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

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

.. _sphx_glr_auto_examples_region_of_interest_PolygonROI.py:


PolygonROI
==========

Use a :class:`~.api.roi.PolygonROI` interactively on a :class:`~.api.signals.Signal2D`.

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.. code-block:: Python

    import hyperspy.api as hs








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Create a signal:

.. GENERATED FROM PYTHON SOURCE LINES 13-15

.. code-block:: Python

    s = hs.data.atomic_resolution_image()








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Create the ROI, here a :class:`~.api.roi.PolygonROI`:

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.. code-block:: Python

    roi = hs.roi.PolygonROI()








.. GENERATED FROM PYTHON SOURCE LINES 20-30

Initializing the ROI with no arguments puts you directly into constructing the 
polygon. Do this by clicking where you want the vertices. Click the first vertex
to complete the polygon. You can reset the polygon by pressing "Esc" and you
can move the entire polygon by shift-clicking and dragging.

An alternative to define the :class:`~.api.roi.PolygonROI` interactively is
to set the vertices of the ROI using the :attr:`~.api.roi.PolygonROI.vertices`.

We can use :meth:`~hyperspy.roi.BaseInteractiveROI.interactive` to add the ROI to the
figure and get the signal from the ROI.

.. GENERATED FROM PYTHON SOURCE LINES 30-35

.. code-block:: Python


    s.plot()
    roi.vertices = [(2, 4.5), (4.5, 4.5), (4.5, 2), (3, 3)]
    s_roi = roi.interactive(s, axes=s.axes_manager.signal_axes)




.. image-sg:: /auto_examples/region_of_interest/images/sphx_glr_PolygonROI_001.png
   :alt:  Signal
   :srcset: /auto_examples/region_of_interest/images/sphx_glr_PolygonROI_001.png
   :class: sphx-glr-single-img





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Then we can extract the ROI from the signal and plot it.

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.. code-block:: Python


    s_roi.plot()




.. image-sg:: /auto_examples/region_of_interest/images/sphx_glr_PolygonROI_002.png
   :alt:  Signal
   :srcset: /auto_examples/region_of_interest/images/sphx_glr_PolygonROI_002.png
   :class: sphx-glr-single-img





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The signal will contain a lot of NaNs, so take this into consideration when
doing further processing. E.g. use :meth:`~.api.signals.BaseSignal.nanmean`
instead of :meth:`~.api.signals.BaseSignal.mean`.

.. GENERATED FROM PYTHON SOURCE LINES 44-48

.. code-block:: Python


    mean_value = s_roi.nanmean(axis=(0,1)).data[0]
    print("Mean value in ROI:", mean_value)





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

 .. code-block:: none

    Mean value in ROI: 5.207270455522169




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In some cases, it is easier to choose the area to remove rather than keep.
By using the ``inverted`` parameter, everything except the ROI will be retained:

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.. code-block:: Python


    s_roi_inv = roi(s, inverted=True)
    s_roi_inv.plot()



.. image-sg:: /auto_examples/region_of_interest/images/sphx_glr_PolygonROI_003.png
   :alt:  Signal
   :srcset: /auto_examples/region_of_interest/images/sphx_glr_PolygonROI_003.png
   :class: sphx-glr-single-img






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

   **Total running time of the script:** (0 minutes 7.639 seconds)


.. _sphx_glr_download_auto_examples_region_of_interest_PolygonROI.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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