ENH: Add VolumeAffineResample interface to wb_command -volume-resample

Author: effigies

nibabies/interfaces/workbench.py

@@ -0,0 +1,79 @@
+from nipype.interfaces.base import CommandLineInputSpec, File, traits, TraitedSpec
+from nipype.interfaces.workbench.base import WBCommand
+
+
+class VolumeAffineResampleInputSpec(CommandLineInputSpec):
+    in_file = File(
+        exists=True,
+        mandatory=True,
+        argstr="%s",
+        position=0,
+        desc="volume to resample",
+    )
+    volume_space = File(
+        exists=True,
+        mandatory=True,
+        argstr="%s",
+        position=1,
+        desc="a volume file in the volume space you want for the output",
+    )
+    method = traits.Enum("CUBIC", "ENCLOSING_VOXEL", "TRILINEAR",
+        mandatory=True,
+        argstr="%s",
+        position=2,
+        desc="The resampling method. The recommended methods are CUBIC "
+             "(cubic spline) for most data, and ENCLOSING_VOXEL for label data.",
+    )
+    out_file = File(
+        name_source=["in_file"],
+        name_template="resampled_%s.nii.gz",
+        keep_extension=True,
+        argstr="%s",
+        position=3,
+        desc="the output volume",
+    )
+    affine = File(
+        exists=True,
+        mandatory=True,
+        argstr="-affine %s",
+        position=4,
+        desc="the affine file to apply",
+        )
+    flirt = traits.Bool(
+        argstr="-flirt %s %s",
+        position=5,
+        desc="Set ``True`` if ``affine`` is a FLIRT affine.",
+        )
+    flirt_source_volume = File(
+        exists=True,
+        desc="the source volume used when generating the affine; defaults to in_file",
+        requires=['flirt'],
+        )
+    flirt_target_volume = File(
+        exists=True,
+        desc="the target volume used when generating the affine; defaults to volume_space",
+        requires=['flirt'],
+        )
+
+
+class VolumeAffineResampleOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc="the output volume")
+
+
+class VolumeAffineResample(WBCommand):
+    """
+    Resample a volume file with an affine transformation.
+    """
+
+    input_spec = VolumeAffineResampleInputSpec
+    output_spec = VolumeAffineResampleOutputSpec
+    _cmd = "wb_command -volume-resample"
+
+    def _format_arg(self, opt, spec, val):
+        if opt == "flirt" and val:
+            val = (
+                self.inputs.flirt_source_volume or self.inputs.in_file,
+                self.inputs.flirt_target_volume or self.inputs.volume_space,
+                )
+        return super()._format_arg(opt, spec, val)
+