Mercurial > repos > greg > drmi

comparison dmri.py @ 39:24c3ca0fd7fa draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Thu, 30 Nov 2017 11:02:43 -0500
parents b054adc68274
children da05d30d0642
comparison
equal deleted inserted replaced
38:b054adc68274 39:24c3ca0fd7fa
4 import shutil 4 import shutil
5 5
6 from dipy.core.gradients import gradient_table 6 from dipy.core.gradients import gradient_table
7 from dipy.data import fetch_stanford_hardi, fetch_stanford_t1, read_stanford_labels 7 from dipy.data import fetch_stanford_hardi, fetch_stanford_t1, read_stanford_labels
8 from dipy.io import read_bvals_bvecs 8 from dipy.io import read_bvals_bvecs
9 from dipy.io.image import save_nifti
9 from matplotlib import pyplot 10 from matplotlib import pyplot
10 11
11 import nibabel 12 import nibabel
12 13
13 parser = argparse.ArgumentParser() 14 parser = argparse.ArgumentParser()
66 pyplot.imshow(data[:, :, axial_middle, 0].T, cmap='gray', origin='lower') 67 pyplot.imshow(data[:, :, axial_middle, 0].T, cmap='gray', origin='lower')
67 pyplot.subplot(1, 2, 2).set_axis_off() 68 pyplot.subplot(1, 2, 2).set_axis_off()
68 pyplot.imshow(data[:, :, axial_middle, 10].T, cmap='gray', origin='lower') 69 pyplot.imshow(data[:, :, axial_middle, 10].T, cmap='gray', origin='lower')
69 pyplot.savefig('data.png', bbox_inches='tight') 70 pyplot.savefig('data.png', bbox_inches='tight')
70 shutil.move('data.png', args.output_png) 71 shutil.move('data.png', args.output_png)
71 # Load the b-values and b-vectors. 72
72 bvals, bvecs = read_bvals_bvecs(fbval, fbvec) 73 if args.drmi_dataset == 'stanford_hardi':
73 gtab = gradient_table(bvals, bvecs) 74 # Load the b-values and b-vectors.
74 # gtab can be used to tell what part of the data is the S0 75 bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
75 # volumes (volumes which correspond to b-values of 0). 76 gtab = gradient_table(bvals, bvecs)
76 S0s = data[:, :, :, gtab.b0s_mask] 77 # gtab can be used to tell what part of the data is the S0
77 # Save this in a new Nifti file. 78 # volumes (volumes which correspond to b-values of 0).
78 nibabel.save(nibabel.Nifti1Image(S0s, img.affine), 'output.nii') 79 S0s = data[:, :, :, gtab.b0s_mask]
80 # Save this in a new Nifti file.
81 nibabel.save(nibabel.Nifti1Image(S0s, img.affine), 'output.nii')
82 else:
83 save_nifti('output.nii', data, img.affine)
84
79 shutil.move('output.nii', args.output_nifti1) 85 shutil.move('output.nii', args.output_nifti1)
80 # Move the entire contents of input_dir to output_nifti1_extra_files. 86 # Move the entire contents of input_dir to output_nifti1_extra_files.
81 move_directory_files(input_dir, args.output_nifti1_extra_files) 87 move_directory_files(input_dir, args.output_nifti1_extra_files)
88