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comparison dmri.py @ 41:da05d30d0642 draft default tip

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author greg
date Thu, 30 Nov 2017 11:09:07 -0500
parents 24c3ca0fd7fa
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40:1e2dad266344 41:da05d30d0642
14 parser = argparse.ArgumentParser() 14 parser = argparse.ArgumentParser()
15 parser.add_argument('--drmi_dataset', dest='drmi_dataset', help='Input dataset') 15 parser.add_argument('--drmi_dataset', dest='drmi_dataset', help='Input dataset')
16 parser.add_argument('--drmi_dataset_type', dest='drmi_dataset_type', help='Input dataset type') 16 parser.add_argument('--drmi_dataset_type', dest='drmi_dataset_type', help='Input dataset type')
17 parser.add_argument('--output_nifti1', dest='output_nifti1', help='Output Nifti1 dataset') 17 parser.add_argument('--output_nifti1', dest='output_nifti1', help='Output Nifti1 dataset')
18 parser.add_argument('--output_nifti1_extra_files', dest='output_nifti1_extra_files', help='Output Nifti1 extra files') 18 parser.add_argument('--output_nifti1_extra_files', dest='output_nifti1_extra_files', help='Output Nifti1 extra files')
19 parser.add_argument('--output_png', dest='output_png', help='Output dataset') 19 parser.add_argument('--output_png', dest='output_png', default=None, help='Output dataset')
20 20
21 args = parser.parse_args() 21 args = parser.parse_args()
22 22
23 def move_directory_files(source_dir, destination_dir, copy=False, remove_source_dir=False): 23 def move_directory_files(source_dir, destination_dir, copy=False, remove_source_dir=False):
24 source_directory = os.path.abspath(source_dir) 24 source_directory = os.path.abspath(source_dir)
58 58
59 data = img.get_data() 59 data = img.get_data()
60 # data is a 4D array where the first 3 dimensions are the i, j, 60 # data is a 4D array where the first 3 dimensions are the i, j,
61 # k voxel coordinates and the last dimension is the number of 61 # k voxel coordinates and the last dimension is the number of
62 # non-weighted (S0s) and diffusion-weighted volumes. 62 # non-weighted (S0s) and diffusion-weighted volumes.
63 # Visualize the results using matplotlib. 63
64 axial_middle = data.shape[2] // 2
65 pyplot.subplot(1, 2, 1).set_axis_off()
66 if args.drmi_dataset == 'stanford_hardi': 64 if args.drmi_dataset == 'stanford_hardi':
65 # Visualize the results using matplotlib.
66 axial_middle = data.shape[2] // 2
67 pyplot.subplot(1, 2, 1).set_axis_off()
67 pyplot.imshow(data[:, :, axial_middle, 0].T, cmap='gray', origin='lower') 68 pyplot.imshow(data[:, :, axial_middle, 0].T, cmap='gray', origin='lower')
68 pyplot.subplot(1, 2, 2).set_axis_off() 69 pyplot.subplot(1, 2, 2).set_axis_off()
69 pyplot.imshow(data[:, :, axial_middle, 10].T, cmap='gray', origin='lower') 70 pyplot.imshow(data[:, :, axial_middle, 10].T, cmap='gray', origin='lower')
70 pyplot.savefig('data.png', bbox_inches='tight') 71 pyplot.savefig('data.png', bbox_inches='tight')
71 shutil.move('data.png', args.output_png) 72 shutil.move('data.png', args.output_png)
72
73 if args.drmi_dataset == 'stanford_hardi':
74 # Load the b-values and b-vectors. 73 # Load the b-values and b-vectors.
75 bvals, bvecs = read_bvals_bvecs(fbval, fbvec) 74 bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
76 gtab = gradient_table(bvals, bvecs) 75 gtab = gradient_table(bvals, bvecs)
77 # gtab can be used to tell what part of the data is the S0 76 # gtab can be used to tell what part of the data is the S0
78 # volumes (volumes which correspond to b-values of 0). 77 # volumes (volumes which correspond to b-values of 0).
83 save_nifti('output.nii', data, img.affine) 82 save_nifti('output.nii', data, img.affine)
84 83
85 shutil.move('output.nii', args.output_nifti1) 84 shutil.move('output.nii', args.output_nifti1)
86 # Move the entire contents of input_dir to output_nifti1_extra_files. 85 # Move the entire contents of input_dir to output_nifti1_extra_files.
87 move_directory_files(input_dir, args.output_nifti1_extra_files) 86 move_directory_files(input_dir, args.output_nifti1_extra_files)
88