Mercurial > repos > greg > drmi
changeset 21:53671fcb9507 draft
Uploaded
| author | greg |
|---|---|
| date | Sun, 05 Nov 2017 07:33:21 -0500 |
| parents | fcdb8f5e9c8f |
| children | 814082359f36 |
| files | dmri.py |
| diffstat | 1 files changed, 6 insertions(+), 4 deletions(-) [+] |
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--- a/dmri.py Sun Nov 05 07:33:10 2017 -0500 +++ b/dmri.py Sun Nov 05 07:33:21 2017 -0500 @@ -10,15 +10,18 @@ from matplotlib import pyplot parser = argparse.ArgumentParser() -parser.add_argument('--input', dest='input', help='Input dataset') +parser.add_argument('--drmi_dataset', dest='drmi_dataset', help='Input dataset') parser.add_argument('--output_nifti1', dest='output_nifti1', help='Output Nifti1 dataset') parser.add_argument('--output_png', dest='output_png', help='Output dataset') args = parser.parse_args() -input_dir = 'sherbrooke_3shell' # Get input data. -fetch_sherbrooke_3shell() +input_dir = args.drmi_dataset +if args.drmi_dataset == 'sherbrooke_3shell': + fetch_sherbrooke_3shell() +elif args.drmi_dataset == 'stanford_hardi': + fetch_stanford_hardi() fdwi = os.path.join(input_dir, 'HARDI193.nii.gz') fbval = os.path.join(input_dir, 'HARDI193.bval') fbvec = os.path.join(input_dir, 'HARDI193.bvec') @@ -30,7 +33,6 @@ # non-weighted (S0s) and diffusion-weighted volumes. # Visualize the results using matplotlib. axial_middle = data.shape[2] // 2 -pyplot.figure('Showing the datasets') pyplot.subplot(1, 2, 1).set_axis_off() pyplot.imshow(data[:, :, axial_middle, 0].T, cmap='gray', origin='lower') pyplot.subplot(1, 2, 2).set_axis_off()