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DOC: switch pylab example mri_with_eeg.py to OO interface + cosmetick fixes
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tacaswell
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matplotlib:master
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afvincent:doc_pylab_examples_mri_with_eeg
Oct 3, 2016
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86bf335
DOC: switch to pyplot OO interface
afvincent 330a807
DOC: cosmetick adjustements (tight_layout, labels and comments)
afvincent 2d65280
Replace (unfortunate) manual xticks with example of MultipleLocator
afvincent 0c204d2
DOC: correct statement in docstring
afvincent d06e572
Switch to triple quotes comment blocks as visual separators
afvincent f5da34f
DOC: structure blocks of code with only a top real comment line
afvincent c8388f9
Close files or use safer access functions
afvincent 38d92b5
Remove top comment 'pcolor vs imshow'
afvincent dfc9cca
Normalize intensity values in [0, 1] and adjust x-ticks
afvincent db3d206
Add a top dosctring and perform small cleaning/fixing ops to mri_with…
afvincent 96ff817
Switch mri_demo.py to OO interface
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,13 +1,19 @@ | ||
| from __future__ import print_function | ||
| """Displays an MRI image.""" | ||
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| import matplotlib.pyplot as plt | ||
| import matplotlib.cbook as cbook | ||
| import matplotlib.cm as cm | ||
| import numpy as np | ||
| # data are 256x256 16 bit integers | ||
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| fig, ax = plt.subplots(num="MRI_demo") | ||
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| # 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) | ||
| dfile.close() | ||
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| plt.imshow(im, cmap=plt.cm.gray) | ||
| plt.axis('off') | ||
| ax.imshow(im, cmap=cm.gray) | ||
| ax.axis('off') | ||
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||
| plt.show() |
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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. | ||
| """ | ||
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| from __future__ import division, print_function | ||
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| import numpy as np | ||
| import matplotlib.pyplot as plt | ||
| import matplotlib.cbook as cbook | ||
| import matplotlib.cm as cm | ||
|
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||
| 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 | ||
|
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||
| 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 | ||
|
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| if 1: # plot the MRI in pcolor | ||
| subplot(221) | ||
| imshow(im, cmap=cm.gray) | ||
| axis('off') | ||
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| 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') | ||
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| if 1: # plot the EEG | ||
| # load the data | ||
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| 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, 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) | ||
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| segs = [] | ||
| for i in range(numRows): | ||
| segs.append(np.hstack((t[:, np.newaxis], data[:, i, np.newaxis]))) | ||
| ticklocs.append(i*dr) | ||
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| offsets = np.zeros((numRows, 2), dtype=float) | ||
| offsets[:, 1] = ticklocs | ||
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| lines = LineCollection(segs, offsets=offsets, | ||
| transOffset=None, | ||
| ) | ||
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| ax.add_collection(lines) | ||
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| # set the yticks to use axes coords on the y axis | ||
| ax.set_yticks(ticklocs) | ||
| ax.set_yticklabels(['PG3', 'PG5', 'PG7', 'PG9']) | ||
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| xlabel('time (s)') | ||
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| show() | ||
| from matplotlib.ticker import MultipleLocator | ||
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| fig = plt.figure("MRI_with_EEG") | ||
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| # 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') | ||
|
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||
| # 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 | ||
|
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| # 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) | ||
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| segs = [] | ||
| for i in range(numRows): | ||
| segs.append(np.hstack((t[:, np.newaxis], data[:, i, np.newaxis]))) | ||
| ticklocs.append(i * dr) | ||
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| offsets = np.zeros((numRows, 2), dtype=float) | ||
| offsets[:, 1] = ticklocs | ||
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| lines = LineCollection(segs, offsets=offsets, transOffset=None) | ||
| ax2.add_collection(lines) | ||
|
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| # Set the yticks to use axes coordinates on the y axis | ||
| ax2.set_yticks(ticklocs) | ||
| ax2.set_yticklabels(['PG3', 'PG5', 'PG7', 'PG9']) | ||
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| ax2.set_xlabel('Time (s)') | ||
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| plt.tight_layout() | ||
| plt.show() | ||
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This file should be closed.
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get_sample_datashould 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.