Merge pull request #2871 from mgxd/enh/ciftismooth

enh: wb cifti-smoothing

Author: effigies

nipype/interfaces/workbench/__init__.py

@@ -3,3 +3,4 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 
 from .metric import MetricResample
+from .cifti import CiftiSmooth

nipype/interfaces/workbench/cifti.py

@@ -0,0 +1,143 @@
+# -*- 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:
+"""This module provides interfaces for workbench CIFTI commands"""
+from __future__ import (print_function, division, unicode_literals,
+                        absolute_import)
+
+from ..base import (TraitedSpec, File, traits, CommandLineInputSpec)
+from .base import WBCommand
+from ... import logging
+
+iflogger = logging.getLogger('nipype.interface')
+
+
+class CiftiSmoothInputSpec(CommandLineInputSpec):
+    in_file = File(
+        exists=True,
+        mandatory=True,
+        argstr="%s",
+        position=0,
+        desc="The input CIFTI file")
+    sigma_surf = traits.Float(
+        mandatory=True,
+        argstr="%s",
+        position=1,
+        desc="the sigma for the gaussian surface smoothing kernel, in mm")
+    sigma_vol = traits.Float(
+        mandatory=True,
+        argstr="%s",
+        position=2,
+        desc="the sigma for the gaussian volume smoothing kernel, in mm")
+    direction = traits.Enum(
+        "ROW",
+        "COLUMN",
+        mandatory=True,
+        argstr="%s",
+        position=3,
+        desc="which dimension to smooth along, ROW or COLUMN")
+    out_file = File(
+        name_source=["in_file"],
+        name_template="smoothed_%s.nii",
+        keep_extension=True,
+        argstr="%s",
+        position=4,
+        desc="The output CIFTI")
+    left_surf = File(
+        exists=True,
+        mandatory=True,
+        position=5,
+        argstr="-left-surface %s",
+        desc="Specify the left surface to use")
+    left_corrected_areas = File(
+        exists=True,
+        position=6,
+        argstr="-left-corrected-areas %s",
+        desc="vertex areas (as a metric) to use instead of computing them from "
+             "the left surface.")
+    right_surf = File(
+        exists=True,
+        mandatory=True,
+        position=7,
+        argstr="-right-surface %s",
+        desc="Specify the right surface to use")
+    right_corrected_areas = File(
+        exists=True,
+        position=8,
+        argstr="-right-corrected-areas %s",
+        desc="vertex areas (as a metric) to use instead of computing them from "
+             "the right surface")
+    cerebellum_surf = 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_surf"],
+        argstr="cerebellum-corrected-areas %s",
+        desc="vertex areas (as a metric) to use instead of computing them from "
+             "the cerebellum surface")
+    cifti_roi = File(
+        exists=True,
+        position=11,
+        argstr="-cifti-roi %s",
+        desc="CIFTI file for ROI smoothing")
+    fix_zeros_vol = traits.Bool(
+        position=12,
+        argstr="-fix-zeros-volume",
+        desc="treat values of zero in the volume as missing data")
+    fix_zeros_surf = traits.Bool(
+        position=13,
+        argstr="-fix-zeros-surface",
+        desc="treat values of zero on the surface as missing data")
+    merged_volume = traits.Bool(
+        position=14,
+        argstr="-merged-volume",
+        desc="smooth across subcortical structure boundaries")
+
+
+class CiftiSmoothOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc="output CIFTI file")
+
+
+class CiftiSmooth(WBCommand):
+    """
+    Smooth a CIFTI file
+
+    The input cifti file must have a brain models mapping on the chosen
+    dimension, columns for .dtseries, and either for .dconn.  By default,
+    data in different structures is smoothed independently (i.e., "parcel
+    constrained" smoothing), so volume structures that touch do not smooth
+    across this boundary.  Specify ``merged_volume`` to ignore these
+    boundaries. Surface smoothing uses the ``GEO_GAUSS_AREA`` smoothing method.
+
+    The ``*_corrected_areas`` options are intended for when it is unavoidable
+    to smooth on group average surfaces, it is only an approximate correction
+    for the reduction of structure in a group average surface.  It is better
+    to smooth the data on individuals before averaging, when feasible.
+
+    The ``fix_zeros_*`` options will treat values of zero as lack of data, and
+    not use that value when generating the smoothed values, but will fill
+    zeros with extrapolated values.  The ROI should have a brain models
+    mapping along columns, exactly matching the mapping of the chosen
+    direction in the input file.  Data outside the ROI is ignored.
+
+    >>> from nipype.interfaces.workbench import CiftiSmooth
+    >>> smooth = CiftiSmooth()
+    >>> smooth.inputs.in_file = 'sub-01_task-rest.dtseries.nii'
+    >>> smooth.inputs.sigma_surf = 4
+    >>> smooth.inputs.sigma_vol = 4
+    >>> smooth.inputs.direction = 'COLUMN'
+    >>> smooth.inputs.right_surf = 'sub-01.R.midthickness.32k_fs_LR.surf.gii'
+    >>> smooth.inputs.left_surf = 'sub-01.L.midthickness.32k_fs_LR.surf.gii'
+    >>> smooth.cmdline
+    'wb_command -cifti-smoothing sub-01_task-rest.dtseries.nii 4.0 4.0 COLUMN \
+    smoothed_sub-01_task-rest.dtseries.nii \
+    -left-surface sub-01.L.midthickness.32k_fs_LR.surf.gii \
+    -right-surface sub-01.R.midthickness.32k_fs_LR.surf.gii'
+    """
+    input_spec = CiftiSmoothInputSpec
+    output_spec = CiftiSmoothOutputSpec
+    _cmd = 'wb_command -cifti-smoothing'

