Mercurial > repos > greg > diffusion_signal_reconstruction

comparison diffusion_signal_reconstruction.py @ 9:dc700deb06c1 draft

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author greg
date Thu, 30 Nov 2017 08:30:06 -0500
parents 85df19d98cd0
children 7bcc39c8ccfd
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8:0c3f09c848be 9:dc700deb06c1
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 import argparse 2 import argparse
3 import os
3 import shutil 4 import shutil
4 5
5 from dipy.data import fetch_sherbrooke_3shell 6 from dipy.data import fetch_sherbrooke_3shell
6 from dipy.data import fetch_stanford_hardi 7 from dipy.data import fetch_stanford_hardi
7 from dipy.data import get_sphere 8 from dipy.data import get_sphere
17 import nibabel 18 import nibabel
18 import numpy 19 import numpy
19 20
20 # http://nipy.org/dipy/examples_built/reconst_dti.html#example-reconst-dti 21 # http://nipy.org/dipy/examples_built/reconst_dti.html#example-reconst-dti
21 parser = argparse.ArgumentParser() 22 parser = argparse.ArgumentParser()
22 parser.add_argument('--drmi_dataset', dest='drmi_dataset', help='Input dataset') 23 parser.add_argument('--input', dest='input', help='Input dataset')
24 parser.add_argument('--input_extra_files_path', dest='input_extra_files_path', help='Input dataset extra files path')
23 parser.add_argument('--output_nifti1_fa', dest='output_nifti1_fa', help='Output fractional anisotropy Nifti1 dataset') 25 parser.add_argument('--output_nifti1_fa', dest='output_nifti1_fa', help='Output fractional anisotropy Nifti1 dataset')
26 parser.add_argument('--output_nifti1_fa_files_path', dest='output_nifti1_fa_files_path', help='Output fractional anisotropy Nifti1 extra files path')
24 parser.add_argument('--output_nifti1_evecs', dest='output_nifti1_evecs', help='Output eigen vectors Nifti1 dataset') 27 parser.add_argument('--output_nifti1_evecs', dest='output_nifti1_evecs', help='Output eigen vectors Nifti1 dataset')
28 parser.add_argument('--output_nifti1_evecs_files_path', dest='output_nifti1_evecs_files_path', help='Output eigen vectors Nifti1 extra files path')
25 parser.add_argument('--output_nifti1_md', dest='output_nifti1_md', help='Output mean diffusivity Nifti1 dataset') 29 parser.add_argument('--output_nifti1_md', dest='output_nifti1_md', help='Output mean diffusivity Nifti1 dataset')
30 parser.add_argument('--output_nifti1_md_files_path', dest='output_nifti1_md_files_path', help='Output mean diffusivity Nifti1 extra files path')
26 parser.add_argument('--output_nifti1_rgb', dest='output_nifti1_rgb', help='Output RGB-map Nifti1 dataset') 31 parser.add_argument('--output_nifti1_rgb', dest='output_nifti1_rgb', help='Output RGB-map Nifti1 dataset')
32 parser.add_argument('--output_nifti1_rgb_files_path', dest='output_nifti1_rgb_files_path', help='Output RGB-map Nifti1 extra files path')
27 parser.add_argument('--output_png_ellipsoids', dest='output_png_ellipsoids', help='Output ellipsoids PNG dataset') 33 parser.add_argument('--output_png_ellipsoids', dest='output_png_ellipsoids', help='Output ellipsoids PNG dataset')
28 parser.add_argument('--output_png_odfs', dest='output_png_odfs', help='Output orientation distribution functions PNG dataset') 34 parser.add_argument('--output_png_odfs', dest='output_png_odfs', help='Output orientation distribution functions PNG dataset')
29 parser.add_argument('--output_png_middle_axial_slice', dest='output_png_middle_axial_slice', help='Output middle axial slice PNG dataset') 35 parser.add_argument('--output_png_middle_axial_slice', dest='output_png_middle_axial_slice', help='Output middle axial slice PNG dataset')
30 36
31 args = parser.parse_args() 37 args = parser.parse_args()
32 38
39 def move_directory_files(source_dir, destination_dir, copy=False, remove_source_dir=False):
40 source_directory = os.path.abspath(source_dir)
41 destination_directory = os.path.abspath(destination_dir)
42 if not os.path.isdir(destination_directory):
43 os.makedirs(destination_directory)
44 for dir_entry in os.listdir(source_directory):
45 source_entry = os.path.join(source_directory, dir_entry)
46 if copy:
47 shutil.copy(source_entry, destination_directory)
48 else:
49 shutil.move(source_entry, destination_directory)
50 if remove_source_dir:
51 os.rmdir(source_directory)
52
33 # Get input data. 53 # Get input data.
