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Sphere subdivide #731

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merged 11 commits into from
Aug 17, 2023
Merged

Sphere subdivide #731

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4b77ad0
add subdivide sphere argument
EliseCos Jul 27, 2023
6e95a7b
Merge branch 'master' into sphere_subdivide
EliseCos Jul 27, 2023
cbf8e87
add test
EliseCos Jul 27, 2023
df0b378
Change default sphere_subdivide
EliseCos Jul 27, 2023
a1aa22b
Change argmument default
EliseCos Jul 27, 2023
7485725
Change default argument
EliseCos Jul 27, 2023
d1445a6
Delete scil_compute_local_tracking_mouse.py
EliseCos Jul 27, 2023
d275991
rm DS_Store
EliseCos Jul 27, 2023
20cc282
Change the subdivide sphere definition
EliseCos Jul 28, 2023
0639811
Add space subdivide sphere argument
EliseCos Jul 28, 2023
be35779
Update scil_compute_local_tracking.py
EliseCos Aug 17, 2023
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7 changes: 5 additions & 2 deletions scripts/scil_compute_local_tracking.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,10 @@ def _build_arg_parser():
choices=['det', 'prob', 'eudx'],
help='Algorithm to use. [%(default)s]')
add_sphere_arg(track_g, symmetric_only=True)

track_g.add_argument('--sub_sphere',
type=int, default=0,
help='Subdivides each face of the sphere into 4^s new faces. '
'[%(default)s]')
add_seeding_options(p)
out_g = add_out_options(p)

Expand All @@ -78,7 +81,7 @@ def _build_arg_parser():

def _get_direction_getter(args):
odf_data = nib.load(args.in_odf).get_fdata(dtype=np.float32)
sphere = HemiSphere.from_sphere(get_sphere(args.sphere))
sphere = HemiSphere.from_sphere(get_sphere(args.sphere)).subdivide(args.sub_sphere)
theta = get_theta(args.theta, args.algo)

non_zeros_count = np.count_nonzero(np.sum(odf_data, axis=-1))
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15 changes: 15 additions & 0 deletions scripts/tests/test_compute_local_tracking.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,21 @@ def test_execution_tracking_fodf(script_runner):
assert ret.success


def test_execution_sphere_subdivide(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_fodf = os.path.join(get_home(), 'tracking',
'fodf.nii.gz')
in_mask = os.path.join(get_home(), 'tracking',
'seeding_mask.nii.gz')

ret = script_runner.run('scil_compute_local_tracking.py', in_fodf,
in_mask, in_mask, 'local_sphere.trk', '--nt', '1000',
'--compress', '0.1', '--sh_basis', 'descoteaux07',
'--min_length', '20', '--max_length', '200',
'--sub_sphere', '2')
assert ret.success


def test_execution_tracking_fodf_no_compression(script_runner):
os.chdir(os.path.expanduser(tmp_dir.name))
in_fodf = os.path.join(get_home(), 'tracking',
Expand Down