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

.. only:: html

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

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

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

.. _sphx_glr_examples_plot_roi_demo.py:


Working with RegionOfInterest objects
=====================================

.. GENERATED FROM PYTHON SOURCE LINES 8-12

Import our packages
We can import a variety of neo objects from neo.core and since an ImageSquence
also uses units let's import quantities which is the "units" library
that neo uses under the hood

.. GENERATED FROM PYTHON SOURCE LINES 12-20

.. code-block:: Python


    import matplotlib.pyplot as plt
    import numpy as np
    from neo.core import CircularRegionOfInterest, RectangularRegionOfInterest, PolygonRegionOfInterest, ImageSequence
    from numpy.random import rand
    import random
    import quantities as pq








.. GENERATED FROM PYTHON SOURCE LINES 21-25

First we create our image_sequence. Let's generate some data
In this simulated dataset we will just make an image that is
100x100 pixels and then we will make 50 frames of this image
finally we will fill with random values for the data

.. GENERATED FROM PYTHON SOURCE LINES 25-38

.. code-block:: Python


    l = []
    for frame in range(50):
        l.append([])
        for y in range(100):
            l[frame].append([])
            for x in range(100):
                l[frame][y].append(random.randint(0, 50))

    # make an ImageSquence in Neo
    image_seq = ImageSequence(l, sampling_rate=500 * pq.Hz, spatial_scale="m", units="V")









.. GENERATED FROM PYTHON SOURCE LINES 39-40

Now we will write a function for plotting an roi

.. GENERATED FROM PYTHON SOURCE LINES 40-52

.. code-block:: Python

    def plot_roi(roi, shape):
        img = rand(120, 100)
        pir = np.array(roi.pixels_in_region()).T
        img[pir[1], pir[0]] = 5

        plt.imshow(img, cmap="gray_r")
        plt.clim(0, 5)

        ax = plt.gca()
        ax.add_artist(shape)









.. GENERATED FROM PYTHON SOURCE LINES 53-54

Finally we will plot each roi to demonstrate how we could high regions of interest

.. GENERATED FROM PYTHON SOURCE LINES 54-75

.. code-block:: Python


    # First a nice circle
    roi = CircularRegionOfInterest(image_sequence=image_seq, x=50.3, y=50.8, radius=30.2)
    shape = plt.Circle(roi.centre, roi.radius, color="r", fill=False)
    plt.subplot(1, 3, 1)
    plot_roi(roi, shape)

    # Next a rectangle
    roi = RectangularRegionOfInterest(image_sequence=image_seq, x=50.3, y=40.2, width=40.1, height=50.3)
    shape = plt.Rectangle((roi.x - roi.width / 2.0, roi.y - roi.height / 2.0), roi.width, roi.height, color="r", fill=False)
    plt.subplot(1, 3, 2)
    plot_roi(roi, shape)

    # Finally we can make a polygon (in this case a triangle)
    roi = PolygonRegionOfInterest(image_seq, (20.3, 30.2), (80.7, 30.1), (55.2, 59.4))
    shape = plt.Polygon(np.array(roi.vertices), closed=True, color="r", fill=False)
    plt.subplot(1, 3, 3)
    plot_roi(roi, shape)

    plt.tight_layout()
    plt.show()



.. image-sg:: /examples/images/sphx_glr_plot_roi_demo_001.png
   :alt: plot roi demo
   :srcset: /examples/images/sphx_glr_plot_roi_demo_001.png
   :class: sphx-glr-single-img






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

   **Total running time of the script:** (0 minutes 0.608 seconds)


.. _sphx_glr_download_examples_plot_roi_demo.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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