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comparison dmri.py @ 11:173c5c07b2f9 draft

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author greg
date Fri, 03 Nov 2017 13:51:40 -0400
parents 5014ba48e15e
children 1467f96db74a
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10:5014ba48e15e 11:173c5c07b2f9
3 import os 3 import os
4 import nibabel 4 import nibabel
5 import shutil 5 import shutil
6 6
7 from dipy.data import fetch_sherbrooke_3shell 7 from dipy.data import fetch_sherbrooke_3shell
8 from matplotlib import pyplot
8 9
9 parser = argparse.ArgumentParser() 10 parser = argparse.ArgumentParser()
10 parser.add_argument('--input', dest='input', help='Input dataset') 11 parser.add_argument('--input', dest='input', help='Input dataset')
11 parser.add_argument('--output', dest='output', help='Output dataset') 12 parser.add_argument('--output', dest='output', help='Output dataset')
12 13
24 # data is a 4D array where the first 3 dimensions are the i, j, 25 # data is a 4D array where the first 3 dimensions are the i, j,
25 # k voxel coordinates and the last dimension is the number of 26 # k voxel coordinates and the last dimension is the number of
26 # non-weighted (S0s) and diffusion-weighted volumes. 27 # non-weighted (S0s) and diffusion-weighted volumes.
27 # Visualize the results using matplotlib. 28 # Visualize the results using matplotlib.
28 axial_middle = data.shape[2] // 2 29 axial_middle = data.shape[2] // 2
29 plt.figure('Showing the datasets') 30 pyplot.figure('Showing the datasets')
30 plt.subplot(1, 2, 1).set_axis_off() 31 pyplot.subplot(1, 2, 1).set_axis_off()
31 plt.imshow(data[:, :, axial_middle, 0].T, cmap='gray', origin='lower') 32 pyplot.imshow(data[:, :, axial_middle, 0].T, cmap='gray', origin='lower')
32 plt.subplot(1, 2, 2).set_axis_off() 33 pyplot.subplot(1, 2, 2).set_axis_off()
33 plt.imshow(data[:, :, axial_middle, 10].T, cmap='gray', origin='lower') 34 pyplot.imshow(data[:, :, axial_middle, 10].T, cmap='gray', origin='lower')
34 plt.show() 35 pyplot.show()
35 plt.savefig(args.output, bbox_inches='tight') 36 pyplot.savefig(args.output, bbox_inches='tight')