nipype/interfaces/workbench/tests/test_auto_CiftiSmooth.py

@@ -0,0 +1,95 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..cifti import CiftiSmooth
+
+
+def test_CiftiSmooth_inputs():
+    input_map = dict(
+        args=dict(argstr='%s', ),
+        cerebellum_corrected_areas=dict(
+            argstr='cerebellum-corrected-areas %s',
+            position=10,
+            requires=['cerebellum_surf'],
+        ),
+        cerebellum_surf=dict(
+            argstr='-cerebellum-surface %s',
+            position=9,
+        ),
+        cifti_roi=dict(
+            argstr='-cifti-roi %s',
+            position=11,
+        ),
+        direction=dict(
+            argstr='%s',
+            mandatory=True,
+            position=3,
+        ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        fix_zeros_surf=dict(
+            argstr='-fix-zeros-surface',
+            position=13,
+        ),
+        fix_zeros_vol=dict(
+            argstr='-fix-zeros-volume',
+            position=12,
+        ),
+        in_file=dict(
+            argstr='%s',
+            mandatory=True,
+            position=0,
+        ),
+        left_corrected_areas=dict(
+            argstr='-left-corrected-areas %s',
+            position=6,
+        ),
+        left_surf=dict(
+            argstr='-left-surface %s',
+            mandatory=True,
+            position=5,
+        ),
+        merged_volume=dict(
+            argstr='-merged-volume',
+            position=14,
+        ),
+        out_file=dict(
+            argstr='%s',
+            keep_extension=True,
+            name_source=['in_file'],
+            name_template='smoothed_%s.nii',
+            position=4,
+        ),
+        right_corrected_areas=dict(
+            argstr='-right-corrected-areas %s',
+            position=8,
+        ),
+        right_surf=dict(
+            argstr='-right-surface %s',
+            mandatory=True,
+            position=7,
+        ),
+        sigma_surf=dict(
+            argstr='%s',
+            mandatory=True,
+            position=1,
+        ),
+        sigma_vol=dict(
+            argstr='%s',
+            mandatory=True,
+            position=2,
+        ),
+    )
+    inputs = CiftiSmooth.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+def test_CiftiSmooth_outputs():
+    output_map = dict(out_file=dict(), )
+    outputs = CiftiSmooth.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value