niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_surf2_vol.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_SURF2_VOL_METADATA = Metadata(
+    id="d846efb04834ca6fcc9a5960307e8d15eacf8fd2.boutiques",
+    name="3dSurf2Vol",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dSurf2VolParameters = typing.TypedDict('V3dSurf2VolParameters', {
+    "__STYX_TYPE__": typing.Literal["3dSurf2Vol"],
+    "spec": InputPathType,
+    "surface_volume": InputPathType,
+    "surf_a": str,
+    "surf_b": typing.NotRequired[str | None],
+    "grid_parent": InputPathType,
+    "map_func": str,
+    "prefix": str,
+    "surf_xyz_1d": typing.NotRequired[InputPathType | None],
+    "sdata_1d": typing.NotRequired[InputPathType | None],
+    "sdata": typing.NotRequired[InputPathType | None],
+    "f_steps": typing.NotRequired[float | None],
+    "f_index": typing.NotRequired[str | None],
+    "f_p1_fr": typing.NotRequired[float | None],
+    "f_pn_fr": typing.NotRequired[float | None],
+    "f_p1_mm": typing.NotRequired[float | None],
+    "f_pn_mm": typing.NotRequired[float | None],
+    "stop_gap": bool,
+    "cmask": typing.NotRequired[str | None],
+    "data_expr": typing.NotRequired[str | None],
+    "datum": typing.NotRequired[str | None],
+    "debug": typing.NotRequired[int | None],
+    "dnode": typing.NotRequired[int | None],
+    "dvoxel": typing.NotRequired[int | None],
+    "noscale": bool,
+    "sxyz_orient_as_gpar": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dSurf2Vol": v_3d_surf2_vol_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "3dSurf2Vol": v_3d_surf2_vol_outputs,
+    }.get(t)
+
+
+class V3dSurf2VolOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_surf2_vol(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output dataset"""
+
+
+def v_3d_surf2_vol_params(
+    spec: InputPathType,
+    surface_volume: InputPathType,
+    surf_a: str,
+    grid_parent: InputPathType,
+    map_func: str,
+    prefix: str,
+    surf_b: str | None = None,
+    surf_xyz_1d: InputPathType | None = None,
+    sdata_1d: InputPathType | None = None,
+    sdata: InputPathType | None = None,
+    f_steps: float | None = None,
+    f_index: str | None = None,
+    f_p1_fr: float | None = None,
+    f_pn_fr: float | None = None,
+    f_p1_mm: float | None = None,
+    f_pn_mm: float | None = None,
+    stop_gap: bool = False,
+    cmask: str | None = None,
+    data_expr: str | None = None,
+    datum: str | None = None,
+    debug: int | None = None,
+    dnode: int | None = None,
+    dvoxel: int | None = None,
+    noscale: bool = False,
+    sxyz_orient_as_gpar: bool = False,
+) -> V3dSurf2VolParameters:
+    """
+    Build parameters.
+    
+    Args:
+        spec: SUMA spec file.
+        surface_volume: AFNI surface volume dataset.
+        surf_a: Specify surface A from spec file.
+        grid_parent: AFNI grid parent dataset.
+        map_func: Surface to dataset function.
+        prefix: Prefix for the output dataset.
+        surf_b: Specify surface B from spec file.
+        surf_xyz_1d: 1D coordinate file.
+        sdata_1d: 1D sub-surface data file.
+        sdata: NIML or GIFTI formatted dataset.
+        f_steps: Partition segments into this many steps.
+        f_index: Index by points or voxels.
+        f_p1_fr: Offset p1 by a fraction of the length.
+        f_pn_fr: Offset pn by a fraction of the length.
+        f_p1_mm: Offset p1 by a distance in mm.
+        f_pn_mm: Offset pn by a distance in mm.
+        stop_gap: Stop when a zero gap has been hit.
+        cmask: Command for dataset mask.
+        data_expr: Apply expression to surface input.
+        datum: Set data type in output dataset.
+        debug: Verbose output level.
+        dnode: Extra output for specified node.
+        dvoxel: Extra output for specified voxel.
+        noscale: No scale factor in output dataset.
