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1 #!/usr/bin/env python
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2 import argparse
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3 import os
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4 import shutil
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5
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6 from dipy.data import fetch_sherbrooke_3shell
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7 from dipy.data import fetch_stanford_hardi
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8 from dipy.data import get_sphere
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9 from dipy.data import read_sherbrooke_3shell
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10 from dipy.data import read_stanford_hardi
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11 from dipy.reconst import dti
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12 from dipy.reconst.dti import color_fa
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13 from dipy.reconst.dti import fractional_anisotropy
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14 from dipy.segment.mask import median_otsu
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15 from dipy.viz import fvtk
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16 from matplotlib import pyplot
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17
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18 import nibabel
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19 import numpy
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20
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21 # http://nipy.org/dipy/examples_built/reconst_dti.html#example-reconst-dti
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22 parser = argparse.ArgumentParser()
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23 parser.add_argument('--input', dest='input', help='Input dataset')
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24 parser.add_argument('--input_extra_files_path', dest='input_extra_files_path', help='Input dataset extra files path')
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25 parser.add_argument('--output_nifti1_fa', dest='output_nifti1_fa', help='Output fractional anisotropy Nifti1 dataset')
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26 parser.add_argument('--output_nifti1_fa_files_path', dest='output_nifti1_fa_files_path', help='Output fractional anisotropy Nifti1 extra files path')
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27 parser.add_argument('--output_nifti1_evecs', dest='output_nifti1_evecs', help='Output eigen vectors Nifti1 dataset')
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28 parser.add_argument('--output_nifti1_evecs_files_path', dest='output_nifti1_evecs_files_path', help='Output eigen vectors Nifti1 extra files path')
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29 parser.add_argument('--output_nifti1_md', dest='output_nifti1_md', help='Output mean diffusivity Nifti1 dataset')
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30 parser.add_argument('--output_nifti1_md_files_path', dest='output_nifti1_md_files_path', help='Output mean diffusivity Nifti1 extra files path')
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31 parser.add_argument('--output_nifti1_rgb', dest='output_nifti1_rgb', help='Output RGB-map Nifti1 dataset')
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32 parser.add_argument('--output_nifti1_rgb_files_path', dest='output_nifti1_rgb_files_path', help='Output RGB-map Nifti1 extra files path')
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33 parser.add_argument('--output_png_ellipsoids', dest='output_png_ellipsoids', help='Output ellipsoids PNG dataset')
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34 parser.add_argument('--output_png_odfs', dest='output_png_odfs', help='Output orientation distribution functions PNG dataset')
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35 parser.add_argument('--output_png_middle_axial_slice', dest='output_png_middle_axial_slice', help='Output middle axial slice PNG dataset')
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36
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37 args = parser.parse_args()
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38
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39 def move_directory_files(source_dir, destination_dir, copy=False, remove_source_dir=False):
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40 source_directory = os.path.abspath(source_dir)
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41 destination_directory = os.path.abspath(destination_dir)
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42 if not os.path.isdir(destination_directory):
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43 os.makedirs(destination_directory)
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44 for dir_entry in os.listdir(source_directory):
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45 source_entry = os.path.join(source_directory, dir_entry)
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46 if copy:
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47 shutil.copy(source_entry, destination_directory)
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48 else:
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49 shutil.move(source_entry, destination_directory)
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50 if remove_source_dir:
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51 os.rmdir(source_directory)
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52
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53 # Get input data.
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54 # TODO: do not hard-code 'stanford_hardi'
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55 input_dir = 'stanford_hardi'
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56 os.mkdir(input_dir)
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57 for f in os.list_dir(args.input_extra_files_path):
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58 shutil.copy(os.path.join(args.input_extra_files_path, f), input_dir)
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59 img, gtab = read_stanford_hardi()
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60
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61 data = img.get_data()
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62 maskdata, mask = median_otsu(data, 3, 1, True, vol_idx=range(10, 50), dilate=2)
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63
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64 axial_middle = data.shape[2] // 2
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65 pyplot.subplot(1, 2, 1).set_axis_off()
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66 pyplot.imshow(data[:, :, axial_middle, 0].T, cmap='gray', origin='lower')
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67 pyplot.subplot(1, 2, 2).set_axis_off()
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68 pyplot.imshow(data[:, :, axial_middle, 10].T, cmap='gray', origin='lower')
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69 pyplot.savefig('middle_axial.png', bbox_inches='tight')
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70 shutil.move('middle_axial.png', args.output_png_middle_axial_slice)
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71
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72 tenmodel = dti.TensorModel(gtab)
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73 tenfit = tenmodel.fit(maskdata)
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74
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75 fa = fractional_anisotropy(tenfit.evals)
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76 fa[numpy.isnan(fa)] = 0
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77 fa_img = nibabel.Nifti1Image(fa.astype(numpy.float32), img.affine)
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78 nibabel.save(fa_img, 'output_fa.nii')
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79 shutil.move('output_fa.nii', args.output_nifti1_fa)
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80 move_directory_files(input_dir, args.output_nifti1_fa_files_path)
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81
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82 evecs_img = nibabel.Nifti1Image(tenfit.evecs.astype(numpy.float32), img.affine)
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83 nibabel.save(evecs_img, 'output_evecs.nii')
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84 shutil.move('output_evecs.nii', args.output_nifti1_evecs)
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85 move_directory_files(input_dir, args.output_nifti1_evecs_files_path)
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86
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87 md1 = dti.mean_diffusivity(tenfit.evals)
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88 nibabel.save(nibabel.Nifti1Image(md1.astype(numpy.float32), img.affine), 'output_md.nii')
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89 shutil.move('output_md.nii', args.output_nifti1_md)
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90 move_directory_files(input_dir, args.output_nifti1_md_files_path)
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91
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92 fa = numpy.clip(fa, 0, 1)
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93 rgb = color_fa(fa, tenfit.evecs)
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94 nibabel.save(nibabel.Nifti1Image(numpy.array(255 * rgb, 'uint8'), img.affine), 'output_rgb.nii')
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95 shutil.move('output_rgb.nii', args.output_nifti1_rgb)
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96 move_directory_files(input_dir, args.output_nifti1_rgb_files_path)
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97
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98 sphere = get_sphere('symmetric724')
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99 ren = fvtk.ren()
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100
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101 evals = tenfit.evals[13:43, 44:74, 28:29]
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102 evecs = tenfit.evecs[13:43, 44:74, 28:29]
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103 cfa = rgb[13:43, 44:74, 28:29]
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104 cfa /= cfa.max()
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105 fvtk.add(ren, fvtk.tensor(evals, evecs, cfa, sphere))
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106 fvtk.record(ren, n_frames=1, out_path='tensor_ellipsoids.png', size=(600, 600))
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107 shutil.move('tensor_ellipsoids.png', args.output_png_ellipsoids)
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108
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109 fvtk.clear(ren)
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110
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111 tensor_odfs = tenmodel.fit(data[20:50, 55:85, 38:39]).odf(sphere)
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112 fvtk.add(ren, fvtk.sphere_funcs(tensor_odfs, sphere, colormap=None))
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113 fvtk.record(ren, n_frames=1, out_path='tensor_odfs.png', size=(600, 600))
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114 shutil.move('tensor_odfs.png', args.output_png_odfs)
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