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Adding legacy options to scil_convert_sh_basis.py #704

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merged 4 commits into from
May 23, 2023
Merged

Adding legacy options to scil_convert_sh_basis.py #704

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e5597a9
Adding legacy options
karanphil Apr 3, 2023
35e099d
Merge branch 'master' of github.com:karanphil/scilpy into sh_basis_le…
karanphil May 17, 2023
519f6a4
Adding link doc
karanphil May 17, 2023
c4ebf9f
Change naming
karanphil May 17, 2023
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19 changes: 16 additions & 3 deletions scilpy/reconst/multi_processes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -425,7 +425,8 @@ def convert_sh_basis_parallel(args):


def convert_sh_basis(shm_coeff, sphere, mask=None,
input_basis='descoteaux07', nbr_processes=None):
input_basis='descoteaux07', nbr_processes=None,
is_input_legacy=True, is_output_legacy=True):
"""Converts spherical harmonic coefficients between two bases

Parameters
Expand All @@ -444,6 +445,16 @@ def convert_sh_basis(shm_coeff, sphere, mask=None,
nbr_processes: int, optional
The number of subprocesses to use.
Default: multiprocessing.cpu_count()
is_input_legacy: bool, optional
If true, this means that the input SH used a legacy basis definition
for backward compatibility with previous ``tournier07`` and
``descoteaux07`` implementations.
Default: True
is_output_legacy: bool, optional
If true, this means that the output SH will use a legacy basis
definition for backward compatibility with previous ``tournier07`` and
``descoteaux07`` implementations.
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Default: True

Returns
-------
Expand All @@ -455,8 +466,10 @@ def convert_sh_basis(shm_coeff, sphere, mask=None,
else 'tournier07'

sh_order = order_from_ncoef(shm_coeff.shape[-1])
B_in, _ = sh_to_sf_matrix(sphere, sh_order, input_basis)
_, invB_out = sh_to_sf_matrix(sphere, sh_order, output_basis)
B_in, _ = sh_to_sf_matrix(sphere, sh_order, input_basis,
legacy=is_input_legacy)
_, invB_out = sh_to_sf_matrix(sphere, sh_order, output_basis,
legacy=is_output_legacy)

data_shape = shm_coeff.shape
if mask is None:
Expand Down
16 changes: 13 additions & 3 deletions scripts/scil_convert_sh_basis.py
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Expand Up @@ -4,7 +4,9 @@
"""
Convert a SH file between the two commonly used bases
('descoteaux07' or 'tournier07'). The specified basis corresponds to the
input data basis.
input data basis. Note that by default, both legacy 'descoteaux07' and
legacy 'tournier07' bases will be assumed. For more information, see
https://dipy.org/documentation/1.4.0./theory/sh_basis/.
"""

import argparse
Expand All @@ -25,9 +27,15 @@ def _build_arg_parser():

p.add_argument('in_sh',
help='Input SH filename. (nii or nii.gz)')

p.add_argument('out_sh',
help='Output SH filename. (nii or nii.gz)')

p.add_argument('--in_sh_is_not_legacy', action='store_true',
help='If set, this means that the input SH are not encoded '
'with the legacy version of their SH basis.')
p.add_argument('--out_sh_is_not_legacy', action='store_true',
help='If set, this means that the output SH will not be '
'encoded with the legacy version of their SH basis.')

add_sh_basis_args(p, mandatory=True)
add_processes_arg(p)
Expand All @@ -48,7 +56,9 @@ def main():

new_data = convert_sh_basis(data, sphere,
input_basis=args.sh_basis,
nbr_processes=args.nbr_processes)
nbr_processes=args.nbr_processes,
is_input_legacy=not args.in_sh_is_not_legacy,
is_output_legacy=not args.out_sh_is_not_legacy)

nib.save(nib.Nifti1Image(new_data, img.affine, header=img.header),
args.out_sh)
Expand Down