Merge pull request #525 from oesteban/enh/524-upstream-nitransforms

ENH: Upstream NiTransforms module from fMRIPrep

docs/requirements.txt

@@ -2,6 +2,7 @@ git+https://github.com/AleksandarPetrov/napoleon.git@0dc3f28a309ad602be5f44a9049
 git+https://github.com/rwblair/sphinxcontrib-versioning.git@39b40b0b84bf872fc398feff05344051bbce0f63#egg=sphinxcontrib-versioning
 nbsphinx
 nipype>=1.3.1
+nitransforms >= 20.0.0rc3,<20.2
 packaging
 pydot>=1.2.3
 pydotplus

niworkflows/interfaces/nitransforms.py

@@ -0,0 +1,81 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""Wrappers of NiTransforms."""
+
+from pathlib import Path
+from nipype.interfaces.base import (
+    TraitedSpec, BaseInterfaceInputSpec, File,
+    SimpleInterface, InputMultiObject,
+    traits, isdefined,
+)
+from nitransforms.manip import TransformChain
+from nitransforms.linear import load as load_affine
+
+XFM_FMT = {
+    ".lta": "fs",
+    ".txt": "itk",
+    ".mat": "itk",
+    ".tfm": "itk",
+}
+
+
+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")
+
+
+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
+
+
+def concatenate_xfms(
+    in_files,
+    out_file,
+    out_inv=None,
+    reference=None,
+    moving=None,
+    fmt="itk"
+):
+    """Concatenate linear transforms."""
+    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)

setup.cfg

@@ -28,6 +28,7 @@ install_requires =
     nibabel >= 3.0.1
     nilearn >= 0.2.6, != 0.5.0, != 0.5.1
     nipype >= 1.3.1
+    nitransforms >= 20.0.0rc3,<20.2
     packaging
     pandas
     pybids >= 0.10.2