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comparison dmri.py @ 0:94f6b3e28c36 draft

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author greg
date Fri, 03 Nov 2017 08:52:47 -0400
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children 6fe81fec6cb9
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-1:000000000000 0:94f6b3e28c36
1 #!/usr/bin/env python
2 import argparse
3 import os
4 import nibabel
5 import shutil
6
7 from dipy.data import fetch_sherbrooke_3shell
8
9 parser = argparse.ArgumentParser()
10 parser.add_argument('--input', dest='input', help='Input dataset')
11 parser.add_argument('--output', dest='output', help='Output dataset')
12
13 args = parser.parse_args()
14
15 def move_directory_files(source_dir, destination_dir, copy=False, remove_source_dir=False):
16 source_directory = os.path.abspath(source_dir)
17 destination_directory = os.path.abspath(destination_dir)
18 if not os.path.isdir(destination_directory):
19 os.makedirs(destination_directory)
20 for dir_entry in os.listdir(source_directory):
21 source_entry = os.path.join(source_directory, dir_entry)
22 if copy:
23 shutil.copy(source_entry, destination_directory)
24 else:
25 shutil.move(source_entry, destination_directory)
26 if remove_source_dir:
27 os.rmdir(source_directory)
28
29 input_dir = 'input_dir'
30 # Get input data.
31 fetch_sherbrooke_3shell()
32 # MNove inputs to working directory.
33 move_directory_files('/home/greg/.dipy', input_dir)
34 fdwi = join(input_dir, 'HARDI193.nii.gz')
35 fbval = join(input_dir, 'HARDI193.bval')
36 fbvec = join(input_dir, 'HARDI193.bvec')
37 # Load the dMRI datasets.
38 img = nibabel.load(fdwi)
39 data = img.get_data()
40 # data is a 4D array where the first 3 dimensions are the i, j,
41 # k voxel coordinates and the last dimension is the number of
42 # non-weighted (S0s) and diffusion-weighted volumes.
43 # Visualize the results using matplotlib.
44 axial_middle = data.shape[2] // 2
45 plt.figure('Showing the datasets')
46 plt.subplot(1, 2, 1).set_axis_off()
47 plt.imshow(data[:, :, axial_middle, 0].T, cmap='gray', origin='lower')
48 plt.subplot(1, 2, 2).set_axis_off()
49 plt.imshow(data[:, :, axial_middle, 10].T, cmap='gray', origin='lower')
50 plt.show()
51 plt.savefig(args.output, bbox_inches='tight')