/usr/bin/dipy_sh_estimate is in python-dipy 0.10.1-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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import nibabel as nib
import numpy as np
from dipy.fixes import argparse
from dipy.reconst.shm import sf_to_sh
from dipy.core.sphere import Sphere
def sh_estimate(sphere_file, directions_file, out_file,
rank=8, smoothness=0.0):
in_nifti = nib.load(sphere_file)
refaff = in_nifti.get_affine()
data = in_nifti.get_data()
vertices = np.loadtxt(directions_file)
sphere = Sphere(xyz=vertices)
odf_sh = sf_to_sh(data, sphere, int(rank), "mrtrix", np.float(smoothness))
sh_out = nib.Nifti1Image(odf_sh.astype(np.float32), refaff)
nib.save(sh_out, out_file)
DESCRIPTION = 'Spherical harmonics (SH) estimation from a sampled '\
'spherical function.'
def buildArgsParser():
p = argparse.ArgumentParser(description=DESCRIPTION,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument(action='store', dest='sphere_file',
help='Input nifti file representing the spherical function\n'
'on N vertices.')
p.add_argument(action='store', dest='directions_file',
help="""Sphere vertices in a text file (Nx3)
x1 x2 x3
...
xN yN zN""")
p.add_argument(action='store', dest='out_file', help='Output nifti file.')
p.add_argument('-n', '--order', action='store', dest='rank',
metavar='int', required=False, default=8,
help='Maximum SH order of estimation (default 8)')
p.add_argument('-l', '--lambda', action='store', dest='smoothness',
metavar='float', required=False, default=0.0,
help='Laplace-Beltrami regularization (default 0.0)')
return p
def main():
parser = buildArgsParser()
args = parser.parse_args()
sphere_file = args.sphere_file
directions_file = args.directions_file
out_file = args.out_file
rank = args.rank
smoothness = args.smoothness
sh_estimate(sphere_file, directions_file, out_file, rank, smoothness)
if __name__ == "__main__":
main()
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