niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_vol2_surf.py

@@ -0,0 +1,653 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_VOL2_SURF_METADATA = Metadata(
+    id="c02eb3df673097f601aee76ef3ab0760f92ddec8.boutiques",
+    name="3dVol2Surf",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dVol2SurfParameters = typing.TypedDict('V3dVol2SurfParameters', {
+    "__STYX_TYPE__": typing.Literal["3dVol2Surf"],
+    "spec_file": InputPathType,
+    "sv": InputPathType,
+    "grid_parent": InputPathType,
+    "map_func": str,
+    "surf_A": str,
+    "surf_B": typing.NotRequired[str | None],
+    "out_1D": typing.NotRequired[str | None],
+    "out_niml": typing.NotRequired[str | None],
+    "use_norms": bool,
+    "norm_len": typing.NotRequired[float | None],
+    "first_node": typing.NotRequired[float | None],
+    "last_node": typing.NotRequired[float | None],
+    "debug_level": typing.NotRequired[float | None],
+    "dnode": typing.NotRequired[float | None],
+    "f_steps": typing.NotRequired[float | None],
+    "f_index": typing.NotRequired[str | None],
+    "f_p1_mm": typing.NotRequired[float | None],
+    "f_pn_mm": typing.NotRequired[float | None],
+    "f_p1_fr": typing.NotRequired[float | None],
+    "f_pn_fr": typing.NotRequired[float | None],
+    "skip_col_nodes": bool,
+    "skip_col_1dindex": bool,
+    "skip_col_i": bool,
+    "skip_col_j": bool,
+    "skip_col_k": bool,
+    "skip_col_vals": bool,
+    "no_headers": bool,
+    "save_seg_coords": typing.NotRequired[str | None],
+    "cmask": typing.NotRequired[str | None],
+    "gp_index": typing.NotRequired[float | None],
+    "oob_index": typing.NotRequired[float | None],
+    "oob_value": typing.NotRequired[float | None],
+    "oom_value": typing.NotRequired[float | None],
+    "outcols_afni_nsd": bool,
+    "outcols_1_result": bool,
+    "outcols_results": bool,
+    "outcols_nsd_format": bool,
+    "help": bool,
+    "hist": bool,
+    "version": bool,
+    "keep_norm_dir": bool,
+    "reverse_norm_dir": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dVol2Surf": v_3d_vol2_surf_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 {
+        "3dVol2Surf": v_3d_vol2_surf_outputs,
+    }.get(t)
+
+
+class V3dVol2SurfOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_vol2_surf(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_1d_file: OutputPathType | None
+    """1D output file"""
+    out_niml_file: OutputPathType | None
+    """NIML output file"""
+    seg_coords_file: OutputPathType | None
+    """Segment coordinates output file"""
+
+
+def v_3d_vol2_surf_params(
+    spec_file: InputPathType,
+    sv: InputPathType,
+    grid_parent: InputPathType,
+    map_func: str,
+    surf_a: str,
+    surf_b: str | None = None,
+    out_1_d: str | None = None,
+    out_niml: str | None = None,
+    use_norms: bool = False,
+    norm_len: float | None = None,
+    first_node: float | None = None,
+    last_node: float | None = None,
+    debug_level: float | None = None,
+    dnode: float | None = None,
+    f_steps: float | None = None,
+    f_index: str | None = None,
+    f_p1_mm: float | None = None,
+    f_pn_mm: float | None = None,
+    f_p1_fr: float | None = None,
+    f_pn_fr: float | None = None,
+    skip_col_nodes: bool = False,
+    skip_col_1dindex: bool = False,
+    skip_col_i: bool = False,
+    skip_col_j: bool = False,
+    skip_col_k: bool = False,
+    skip_col_vals: bool = False,
+    no_headers: bool = False,
+    save_seg_coords: str | None = None,
+    cmask: str | None = None,
+    gp_index: float | None = None,
+    oob_index: float | None = None,
+    oob_value: float | None = None,
+    oom_value: float | None = None,
+    outcols_afni_nsd: bool = False,
+    outcols_1_result: bool = False,
+    outcols_results: bool = False,
+    outcols_nsd_format: bool = False,
+    help_: bool = False,
+    hist: bool = False,
+    version: bool = False,
+    keep_norm_dir: bool = False,
+    reverse_norm_dir: bool = False,
+) -> V3dVol2SurfParameters:
+    """
+    Build parameters.
+    
+    Args:
+        spec_file: SUMA spec file.
+        sv: AFNI volume dataset mapped by the surface.
+        grid_parent: AFNI volume dataset used as a grid and orientation master\
+            for output.
+        map_func: Filter for values along the segment.
+        surf_a: Name of surface A from the spec file.
+        surf_b: Name of surface B from the spec file.