+        sxyz_orient_as_gpar: Assume grid parent orientation for surface xyz.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dSurf2Vol",
+        "spec": spec,
+        "surface_volume": surface_volume,
+        "surf_a": surf_a,
+        "grid_parent": grid_parent,
+        "map_func": map_func,
+        "prefix": prefix,
+        "stop_gap": stop_gap,
+        "noscale": noscale,
+        "sxyz_orient_as_gpar": sxyz_orient_as_gpar,
+    }
+    if surf_b is not None:
+        params["surf_b"] = surf_b
+    if surf_xyz_1d is not None:
+        params["surf_xyz_1d"] = surf_xyz_1d
+    if sdata_1d is not None:
+        params["sdata_1d"] = sdata_1d
+    if sdata is not None:
+        params["sdata"] = sdata
+    if f_steps is not None:
+        params["f_steps"] = f_steps
+    if f_index is not None:
+        params["f_index"] = f_index
+    if f_p1_fr is not None:
+        params["f_p1_fr"] = f_p1_fr
+    if f_pn_fr is not None:
+        params["f_pn_fr"] = f_pn_fr
+    if f_p1_mm is not None:
+        params["f_p1_mm"] = f_p1_mm
+    if f_pn_mm is not None:
+        params["f_pn_mm"] = f_pn_mm
+    if cmask is not None:
+        params["cmask"] = cmask
+    if data_expr is not None:
+        params["data_expr"] = data_expr
+    if datum is not None:
+        params["datum"] = datum
+    if debug is not None:
+        params["debug"] = debug
+    if dnode is not None:
+        params["dnode"] = dnode
+    if dvoxel is not None:
+        params["dvoxel"] = dvoxel
+    return params
+
+
+def v_3d_surf2_vol_cargs(
+    params: V3dSurf2VolParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("3dSurf2Vol")
+    cargs.extend([
+        "-spec",
+        execution.input_file(params.get("spec"))
+    ])
+    cargs.extend([
+        "-sv",
+        execution.input_file(params.get("surface_volume"))
+    ])
+    cargs.extend([
+        "-surf_A",
+        params.get("surf_a")
+    ])
+    if params.get("surf_b") is not None:
+        cargs.extend([
+            "-surf_B",
+            params.get("surf_b")
+        ])
+    cargs.extend([
+        "-grid_parent",
+        execution.input_file(params.get("grid_parent"))
+    ])
+    cargs.extend([
+        "-map_func",
+        params.get("map_func")
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("surf_xyz_1d") is not None:
+        cargs.extend([
+            "-surf_xyz_1D",
+            execution.input_file(params.get("surf_xyz_1d"))
+        ])
+    if params.get("sdata_1d") is not None:
+        cargs.extend([
+            "-sdata_1D",
+            execution.input_file(params.get("sdata_1d"))
+        ])
+    if params.get("sdata") is not None:
+        cargs.extend([
+            "-sdata",
+            execution.input_file(params.get("sdata"))
+        ])
+    if params.get("f_steps") is not None:
+        cargs.extend([
+            "-f_steps",
+            str(params.get("f_steps"))
+        ])
+    if params.get("f_index") is not None:
+        cargs.extend([
+            "-f_index",
+            params.get("f_index")
+        ])
+    if params.get("f_p1_fr") is not None:
+        cargs.extend([
+            "-f_p1_fr",
+            str(params.get("f_p1_fr"))
+        ])
+    if params.get("f_pn_fr") is not None:
+        cargs.extend([
+            "-f_pn_fr",
+            str(params.get("f_pn_fr"))
+        ])
+    if params.get("f_p1_mm") is not None:
+        cargs.extend([
+            "-f_p1_mm",
+            str(params.get("f_p1_mm"))
+        ])
+    if params.get("f_pn_mm") is not None:
+        cargs.extend([
+            "-f_pn_mm",
+            str(params.get("f_pn_mm"))
+        ])
+    if params.get("stop_gap"):
+        cargs.append("-stop_gap")
+    if params.get("cmask") is not None:
+        cargs.extend([
+            "-cmask",
+            params.get("cmask")
+        ])
+    if params.get("data_expr") is not None:
+        cargs.extend([
+            "-data_expr",
+            params.get("data_expr")
+        ])
+    if params.get("datum") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("datum")
+        ])
+    if params.get("debug") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug"))
+        ])
+    if params.get("dnode") is not None:
+        cargs.extend([
+            "-dnode",
+            str(params.get("dnode"))
+        ])