54 # TODO: do not hard-code 'stanford_hardi'
55 input_dir = 'stanford_hardi'
56 os.mkdir(input_dir)
34 input_dir = args.drmi_dataset 57 input_dir = args.drmi_dataset
35 if input_dir == 'sherbrooke_3shell': 58 for f in os.list_dir(args.input_extra_files_path):
36 fetch_sherbrooke_3shell() 59 shutil.copy(f, input_dir)
37 img, gtab = read_sherbrooke_3shell() 60 fetch_stanford_hardi()
38 elif input_dir == 'stanford_hardi': 61 img, gtab = read_stanford_hardi()
39 fetch_stanford_hardi()
40 img, gtab = read_stanford_hardi()
41 62
42 data = img.get_data() 63 data = img.get_data()
43 maskdata, mask = median_otsu(data, 3, 1, True, vol_idx=range(10, 50), dilate=2) 64 maskdata, mask = median_otsu(data, 3, 1, True, vol_idx=range(10, 50), dilate=2)
44 65
45 axial_middle = data.shape[2] // 2 66 axial_middle = data.shape[2] // 2
56 fa = fractional_anisotropy(tenfit.evals) 77 fa = fractional_anisotropy(tenfit.evals)
57 fa[numpy.isnan(fa)] = 0 78 fa[numpy.isnan(fa)] = 0
58 fa_img = nibabel.Nifti1Image(fa.astype(numpy.float32), img.affine) 79 fa_img = nibabel.Nifti1Image(fa.astype(numpy.float32), img.affine)
59 nibabel.save(fa_img, 'output_fa.nii') 80 nibabel.save(fa_img, 'output_fa.nii')
60 shutil.move('output_fa.nii', args.output_nifti1_fa) 81 shutil.move('output_fa.nii', args.output_nifti1_fa)
82 move_directory_files(input_dir, args.output_nifti1_fa_files_path)
61 83
62 evecs_img = nibabel.Nifti1Image(tenfit.evecs.astype(numpy.float32), img.affine) 84 evecs_img = nibabel.Nifti1Image(tenfit.evecs.astype(numpy.float32), img.affine)
63 nibabel.save(evecs_img, 'output_evecs.nii') 85 nibabel.save(evecs_img, 'output_evecs.nii')
64 shutil.move('output_evecs.nii', args.output_nifti1_evecs) 86 shutil.move('output_evecs.nii', args.output_nifti1_evecs)
87 move_directory_files(input_dir, args.output_nifti1_evecs_files_path)
65 88
66 md1 = dti.mean_diffusivity(tenfit.evals) 89 md1 = dti.mean_diffusivity(tenfit.evals)
67 nibabel.save(nibabel.Nifti1Image(md1.astype(numpy.float32), img.affine), 'output_md.nii') 90 nibabel.save(nibabel.Nifti1Image(md1.astype(numpy.float32), img.affine), 'output_md.nii')
68 shutil.move('output_md.nii', args.output_nifti1_md) 91 shutil.move('output_md.nii', args.output_nifti1_md)
92 move_directory_files(input_dir, args.output_nifti1_md_files_path)
69 93
70 fa = numpy.clip(fa, 0, 1) 94 fa = numpy.clip(fa, 0, 1)
71 rgb = color_fa(fa, tenfit.evecs) 95 rgb = color_fa(fa, tenfit.evecs)
72 nibabel.save(nibabel.Nifti1Image(numpy.array(255 * rgb, 'uint8'), img.affine), 'output_rgb.nii') 96 nibabel.save(nibabel.Nifti1Image(numpy.array(255 * rgb, 'uint8'), img.affine), 'output_rgb.nii')
73 shutil.move('output_rgb.nii', args.output_nifti1_rgb) 97 shutil.move('output_rgb.nii', args.output_nifti1_rgb)
98 move_directory_files(input_dir, args.output_nifti1_rgb_files_path)
74 99
75 sphere = get_sphere('symmetric724') 100 sphere = get_sphere('symmetric724')
76 ren = fvtk.ren() 101 ren = fvtk.ren()
77 102
78 evals = tenfit.evals[13:43, 44:74, 28:29] 103 evals = tenfit.evals[13:43, 44:74, 28:29]