# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
#
# Copyright 2021 The NiPreps Developers <nipreps@gmail.com>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# We support and encourage derived works from this project, please read
# about our expectations at
#
# https://www.nipreps.org/community/licensing/
#
"""Wrappers of NiTransforms."""
from pathlib import Path
from nipype.interfaces.base import (
BaseInterfaceInputSpec,
File,
InputMultiObject,
SimpleInterface,
TraitedSpec,
isdefined,
traits,
)
from nipype.utils.filemanip import fname_presuffix
XFM_FMT = {
'.lta': 'fs',
'.txt': 'itk',
'.mat': 'itk',
'.tfm': 'itk',
}
class _ConvertAffineInputSpec(BaseInterfaceInputSpec):
in_xfm = File(exists=True, desc='input transform piles')
inverse = traits.Bool(False, usedefault=True, desc='generate inverse')
in_fmt = traits.Enum('auto', 'itk', 'fs', 'fsl', usedefault=True, desc='input format')
out_fmt = traits.Enum('itk', 'fs', 'fsl', usedefault=True, desc='output format')
reference = File(exists=True, desc='reference file')
moving = File(exists=True, desc='moving file')
class _ConvertAffineOutputSpec(TraitedSpec):
out_xfm = File(exists=True, desc='output, combined transform')
out_inv = File(desc='output, combined transform')
[docs]
class ConvertAffine(SimpleInterface):
"""Write a single, flattened transform file."""
input_spec = _ConvertAffineInputSpec
output_spec = _ConvertAffineOutputSpec
def _run_interface(self, runtime):
from nitransforms.linear import load as load_affine
ext = {
'fs': 'lta',
'itk': 'txt',
'fsl': 'mat',
}[self.inputs.out_fmt]
in_fmt = self.inputs.in_fmt
if in_fmt == 'auto':
in_fmt = {
'.lta': 'fs',
'.mat': 'fsl',
'.txt': 'itk',
}[Path(self.inputs.in_xfm).suffix]
reference = self.inputs.reference or None
moving = self.inputs.moving or None
affine = load_affine(self.inputs.in_xfm, fmt=in_fmt, reference=reference, moving=moving)
out_file = fname_presuffix(
self.inputs.in_xfm,
suffix=f'_fwd.{ext}',
newpath=runtime.cwd,
use_ext=False,
)
self._results['out_xfm'] = out_file
affine.to_filename(out_file, moving=moving, fmt=self.inputs.out_fmt)
if self.inputs.inverse:
inv_affine = ~affine
if moving is not None:
inv_affine.reference = moving
out_inv = fname_presuffix(
self.inputs.in_xfm,
suffix=f'_inv.{ext}',
newpath=runtime.cwd,
use_ext=False,
)
self._results['out_inv'] = out_inv
inv_affine.to_filename(out_inv, moving=reference, fmt=self.inputs.out_fmt)
return runtime
class _ConcatenateXFMsInputSpec(BaseInterfaceInputSpec):
in_xfms = InputMultiObject(File(exists=True), desc='input transform piles')
inverse = traits.Bool(False, usedefault=True, desc='generate inverse')
out_fmt = traits.Enum('itk', 'fs', usedefault=True, desc='output format')
reference = File(
exists=True,
desc='reference file (only for writing LTA format, if not concatenating another LTA).',
)
moving = File(
exists=True,
desc='moving file (only for writing LTA format, if not concatenating another LTA).',
)
class _ConcatenateXFMsOutputSpec(TraitedSpec):
out_xfm = File(exists=True, desc='output, combined transform')
out_inv = File(desc='output, combined transform')
[docs]
class ConcatenateXFMs(SimpleInterface):
"""Write a single, flattened transform file."""
input_spec = _ConcatenateXFMsInputSpec
output_spec = _ConcatenateXFMsOutputSpec
def _run_interface(self, runtime):
out_ext = 'lta' if self.inputs.out_fmt == 'fs' else 'tfm'
reference = self.inputs.reference if isdefined(self.inputs.reference) else None
moving = self.inputs.moving if isdefined(self.inputs.moving) else None
out_file = Path(runtime.cwd) / f'out_fwd.{out_ext}'
self._results['out_xfm'] = str(out_file)
out_inv = None
if self.inputs.inverse:
out_inv = Path(runtime.cwd) / f'out_inv.{out_ext}'
self._results['out_inv'] = str(out_inv)
concatenate_xfms(
self.inputs.in_xfms,
out_file,
out_inv,
reference=reference,
moving=moving,
fmt=self.inputs.out_fmt,
)
return runtime
[docs]
def concatenate_xfms(in_files, out_file, out_inv=None, reference=None, moving=None, fmt='itk'):
"""Concatenate linear transforms."""
from nitransforms.linear import load as load_affine
from nitransforms.manip import TransformChain
xfm = TransformChain(
[load_affine(f, fmt=XFM_FMT[Path(f).suffix]) for f in in_files]
).asaffine()
if reference is not None and not xfm.reference:
xfm.reference = reference
xfm.to_filename(out_file, moving=moving, fmt=fmt)
if out_inv is not None:
inv_xfm = ~xfm
if moving is not None:
inv_xfm.reference = moving
inv_xfm.to_filename(out_inv, moving=reference, fmt=fmt)