Logo Search packages:      
Sourcecode: matplotlib version File versions

mri_with_eeg.py

#!/usr/bin/env python
"""
This now uses the imshow command instead of pcolor which *is much
faster*
"""
from __future__ import division

import numpy as np

from matplotlib.pyplot import *
from matplotlib.collections import LineCollection

# I use if 1 to break up the different regions of code visually

if 1:   # load the data
    # data are 256x256 16 bit integers
    dfile = '../data/s1045.ima'
    im = np.fromstring(file(dfile, 'rb').read(), np.uint16).astype(float)
    im.shape = 256, 256

if 1: # plot the MRI in pcolor
    subplot(221)
    imshow(im, cmap=cm.jet)
    axis('off')

if 1:  # plot the histogram of MRI intensity
    subplot(222)
    im = np.ravel(im)
    im = im[np.nonzero(im)] # ignore the background
    im = im/(2.0**15) # normalize
    hist(im, 100)
    xticks([-1, -.5, 0, .5, 1])
    yticks([])
    xlabel('intensity')
    ylabel('MRI density')

if 1:   # plot the EEG
    # load the data

    numSamples, numRows = 800,4
    data = np.fromstring(file('../data/eeg.dat', 'rb').read(), float)
    data.shape = numSamples, numRows
    t = 10.0 * np.arange(numSamples, dtype=float)/numSamples
    ticklocs = []
    ax = subplot(212)
    xlim(0,10)
    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
    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,
                           )

    ax.add_collection(lines)

    # set the yticks to use axes coords on the y axis
    ax.set_yticks(ticklocs)
    ax.set_yticklabels(['PG3', 'PG5', 'PG7', 'PG9'])

    xlabel('time (s)')

show()

Generated by  Doxygen 1.6.0   Back to index