+    if params.get("dvoxel") is not None:
+        cargs.extend([
+            "-dvoxel",
+            str(params.get("dvoxel"))
+        ])
+    if params.get("noscale"):
+        cargs.append("-noscale")
+    if params.get("sxyz_orient_as_gpar"):
+        cargs.append("-sxyz_orient_as_gpar")
+    return cargs
+
+
+def v_3d_surf2_vol_outputs(
+    params: V3dSurf2VolParameters,
+    execution: Execution,
+) -> V3dSurf2VolOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = V3dSurf2VolOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + "+*[gz]"),
+    )
+    return ret
+
+
+def v_3d_surf2_vol_execute(
+    params: V3dSurf2VolParameters,
+    execution: Execution,
+) -> V3dSurf2VolOutputs:
+    """
+    Map data from a surface domain to an AFNI volume domain.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dSurf2VolOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_surf2_vol_cargs(params, execution)
+    ret = v_3d_surf2_vol_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_surf2_vol(
+    spec: InputPathType,
+    surface_volume: InputPathType,
+    surf_a: str,
+    grid_parent: InputPathType,
+    map_func: str,
+    prefix: str,
+    surf_b: str | None = None,
+    surf_xyz_1d: InputPathType | None = None,
+    sdata_1d: InputPathType | None = None,
+    sdata: InputPathType | None = None,
+    f_steps: float | None = None,
+    f_index: str | None = None,
+    f_p1_fr: float | None = None,
+    f_pn_fr: float | None = None,
+    f_p1_mm: float | None = None,
+    f_pn_mm: float | None = None,
+    stop_gap: bool = False,
+    cmask: str | None = None,
+    data_expr: str | None = None,
+    datum: str | None = None,
+    debug: int | None = None,
+    dnode: int | None = None,
+    dvoxel: int | None = None,
+    noscale: bool = False,
+    sxyz_orient_as_gpar: bool = False,
+    runner: Runner | None = None,
+) -> V3dSurf2VolOutputs:
+    """
+    Map data from a surface domain to an AFNI volume domain.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        spec: SUMA spec file.
+        surface_volume: AFNI surface volume dataset.
+        surf_a: Specify surface A from spec file.
+        grid_parent: AFNI grid parent dataset.
+        map_func: Surface to dataset function.
+        prefix: Prefix for the output dataset.
+        surf_b: Specify surface B from spec file.
+        surf_xyz_1d: 1D coordinate file.
+        sdata_1d: 1D sub-surface data file.
+        sdata: NIML or GIFTI formatted dataset.
+        f_steps: Partition segments into this many steps.
+        f_index: Index by points or voxels.
+        f_p1_fr: Offset p1 by a fraction of the length.
+        f_pn_fr: Offset pn by a fraction of the length.
+        f_p1_mm: Offset p1 by a distance in mm.
+        f_pn_mm: Offset pn by a distance in mm.
+        stop_gap: Stop when a zero gap has been hit.
+        cmask: Command for dataset mask.
+        data_expr: Apply expression to surface input.
+        datum: Set data type in output dataset.
+        debug: Verbose output level.
+        dnode: Extra output for specified node.
+        dvoxel: Extra output for specified voxel.
+        noscale: No scale factor in output dataset.
+        sxyz_orient_as_gpar: Assume grid parent orientation for surface xyz.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dSurf2VolOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SURF2_VOL_METADATA)
+    params = v_3d_surf2_vol_params(
+        spec=spec,
+        surface_volume=surface_volume,
+        surf_a=surf_a,
+        surf_b=surf_b,
+        grid_parent=grid_parent,
+        map_func=map_func,
+        prefix=prefix,
+        surf_xyz_1d=surf_xyz_1d,
+        sdata_1d=sdata_1d,
+        sdata=sdata,
+        f_steps=f_steps,
+        f_index=f_index,
+        f_p1_fr=f_p1_fr,
+        f_pn_fr=f_pn_fr,
+        f_p1_mm=f_p1_mm,
+        f_pn_mm=f_pn_mm,
+        stop_gap=stop_gap,
+        cmask=cmask,
+        data_expr=data_expr,
+        datum=datum,
+        debug=debug,
+        dnode=dnode,
+        dvoxel=dvoxel,
+        noscale=noscale,
+        sxyz_orient_as_gpar=sxyz_orient_as_gpar,
+    )
+    return v_3d_surf2_vol_execute(params, execution)
+
+
+__all__ = [
+    "V3dSurf2VolOutputs",
+    "V3dSurf2VolParameters",
+    "V_3D_SURF2_VOL_METADATA",
+    "v_3d_surf2_vol",
+    "v_3d_surf2_vol_params",
+]