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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90 changes: 46 additions & 44 deletions examples/pylab_examples/mri_with_eeg.py
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Original file line number Diff line number Diff line change
@@ -1,77 +1,79 @@
"""
This now uses the imshow command instead of pcolor which *is much
faster*
"""Displays a set of subplots with an MRI image, its intensity histogram and
some EEG traces.

NB: ones uses the imshow command instead of pcolor which *is much faster*.
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Delete this comment line. Even mentioning pcolor here is confusing. I suspect the line dates back to the very earliest days, when imshow was first added to mpl.

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You were right (see 6721163). I have removed it.

"""

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.pyplot import *
from matplotlib.collections import LineCollection
import matplotlib.cbook as cbook
# I use if 1 to break up the different regions of code visually
from matplotlib.ticker import MultipleLocator

if 1: # load the data
# data are 256x256 16 bit integers
# 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
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I really dislike this syntay. Can we get rid of this? It is using python code for documentation purposes.
Having comments should be enough to break the different regions of the code visually.

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@afvincent afvincent Sep 28, 2016 •
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I pushed a new commit (d06e572) that get rid of this idiom.

# 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
im.shape = (256, 256)

if 1: # plot the MRI in pcolor
subplot(221)
imshow(im, cmap=cm.gray)
axis('off')
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
subplot(222)
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/(2.0**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
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)
print('Loading EEG %s' % eegfile)
data = np.fromstring(open(eegfile, 'rb').read(), float)
data.shape = numSamples, numRows
t = 10.0 * np.arange(numSamples, dtype=float)/numSamples
data.shape = (numSamples, numRows)
t = 10.0 * np.arange(numSamples) / numSamples
ticklocs = []
ax = subplot(212)
xlim(0, 10)
xticks(np.arange(10))
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.
dr = (dmax - dmin) * 0.7 # Crowd them a bit.
y0 = dmin
y1 = (numRows - 1) * dr + dmax
ylim(y0, y1)
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)
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)
lines = LineCollection(segs, offsets=offsets, transOffset=None)
ax2.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'])
# Set the yticks to use axes coords on the y axis
ax2.set_yticks(ticklocs)
ax2.set_yticklabels(['PG3', 'PG5', 'PG7', 'PG9'])

xlabel('time (s)')
ax2.set_xlabel('Time (s)')

show()
plt.tight_layout()
plt.show()
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