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ENH: CiftiSeparate
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‎nibabies/interfaces/workbench.py

+168-1
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
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from nipype.interfaces.base import CommandLineInputSpec, File, traits, TraitedSpec, Str
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from nipype.interfaces.base.traits_extension import InputMultiObject
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from nipype.interfaces.base.traits_extension import InputMultiObject, OutputMultiObject, isdefined
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from nipype.interfaces.workbench.base import WBCommand
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@@ -940,6 +940,173 @@ class CiftiResample(WBCommand):
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_cmd = "wb_command -cifti-resample"
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class CiftiSeparateInputSpec(CommandLineInputSpec):
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in_file = File(
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exists=True,
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mandatory=True,
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argstr="%s",
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position=0,
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desc="the cifti to separate a component of",
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)
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direction = traits.Enum(
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"ROW",
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"COLUMN",
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mandatory=True,
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argstr="%s",
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position=1,
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desc="which dimension to smooth along, ROW or COLUMN",
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)
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volume_all_file = File(
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argstr="-volume-all %s",
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position=2,
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desc="separate all volume structures into a volume file",
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)
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volume_all_roi = File(
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argstr="-roi %s",
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position=3,
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requires=["volume_all_file"],
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desc="output the roi of which voxels have data",
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)
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volume_all_label = File(
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argstr="-label %s",
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position=4,
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requires=["volume_all_file"],
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desc="output a volume label file indicating the location of structures",
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)
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volume_all_crop = traits.Bool(
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argstr="-crop",
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position=5,
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requires=["volume_all_file"],
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desc="crop volume to the size of the data rather than using the original volume size",
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)
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# the following can be repeated
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label = InputMultiObject(
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traits.Either(
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traits.Tuple(traits.Enum(VALID_STRUCTURES), File()),
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traits.Tuple(traits.Enum(VALID_STRUCTURES), File(), File()),
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),
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argstr="%s",
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position=6,
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desc="separate one or more surface models into a surface label file",
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)
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metric = InputMultiObject(
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traits.Either(
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traits.Tuple(traits.Enum(VALID_STRUCTURES), File()),
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traits.Tuple(traits.Enum(VALID_STRUCTURES), File(), File()), # -roi
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),
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argstr="%s",
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position=7,
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desc="separate one or more surface models into a metric file",
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)
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volume = InputMultiObject(
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traits.Either(
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traits.Tuple(traits.Enum(VALID_STRUCTURES), File()),
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traits.Tuple(traits.Enum(VALID_STRUCTURES), File(), File()), # -roi
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traits.Tuple(traits.Enum(VALID_STRUCTURES, File(), traits.Bool)), # -crop
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traits.Tuple(traits.Enum(VALID_STRUCTURES), File(), File(), traits.Bool), # -roi -crop
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),
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argstr="%s",
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position=8,
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desc="separate one or more volume structures into a volume file",
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)
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class CiftiSeparateOutputSpec(TraitedSpec):
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volume_all_file = File(desc="File containing all volume structures")
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volume_all_roi_file = File(desc="Output the roi of which voxels have data")
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volume_all_label_file = File(
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desc="output a volume label file indicating the location of structures"
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)
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label_files = OutputMultiObject(File(), desc="Output label files")
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label_roi_files = OutputMultiObject(File(), desc="Output label rois files")
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metric_files = OutputMultiObject(File(), desc="Output metric files")
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metric_roi_files = OutputMultiObject(File(), desc="Output metric rois files")
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volume_files = OutputMultiObject(File(), desc="Output volume files")
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volume_roi_files = OutputMultiObject(File(), desc="Output volume roi files")
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class CiftiSeparate(WBCommand):
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"""
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Extract left or right hemisphere surface from CIFTI file (.dtseries)
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other structure can also be extracted
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The input cifti file must have a brain models mapping on the chosen
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dimension, columns for .dtseries.
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>>> separate = CiftiSeparate()
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>>> separate.inputs.in_file = data_dir / "func.dtseries.nii"
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>>> separate.inputs.direction = "COLUMN"
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>>> separate.inputs.volume_all_file = "volume_all.nii.gz"
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>>> separate.cmdline #doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
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'wb_command -cifti-separate .../func.dtseries.nii COLUMN \
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-volume-all volume_all.nii.gz'
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Metrics, labels, and volumes can also be freely extracted
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>>> separate.inputs.metric = [("CORTEX_LEFT", "cortexleft.func.gii")]
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>>> separate.inputs.volume = [("HIPPOCAMPUS_LEFT", "hippoL.nii.gz"), \
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("HIPPOCAMPUS_RIGHT", "hippoR.nii.gz", "hippoR.roi.nii.gz")]
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>>> separate.cmdline #doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
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'wb_command -cifti-separate .../func.dtseries.nii COLUMN \
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-volume-all volume_all.nii.gz -metric CORTEX_LEFT cortexleft.func.gii \
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-volume HIPPOCAMPUS_LEFT hippoL.nii.gz \
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-volume HIPPOCAMPUS_RIGHT hippoR.nii.gz -roi hippoR.roi.nii.gz'
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"""
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input_spec = CiftiSeparateInputSpec
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output_spec = CiftiSeparateOutputSpec
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_cmd = "wb_command -cifti-separate"
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_label_roi_files = []
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_metric_roi_files = []
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_volume_roi_files = []
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def _format_arg(self, name, trait_spec, value):
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if name in ("label", "metric", "volume"):
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cmds = []
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for i, val in enumerate(value):
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if len(val) == 3:
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if val[-1] is True:
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val = val[:-1] + ("-crop",)
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else:
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val = val[:-1] + ("-roi", val[-1])
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self._set_roi_file(name, val[-1])
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elif len(val) == 4:
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val = val[:-2] + ("-roi", val[-2]) + ("crop") if val[-1] is True else ()
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self._set_roi_file(name, val[-2])
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cmds.append(" ".join((f"-{name}",) + val))
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return trait_spec.argstr % " ".join(cmds)
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return super()._format_arg(name, trait_spec, value)
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def _list_outputs(self):
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outputs = super()._list_outputs()
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if self.inputs.volume_all_file:
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outputs["volume_all_file"] = self.inputs.volume_all_file
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if self.inputs.volume_all_roi_file:
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outputs["volume_all_roi_file"] = self.inputs.volume_all_roi_file
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if self.inputs.volume_all_label_file:
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outputs["volume_all_label_file"] = self.inputs.volume_all_label_file
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if self.inputs.label:
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for label in self.inputs.label:
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outputs["label_files"] = (outputs["label_files"] or []) + \
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self._gen_filename(label[2])
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if self._label_roi_files:
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outputs["label_roi_files"] = self._label_roi_files
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if self.inputs.metric:
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for metric in self.inputs.metric:
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outputs["metric_files"] = (outputs["metric_files"] or []) + \
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self._gen_filename(metric[2])
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if self._metric_roi_files:
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outputs["metric_roi_files"] = self._metric_roi_files
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if self.inputs.volume:
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for volume in self.inputs.volume:
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outputs["volume_files"] = (outputs["volume_files"] or []) + \
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self._gen_filename(volume[2])
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if self._volume_roi_files:
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outputs["volume_roi_files"] = self._volume_roi_files
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def _set_roi_file(self, name, file):
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rois = getattr(self, f"_{name}_roi_files")
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rois.append(self._gen_filename(file))
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class VolumeAffineResampleInputSpec(CommandLineInputSpec):
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in_file = File(
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exists=True,

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