Mercurial > repos > greg > fast_fiber_tracking

comparison fast_fiber_tracking.py @ 3:63aa79b5ebd6 draft

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author greg
date Thu, 30 Nov 2017 09:10:46 -0500
parents 4e3d4331fa58
children 66b5ff1ff984
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2:a695440febc0 3:63aa79b5ebd6
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
18 from dipy.viz import actor, window 19 from dipy.viz import actor, window
19 20
20 import numpy as np 21 import numpy as np
21 22
22 parser = argparse.ArgumentParser() 23 parser = argparse.ArgumentParser()
23 parser.add_argument('--drmi_dataset', dest='drmi_dataset', help='Input dataset') 24 parser.add_argument('--input', dest='input', help='Input dataset')
24 parser.add_argument('--output_csd_direction_field', dest='output_csd_direction_field', help='Output csd direction field dataset') 25 parser.add_argument('--output_csd_direction_field', dest='output_csd_direction_field', help='Output csd direction field dataset')
25 parser.add_argument('--output_det_streamlines', dest='output_det_streamlines', help='Output det streamlines dataset') 26 parser.add_argument('--output_det_streamlines', dest='output_det_streamlines', help='Output det streamlines dataset')
26 parser.add_argument('--output_fa_map', dest='output_fa_map', help='Output fa map dataset') 27 parser.add_argument('--output_fa_map', dest='output_fa_map', help='Output fa map dataset')
28 parser.add_argument('--output_fa_map_files_path', dest='output_fa_map_files_path', help='Output fa map extra files path')
27 29
28 args = parser.parse_args() 30 args = parser.parse_args()
31
32 def move_directory_files(source_dir, destination_dir, copy=False, remove_source_dir=False):
33 source_directory = os.path.abspath(source_dir)
34 destination_directory = os.path.abspath(destination_dir)
35 if not os.path.isdir(destination_directory):
36 os.makedirs(destination_directory)
37 for dir_entry in os.listdir(source_directory):
38 source_entry = os.path.join(source_directory, dir_entry)
39 if copy:
40 shutil.copy(source_entry, destination_directory)
41 else:
42 shutil.move(source_entry, destination_directory)
43 if remove_source_dir:
44 os.rmdir(source_directory)
29 45
30 interactive = False 46 interactive = False
31 47
32 # Get input data. 48 # Get input data.
33 input_dir = args.drmi_dataset 49 # TODO: do not hard-code 'stanford_hardi'
34 if input_dir == 'sherbrooke_3shell': 50 input_dir = 'stanford_hardi'
35 fetch_sherbrooke_3shell() 51 os.mkdir(input_dir)
36 img, gtab = read_sherbrooke_3shell() 52 for f in os.listdir(args.input_extra_files_path):
37 elif input_dir == 'stanford_hardi': 53 shutil.copy(os.path.join(args.input_extra_files_path, f), input_dir)
38 fetch_stanford_hardi() 54 img, gtab = read_stanford_hardi()
39 img, gtab = read_stanford_hardi()
40 55
41 data = img.get_data() 56 data = img.get_data()
42 maskdata, mask = median_otsu(data, 3, 1, False, vol_idx=range(10, 50), dilate=2) 57 maskdata, mask = median_otsu(data, 3, 1, False, vol_idx=range(10, 50), dilate=2)
43 58
44 response, ratio = auto_response(gtab, data, roi_radius=10, fa_thr=0.7) 59 response, ratio = auto_response(gtab, data, roi_radius=10, fa_thr=0.7)
66 window.record(ren, out_path='det_streamlines.png', size=(900, 900)) 81 window.record(ren, out_path='det_streamlines.png', size=(900, 900))
67 shutil.move('det_streamlines.png', args.output_det_streamlines) 82 shutil.move('det_streamlines.png', args.output_det_streamlines)
68 83
69 save_nifti('fa_map.nii', fa, img.affine) 84 save_nifti('fa_map.nii', fa, img.affine)
70 shutil.move('fa_map.nii', args.output_fa_map) 85 shutil.move('fa_map.nii', args.output_fa_map)
86 move_directory_files(input_dir, args.output_fa_map_files_path, copy=True)