ENH: Add Reorient interface

Author: effigies

nipype/interfaces/image.py

@@ -0,0 +1,98 @@
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+import numpy as np
+import nibabel as nb
+
+from ..utils.filemanip import fname_presuffix
+from .base import (SimpleInterface, TraitedSpec, BaseInterfaceInputSpec,
+                   traits, File)
+
+_axes = ('RL', 'AP', 'SI')
+_orientations = tuple(
+    ''.join((x[i], y[j], z[k]))
+    for x in _axes for y in _axes for z in _axes
+    if x != y != z != x
+    for i in (0, 1) for j in (0, 1) for k in (0, 1))
+
+
+class ReorientInputSpec(BaseInterfaceInputSpec):
+    in_file = File(exists=True, mandatory=True, desc='Input image')
+    orientation = traits.Enum(_orientations, usedefault=True,
+                              desc='Target axis orientation')
+
+
+class ReorientOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='Reoriented image')
+    transform = File(exists=True,
+                     desc='Affine transform from input orientation to output')
+
+
+class Reorient(SimpleInterface):
+    """Reorient an image
+    """
+    input_spec = ReorientInputSpec
+    output_spec = ReorientOutputSpec
+
+    def _run_interface(self, runtime):
+        from nibabel.orientations import (
+            axcodes2ornt, ornt_transform, inv_ornt_aff)
+
+        fname = self.inputs.in_file
+        orig_img = nb.load(fname)
+
+        # Find transform from current (approximate) orientation to
+        # target, in nibabel orientation matrix and affine forms
+        orig_ornt = nb.io_orientation(orig_img.affine)
+        targ_ornt = axcodes2ornt(self.inputs.orientation)
+        transform = ornt_transform(orig_ornt, targ_ornt)
+        affine_xfm = inv_ornt_aff(transform, orig_img.shape)
+
+        # Check can be eliminated when minimum nibabel version >= 2.2
+        if hasattr(orig_img, 'as_reoriented'):
+            reoriented = orig_img.as_reoriented(transform)
+        else:
+            reoriented = _as_reoriented_backport(orig_img, transform)
+
+        # Image may be reoriented
+        if reoriented is not orig_img:
+            out_name = fname_presuffix(fname, suffix='_ras',
+                                       newpath=runtime.cwd)
+            reoriented.to_filename(out_name)
+        else:
+            out_name = fname
+
+        mat_name = fname_presuffix(fname, suffix='.mat',
+                                   newpath=runtime.cwd, use_ext=False)
+        np.savetxt(mat_name, affine_xfm, fmt='%.08f')
+
+        self._results['out_file'] = out_name
+        self._results['transform'] = mat_name
+
+        return runtime
+
+
+def _as_reoriented_backport(img, ornt):
+    """Backport of img.as_reoriented as of nibabel 2.2.0"""
+    from nibabel.orientations import inv_ornt_aff
+    if np.array_equal(ornt, [[0, 1], [1, 1], [2, 1]]):
+        return img
+
+    t_arr = nb.apply_orientation(img.get_data(), ornt)
+    new_aff = img.affine.dot(inv_ornt_aff(ornt, img.shape))
+    reoriented = img.__class__(t_arr, new_aff, img.header)
+
+    if isinstance(reoriented, nb.Nifti1Pair):
+        # Also apply the transform to the dim_info fields
+        new_dim = list(reoriented.header.get_dim_info())
+        for idx, value in enumerate(new_dim):
+            # For each value, leave as None if it was that way,
+            # otherwise check where we have mapped it to
+            if value is None:
+                continue
+            new_dim[idx] = np.where(ornt[:, 0] == idx)[0]
+
+        reoriented.header.set_dim_info(*new_dim)
+
+    return reoriented