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comparison dmri.py @ 14:2b914b6a0c83 draft

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author greg
date Fri, 03 Nov 2017 14:13:37 -0400
parents 1467f96db74a
children b9fbc233c9c2
comparison
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13:85b0aa4ab75f 14:2b914b6a0c83
2 import argparse 2 import argparse
3 import os 3 import os
4 import nibabel 4 import nibabel
5 import shutil 5 import shutil
6 6
7 from dipy.core.gradients import gradient_table
7 from dipy.data import fetch_sherbrooke_3shell 8 from dipy.data import fetch_sherbrooke_3shell
9 from dipy.io import read_bvals_bvecs
8 from matplotlib import pyplot 10 from matplotlib import pyplot
9 11
10 parser = argparse.ArgumentParser() 12 parser = argparse.ArgumentParser()
11 parser.add_argument('--input', dest='input', help='Input dataset') 13 parser.add_argument('--input', dest='input', help='Input dataset')
12 parser.add_argument('--output', dest='output', help='Output dataset') 14 parser.add_argument('--output_gtab', dest='output_gtab', help='Output gradient table dataset')
15 parser.add_argument('--output_png', dest='output_png', help='Output dataset')
13 16
14 args = parser.parse_args() 17 args = parser.parse_args()
15 18
16 input_dir = 'sherbrooke_3shell' 19 input_dir = 'sherbrooke_3shell'
17 # Get input data. 20 # Get input data.
31 pyplot.subplot(1, 2, 1).set_axis_off() 34 pyplot.subplot(1, 2, 1).set_axis_off()
32 pyplot.imshow(data[:, :, axial_middle, 0].T, cmap='gray', origin='lower') 35 pyplot.imshow(data[:, :, axial_middle, 0].T, cmap='gray', origin='lower')
33 pyplot.subplot(1, 2, 2).set_axis_off() 36 pyplot.subplot(1, 2, 2).set_axis_off()
34 pyplot.imshow(data[:, :, axial_middle, 10].T, cmap='gray', origin='lower') 37 pyplot.imshow(data[:, :, axial_middle, 10].T, cmap='gray', origin='lower')
35 pyplot.savefig('data.png', bbox_inches='tight') 38 pyplot.savefig('data.png', bbox_inches='tight')
36 shutil.move('data.png', args.output) 39 shutil.move('data.png', args.output_png)
40 # Load the b-values and b-vectors.
41 bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
42 gtab = gradient_table(bvals, bvecs)
43 with open(args.output_gtab) as fh:
44 fh.write(gtab.info)