+        out_1_d: Specify a 1D file for the output.
+        out_niml: Specify a niml file for the output.
+        use_norms: Use normals for second surface.
+        norm_len: Length for node normals.
+        first_node: Skip all previous nodes.
+        last_node: Skip all following nodes.
+        debug_level: Verbose output level.
+        dnode: Node for debug.
+        f_steps: Number of steps along each segment (defines the number of\
+            evenly spaced points along each segment).
+        f_index: Whether to use all segment point values or only those\
+            corresponding to unique volume voxels.
+        f_p1_mm: Distance in millimeters to add to the first point of each line\
+            segment.
+        f_pn_mm: Distance in millimeters to add to the second point of each\
+            line segment.
+        f_p1_fr: Fractional distance to add to the first point of each line\
+            segment.
+        f_pn_fr: Fractional distance to add to the second point of each line\
+            segment.
+        skip_col_nodes: Do not output node column.
+        skip_col_1dindex: Do not output 1dindex column.
+        skip_col_i: Do not output i column.
+        skip_col_j: Do not output j column.
+        skip_col_k: Do not output k column.
+        skip_col_vals: Do not output vals column.
+        no_headers: Do not output column headers.
+        save_seg_coords: Save segment coordinates to a file.
+        cmask: Command for dataset mask.
+        gp_index: Choose grid_parent sub-brick.
+        oob_index: Specify default index for out of bounds nodes.
+        oob_value: Specify default value for out of bounds nodes.
+        oom_value: Specify default value for out of mask nodes.
+        outcols_afni_nsd: Output nodes and one result column.
+        outcols_1_result: Output only one result column.
+        outcols_results: Output only all result columns.
+        outcols_nsd_format: Output nodes and all results (NI_SURF_DSET format).
+        help_: Show this help.
+        hist: Show revision history.
+        version: Show version information.
+        keep_norm_dir: Keep the direction of the normals.
+        reverse_norm_dir: Reverse the normal directions.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dVol2Surf",
+        "spec_file": spec_file,
+        "sv": sv,
+        "grid_parent": grid_parent,
+        "map_func": map_func,
+        "surf_A": surf_a,
+        "use_norms": use_norms,
+        "skip_col_nodes": skip_col_nodes,
+        "skip_col_1dindex": skip_col_1dindex,
+        "skip_col_i": skip_col_i,
+        "skip_col_j": skip_col_j,
+        "skip_col_k": skip_col_k,
+        "skip_col_vals": skip_col_vals,
+        "no_headers": no_headers,
+        "outcols_afni_nsd": outcols_afni_nsd,
+        "outcols_1_result": outcols_1_result,
+        "outcols_results": outcols_results,
+        "outcols_nsd_format": outcols_nsd_format,
+        "help": help_,
+        "hist": hist,
+        "version": version,
+        "keep_norm_dir": keep_norm_dir,
+        "reverse_norm_dir": reverse_norm_dir,
+    }
+    if surf_b is not None:
+        params["surf_B"] = surf_b
+    if out_1_d is not None:
+        params["out_1D"] = out_1_d
+    if out_niml is not None:
+        params["out_niml"] = out_niml
+    if norm_len is not None:
+        params["norm_len"] = norm_len
+    if first_node is not None:
+        params["first_node"] = first_node
+    if last_node is not None:
+        params["last_node"] = last_node
+    if debug_level is not None:
+        params["debug_level"] = debug_level
+    if dnode is not None:
+        params["dnode"] = dnode
+    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_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 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 save_seg_coords is not None:
+        params["save_seg_coords"] = save_seg_coords
+    if cmask is not None:
+        params["cmask"] = cmask
+    if gp_index is not None:
+        params["gp_index"] = gp_index
+    if oob_index is not None:
+        params["oob_index"] = oob_index
+    if oob_value is not None:
+        params["oob_value"] = oob_value
+    if oom_value is not None:
+        params["oom_value"] = oom_value
+    return params
+
+
+def v_3d_vol2_surf_cargs(
+    params: V3dVol2SurfParameters,
+    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("3dVol2Surf")
+    cargs.append(execution.input_file(params.get("spec_file")))
+    cargs.extend([
+        "-sv",
+        execution.input_file(params.get("sv"))
+    ])
+    cargs.extend([
+        "-grid_parent",
+        execution.input_file(params.get("grid_parent"))
+    ])
+    cargs.extend([
+        "-map_func",
+        params.get("map_func")
+    ])
+    cargs.extend([
+        "-surf_A",
+        params.get("surf_A")
+    ])
+    if params.get("surf_B") is not None:
+        cargs.extend([
+            "-surf_B",
+            params.get("surf_B")
+        ])
+    if params.get("out_1D") is not None:
+        cargs.extend([
