8000 DOC: switch pylab example `mri_with_eeg.py` to OO interface + cosmetick fixes by afvincent · Pull Request #7192 · matplotlib/matplotlib · GitHub
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DOC: switch pylab example mri_with_eeg.py to OO interface + cosmetick fixes #7192

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Merged
merged 11 commits into from
Oct 3, 2016
Merged

DOC: switch pylab example mri_with_eeg.py to OO interface + cosmetick fixes #7192

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86bf335
DOC: switch to pyplot OO interface
afvincent Sep 28, 2016
330a807
DOC: cosmetick adjustements (tight_layout, labels and comments)
afvincent Sep 28, 2016
2d65280
Replace (unfortunate) manual xticks with example of MultipleLocator
afvincent Sep 28, 2016
0c204d2
DOC: correct statement in docstring
afvincent Sep 28, 2016
d06e572
Switch to triple quotes comment blocks as visual separators
afvincent Sep 28, 2016
f5da34f
DOC: structure blocks of code with only a top real comment line
afvincent Sep 30, 2016
c8388f9
Close files or use safer access functions
afvincent Oct 1, 2016
38d92b5
Remove top comment 'pcolor vs imshow'
afvincent Oct 2, 2016
dfc9cca
Normalize intensity values in [0, 1] and adjust x-ticks
afvincent Oct 2, 2016
db3d206
Add a top dosctring and perform small cleaning/fixing ops to mri_with…
afvincent Oct 2, 2016
96ff817
Switch mri_demo.py to OO interface
afvincent Oct 2, 2016
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Switch to triple quotes comment blocks as visual separators
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@afvincent
afvincent committed Sep 28, 2016
commit d06e57283f97d6d014085dd8f24e73c7f9c39f22
125 changes: 67 additions & 58 deletions examples/pylab_examples/mri_with_eeg.py
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Expand Up @@ -14,66 +14,75 @@
from matplotlib.collections import LineCollection
from matplotlib.ticker import MultipleLocator

# NB: one uses "if 1:" to break up the different regions of code visually
fig = plt.figure("MRI_with_EEG")

if 1: # Load the data
# Data are 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)

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

if 1: # 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**15) # Normalize
ax1.hist(im, 100)
ax1.xaxis.set_major_locator(MultipleLocator(0.5))
ax1.set_yticks([])
ax1.set_xlabel('Intensity')
ax1.set_ylabel('MRI density')

if 1: # Plot the EEG
# Load the data
numSamples, numRows = 800, 4
eegfile = cbook.get_sample_data('eeg.dat', asfileobj=False)
print('Loading EEG %s' % eegfile)
data = np.fromstring(open(eegfile, 'rb').read(), float)
data.shape = (numSamples, numRows)
t = 10.0 * np.arange(numSamples) / numSamples
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 coords on the y axis
ax2.set_yticks(ticklocs)
ax2.set_yticklabels(['PG3', 'PG5', 'PG7', 'PG9'])

ax2.set_xlabel('Time (s)')
"""
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I am sorry, but I still don't like this. This is also python code, meant for a specific purpose. Can you switch to comments?

Load the data
"""
# Data are 256x256 16 bit integers
dfile = cbook.get_sample_data('s1045.ima.gz')
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This file should be closed.

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get_sample_data should probably be deprecated and replaced with something with a sane interface.
In any case, python will close that file automatically at the end of the script without problems considering it is a read-only file.

im = np.fromstring(dfile.read(), np.uint16).astype(float)
im.shape = (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**15) # Normalize
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So this is how it was originally, but I'm not sure if it's right. The intensities go over 1 and a uint16 should have a maximum of 2**16, but maybe this just how MRIs are defined? I don't know, but it seems odd.

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ping @matthew-brett our resident expert on MRI :)

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I agree that this normalization seemed weird to me too but I did not feel comfortable changing it to (2**16 - 1) as I do not know anything about MRI. PS: anyway, currently there are no units for the MRI...

ax1.hist(im, 100)
ax1.xaxis.set_major_locator(MultipleLocator(0.5))
ax1.set_yticks([])
ax1.set_xlabel('Intensity')
ax1.set_ylabel('MRI density')

"""
Plot the EEG
"""
# Load the data
numSamples, numRows = 800, 4
eegfile = cbook.get_sample_data('eeg.dat', asfileobj=False)
print('Loading EEG %s' % eegfile)
data = np.fromstring(open(eegfile, 'rb').read(), float)
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Leaky open; can use np.fromfile(eegfile, float) instead

data.shape = (numSamples, numRows)
t = 10.0 * np.arange(numSamples) / numSamples

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 coords 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()
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