

.. _sphx_glr_gallery_pylab_examples_mri_with_eeg.py:


============
MRI With EEG
============

Displays a set of subplots with an MRI image, its intensity
histogram and some EEG traces.




.. image:: /gallery/pylab_examples/images/sphx_glr_mri_with_eeg_001.png
    :align: center





.. code-block:: python


    from __future__ import division, print_function

    import numpy as np
    import matplotlib.pyplot as plt
    import matplotlib.cbook as cbook
    import matplotlib.cm as cm

    from matplotlib.collections import LineCollection
    from matplotlib.ticker import MultipleLocator

    fig = plt.figure("MRI_with_EEG")

    # Load the MRI data (256x256 16 bit integers)
    with cbook.get_sample_data('s1045.ima.gz') as dfile:
        im = np.fromstring(dfile.read(), np.uint16).reshape((256, 256))

    # Plot the MRI image
    ax0 = fig.add_subplot(2, 2, 1)
    ax0.imshow(im, cmap=cm.gray)
    ax0.axis('off')

    # Plot the histogram of MRI intensity
    ax1 = fig.add_subplot(2, 2, 2)
    im = np.ravel(im)
    im = im[np.nonzero(im)]  # Ignore the background
    im = im / (2**16 - 1)  # Normalize
    ax1.hist(im, bins=100)
    ax1.xaxis.set_major_locator(MultipleLocator(0.4))
    ax1.minorticks_on()
    ax1.set_yticks([])
    ax1.set_xlabel('Intensity (a.u.)')
    ax1.set_ylabel('MRI density')

    # Load the EEG data
    numSamples, numRows = 800, 4
    with cbook.get_sample_data('eeg.dat') as eegfile:
        data = np.fromfile(eegfile, dtype=float)
    data.shape = (numSamples, numRows)
    t = 10.0 * np.arange(numSamples) / numSamples

    # Plot the EEG
    ticklocs = []
    ax2 = fig.add_subplot(2, 1, 2)
    ax2.set_xlim(0, 10)
    ax2.set_xticks(np.arange(10))
    dmin = data.min()
    dmax = data.max()
    dr = (dmax - dmin) * 0.7  # Crowd them a bit.
    y0 = dmin
    y1 = (numRows - 1) * dr + dmax
    ax2.set_ylim(y0, y1)

    segs = []
    for i in range(numRows):
        segs.append(np.hstack((t[:, np.newaxis], data[:, i, np.newaxis])))
        ticklocs.append(i * dr)

    offsets = np.zeros((numRows, 2), dtype=float)
    offsets[:, 1] = ticklocs

    lines = LineCollection(segs, offsets=offsets, transOffset=None)
    ax2.add_collection(lines)

    # Set the yticks to use axes coordinates on the y axis
    ax2.set_yticks(ticklocs)
    ax2.set_yticklabels(['PG3', 'PG5', 'PG7', 'PG9'])

    ax2.set_xlabel('Time (s)')


    plt.tight_layout()
    plt.show()

**Total running time of the script:** ( 0 minutes  0.176 seconds)



.. container:: sphx-glr-footer


  .. container:: sphx-glr-download

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



  .. container:: sphx-glr-download

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

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

    `Generated by Sphinx-Gallery <https://sphinx-gallery.readthedocs.io>`_
