feat: Add affine converter interface

Author: effigies

fmriprep/interfaces/nitransforms.py

@@ -0,0 +1,101 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2025 The NiPreps Developers <[email protected]>
+#
+# 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,
+    SimpleInterface,
+    TraitedSpec,
+    traits,
+)
+from nipype.utils.filemanip import fname_presuffix
+
+
+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')
+
+
+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_xfm
+        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