced axes
3. Calibrated Coordinates with unevenly spaced axes (e.g. corrected for the Ewald sphere)

.. GENERATED FROM PYTHON SOURCE LINES 14-23

.. code-block:: Python


    import pyxem as pxm
    from skimage.morphology import disk


    s = pxm.signals.Diffraction2D(disk((10)))
    s.calibration.center = None
    print(s.calibration.center)





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    [10.0, 10.0]




.. GENERATED FROM PYTHON SOURCE LINES 24-26

.. code-block:: Python


    s.plot(axes_ticks=True)



.. image-sg:: /examples/standards/images/sphx_glr_pixel_coodinates_001.png
   :alt:  Signal
   :srcset: /examples/standards/images/sphx_glr_pixel_coodinates_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 27-31

From the plot above you can see that hyperspy automatically sets the axes ticks to be centered
on each pixel. This means that for a 21x21 pixel image, the center is at (-10, -10) in pixel coordinates.
if we change the scale using the calibration function it will automatically adjust the center.  Here it is
now (-1, -1)

.. GENERATED FROM PYTHON SOURCE LINES 31-38

.. code-block:: Python


    s.calibration.scale = 0.1
    s.calibration.units = "nm$^{-1}$"
    s.plot(axes_ticks=True)
    print(s.calibration.center)





.. image-sg:: /examples/standards/images/sphx_glr_pixel_coodinates_002.png
   :alt:  Signal
   :srcset: /examples/standards/images/sphx_glr_pixel_coodinates_002.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    [10.0, 10.0]




.. GENERATED FROM PYTHON SOURCE LINES 39-43

Azimuthal Integration
---------------------

Now if we do integrate this dataset it will choose the appropriate center based on the center pixel.

.. GENERATED FROM PYTHON SOURCE LINES 43-47

.. code-block:: Python


    az = s.get_azimuthal_integral2d(npt=30)
    az.plot()




.. image-sg:: /examples/standards/images/sphx_glr_pixel_coodinates_003.png
   :alt:  Signal
   :srcset: /examples/standards/images/sphx_glr_pixel_coodinates_003.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none


      0%|          | 0/2 [00:00<?, ?it/s]
     50%|█████     | 1/2 [00:02<00:02,  2.66s/it]
    100%|██████████| 2/2 [00:02<00:00,  1.33s/it]




.. GENERATED FROM PYTHON SOURCE LINES 48-53

Non-Linear Axes
---------------

Now consider the case where we have non-linear axes. In this case the center is still (10,10)
but things are streatched based on the effects of the Ewald Sphere.

.. GENERATED FROM PYTHON SOURCE LINES 53-62

.. code-block:: Python


    s.calibration.beam_energy = 200
    s.calibration.detector(pixel_size=0.1, detector_distance=3)
    print(s.calibration.center)
    s.plot()

    az = s.get_azimuthal_integral2d(npt=30)
    az.plot()




.. rst-class:: sphx-glr-horizontal


    *

      .. image-sg:: /examples/standards/images/sphx_glr_pixel_coodinates_004.png
         :alt:  Signal
         :srcset: /examples/standards/images/sphx_glr_pixel_coodinates_004.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /examples/standards/images/sphx_glr_pixel_coodinates_005.png
         :alt:  Signal
         :srcset: /examples/standards/images/sphx_glr_pixel_coodinates_005.png
         :class: sphx-glr-multi-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    [np.int64(10), np.int64(10)]

      0%|          | 0/2 [00:00<?, ?it/s]
    100%|██████████| 2/2 [00:00<00:00, 1491.84it/s]




.. GENERATED FROM PYTHON SOURCE LINES 63-64

sphinx_gallery_thumbnail_number = 4


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

   **Total running time of the script:** (0 minutes 7.773 seconds)


.. _sphx_glr_download_examples_standards_pixel_coodinates.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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