.. _pylab_examples-mri_with_eeg:

pylab_examples example code: mri_with_eeg.py
============================================



.. plot:: /home/tcaswell/src/p/matplotlib/doc/mpl_examples/pylab_examples/mri_with_eeg.py

::

    """Displays a set of subplots with an MRI image, its intensity histogram and
    some EEG traces.
    """
    
    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)
    dfile = cbook.get_sample_data('s1045.ima.gz')
    im = np.fromstring(dfile.read(), np.uint16).astype(float)
    im.shape = (256, 256)
    dfile.close()
    
    # 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
    eegfile = cbook.get_sample_data('eeg.dat', asfileobj=False)
    print('Loading EEG %s' % 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()
    

Keywords: python, matplotlib, pylab, example, codex (see :ref:`how-to-search-examples`)