# note, this is currentl *very slow*. I'm working on improving the
# efficiency of pcolor. If you want to run this example and your
# computer is not very fast, I suggest you grab a cup of coffee while
# it runs. Look for major improvments in pcolor in future releases of
# matplotlib when we add image handling capability in extension module
# code
from __future__ import division
from matplotlib.matlab import *
from matplotlib.lines import Line2D
from matplotlib.transforms import Transform, Bound1D
# 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 = fromstring(file(dfile, 'rb').read(), Int16).astype(Float)
im.shape = 256, 256
# flip upside down
im = array([im[i] for i in arange(255,-1,-1)])
if 1: # plot the MRI in pcolor
subplot(221)
pcolor(im, shading='flat')
axis('off')
if 1: # plot the histogram of MRI intensity
subplot(222)
im.shape = 256*256,
im = take(im, nonzero(im)) # ignore the background
im = im/(2.0**15) # normalize
hist(im, 100)
set(gca(), 'xticks', [-1, -.5, 0, .5, 1])
set(gca(), 'yticks', [])
xlabel('intensity')
ylabel('MRI density')
if 1: # plot the EEG
# load the data
numSamples, numRows = 800,4
data = fromstring(file('data/eeg.dat', 'rb').read(), Float)
data.shape = numSamples, numRows
t = arange(numSamples)/float(numSamples)*10.0
ticklocs = []
ax = subplot(212)
height = 72 # height of one EEG in pixels
# transform data to axes coord (0,1)
transy = Transform(Bound1D(-.05,.05), Bound1D(-.2,.2))
for i in range(numRows):
thisLine = Line2D(
ax.dpi, ax.bbox, t, data[:,i]-data[0,i],
transx=ax.xaxis.transData,
transy=transy)
offset = (i+1)/(numRows+1)
thisLine.set_vertical_offset(offset, ax.yaxis.transAxis)
ax.add_line(thisLine)
ticklocs.append(offset)
set(gca(), 'xlim', [0,10])
set(gca(), 'xticks', arange(10))
yticks = set(gca(), 'yticks', ticklocs)
set(gca(), 'yticklabels', ['PG3', 'PG5', 'PG7', 'PG9'])
# set the yticks to use axes coords on the y axis
set(yticks, 'transform', ax.yaxis.transAxis)
xlabel('time (s)')
savefig('mri_with_eeg_small.png', dpi=60)
savefig('mri_with_eeg_large.png', dpi=120)
show()
