Merge pull request #50 from mgxd/enh/cifti-dilate

ENH: CiftiDilate interface

nibabies/interfaces/workbench.py

@@ -0,0 +1,134 @@
+from nipype.interfaces.base import CommandLineInputSpec, File, traits, TraitedSpec
+from nipype.interfaces.workbench.base import WBCommand
+
+
+class CiftiDilateInputSpec(CommandLineInputSpec):
+    in_file = File(
+        exists=True,
+        mandatory=True,
+        argstr="%s",
+        position=0,
+        desc="The input CIFTI file",
+    )
+    direction = traits.Enum(
+        "ROW",
+        "COLUMN",
+        mandatory=True,
+        argstr="%s",
+        position=1,
+        desc="Which dimension to dilate along, ROW or COLUMN",
+    )
+    surface_distance = traits.Int(
+        mandatory=True,
+        argstr="%d",
+        position=2,
+        desc="The distance to dilate on surfaces, in mm",
+    )
+    volume_distance = traits.Int(
+        mandatory=True,
+        argstr="%d",
+        position=3,
+        desc="The distance to dilate in the volume, in mm",
+    )
+    out_file = File(
+        name_source=["in_file"],
+        name_template="dilated_%s.nii",
+        keep_extension=True,
+        argstr="%s",
+        position=4,
+        desc="The dilated CIFTI file",
+    )
+    left_surface = File(
+        exists=True,
+        position=5,
+        argstr="-left-surface %s",
+        desc="Specify the left surface to use",
+    )
+    left_corrected_areas = File(
+        exists=True,
+        position=6,
+        requires=["left_surface"],
+        argstr="-left-corrected-areas %s",
+        desc="vertex areas (as a metric) to use instead of computing them from the left surface.",
+    )
+    right_surface = File(
+        exists=True,
+        position=7,
+        argstr="-right-surface %s",
+        desc="Specify the right surface to use",
+    )
+    right_corrected_areas = File(
+        exists=True,
+        position=8,
+        requires=["right_surface"],
+        argstr="-right-corrected-areas %s",
+        desc="vertex areas (as a metric) to use instead of computing them from the right surface",
+    )
+    cerebellum_surface = File(
+        exists=True,
+        position=9,
+        argstr="-cerebellum-surface %s",
+        desc="specify the cerebellum surface to use",
+    )
+    cerebellum_corrected_areas = File(
+        exists=True,
+        position=10,
+        requires=["cerebellum_surface"],
+        argstr="-cerebellum-corrected-areas %s",
+        desc="vertex areas (as a metric) to use instead of computing them from the cerebellum "
+        "surface",
+    )
+    bad_brainordinate_roi = File(
+        exists=True,
+        position=11,
+        argstr="-bad-brainordinate-roi %s",
+        desc="CIFTI dscalar or dtseries file, positive values denote brainordinates to have their "
+        "values replaced",
+    )
+    nearest = traits.Bool(
+        position=12,
+        argstr="-nearest",
+        desc="Use nearest good value instead of a weighted average",
+    )
+    merged_volume = traits.Bool(
+        position=13,
+        argstr="-merged-volume",
+        desc="treat volume components as if they were a single component",
+    )
+    legacy_mode = traits.Bool(
+        position=14,
+        argstr="-legacy-mode",
+        desc="Use the math from v1.3.2 and earlier for weighted dilation",
+    )
+
+
+class CiftiDilateOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc="Dilated CIFTI file")
+
+
+class CiftiDilate(WBCommand):
+    """
+    Dilate a CIFTI file.
+
+    For all data values designated as bad, if they neighbor a good value or
+    are within the specified distance of a good value in the same kind of
+    model, replace the value with a distance weighted average of nearby good
+    values, otherwise set the value to zero.  If -nearest is specified, it
+    will use the value from the closest good value within range instead of a
+    weighted average.  When the input file contains label data, nearest
+    dilation is used on the surface, and weighted popularity is used in the
+    volume.
+
+    The -*-corrected-areas options are intended for dilating on group average
+    surfaces, but it is only an approximate correction for the reduction of
+    structure in a group average surface.
+
+    If -bad-brainordinate-roi is specified, all values, including those with
+    value zero, are good, except for locations with a positive value in the
+    ROI.  If it is not specified, only values equal to zero are bad.
+
+    """
+
+    input_spec = CiftiDilateInputSpec
+    output_spec = CiftiDilateOutputSpec
+    _cmd = "wb_command -cifti-dilate"