+            "-out_1D",
+            params.get("out_1D")
+        ])
+    if params.get("out_niml") is not None:
+        cargs.extend([
+            "-out_niml",
+            params.get("out_niml")
+        ])
+    if params.get("use_norms"):
+        cargs.append("-use_norms")
+    if params.get("norm_len") is not None:
+        cargs.extend([
+            "-norm_len",
+            str(params.get("norm_len"))
+        ])
+    if params.get("first_node") is not None:
+        cargs.extend([
+            "-first_node",
+            str(params.get("first_node"))
+        ])
+    if params.get("last_node") is not None:
+        cargs.extend([
+            "-last_node",
+            str(params.get("last_node"))
+        ])
+    if params.get("debug_level") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug_level"))
+        ])
+    if params.get("dnode") is not None:
+        cargs.extend([
+            "-dnode",
+            str(params.get("dnode"))
+        ])
+    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_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("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("skip_col_nodes"):
+        cargs.append("-skip_col_nodes")
+    if params.get("skip_col_1dindex"):
+        cargs.append("-skip_col_1dindex")
+    if params.get("skip_col_i"):
+        cargs.append("-skip_col_i")
+    if params.get("skip_col_j"):
+        cargs.append("-skip_col_j")
+    if params.get("skip_col_k"):
+        cargs.append("-skip_col_k")
+    if params.get("skip_col_vals"):
+        cargs.append("-skip_col_vals")
+    if params.get("no_headers"):
+        cargs.append("-no_headers")
+    if params.get("save_seg_coords") is not None:
+        cargs.extend([
+            "-save_seg_coords",
+            params.get("save_seg_coords")
+        ])
+    if params.get("cmask") is not None:
+        cargs.extend([
+            "-cmask",
+            params.get("cmask")
+        ])
+    if params.get("gp_index") is not None:
+        cargs.extend([
+            "-gp_index",
+            str(params.get("gp_index"))
+        ])
+    if params.get("oob_index") is not None:
+        cargs.extend([
+            "-oob_index",
+            str(params.get("oob_index"))
+        ])
+    if params.get("oob_value") is not None:
+        cargs.extend([
+            "-oob_value",
+            str(params.get("oob_value"))
+        ])
+    if params.get("oom_value") is not None:
+        cargs.extend([
+            "-oom_value",
+            str(params.get("oom_value"))
+        ])
+    if params.get("outcols_afni_nsd"):
+        cargs.append("-outcols_afni_NSD")
+    if params.get("outcols_1_result"):
+        cargs.append("-outcols_1_result")
+    if params.get("outcols_results"):
+        cargs.append("-outcols_results")
+    if params.get("outcols_nsd_format"):
+        cargs.append("-outcols_NSD_format")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("hist"):
+        cargs.append("-hist")
+    if params.get("version"):
+        cargs.append("-version")
+    if params.get("keep_norm_dir"):
+        cargs.append("-keep_norm_dir")
+    if params.get("reverse_norm_dir"):
+        cargs.append("-reverse_norm_dir")
+    return cargs
+
+
+def v_3d_vol2_surf_outputs(
+    params: V3dVol2SurfParameters,
+    execution: Execution,
+) -> V3dVol2SurfOutputs:
+    """
+    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 = V3dVol2SurfOutputs(
+        root=execution.output_file("."),
+        out_1d_file=execution.output_file(params.get("out_1D")) if (params.get("out_1D") is not None) else None,
+        out_niml_file=execution.output_file(params.get("out_niml")) if (params.get("out_niml") is not None) else None,
+        seg_coords_file=execution.output_file(params.get("save_seg_coords")) if (params.get("save_seg_coords") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_vol2_surf_execute(
+    params: V3dVol2SurfParameters,
+    execution: Execution,
+) -> V3dVol2SurfOutputs:
+    """
+    Map data from a volume domain to a surface domain.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dVol2SurfOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_vol2_surf_cargs(params, execution)
+    ret = v_3d_vol2_surf_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_vol2_surf(
+    spec_file: InputPathType,
+    sv: InputPathType,
+    grid_parent: InputPathType,
+    map_func: str,
+    surf_a: str,
+    surf_b: str | None = None,
+    out_1_d: str | None = None,
+    out_niml: str | None = None,
+    use_norms: bool = False,
+    norm_len: float | None = None,
+    first_node: float | None = None,
+    last_node: float | None = None,
+    debug_level: float | None = None,
+    dnode: float | None = None,
+    f_steps: float | None = None,
+    f_index: str | None = None,
+    f_p1_mm: float | None = None,
+    f_pn_mm: float | None = None,
+    f_p1_fr: float | None = None,
+    f_pn_fr: float | None = None,
+    skip_col_nodes: bool = False,
+    skip_col_1dindex: bool = False,
+    skip_col_i: bool = False,
+    skip_col_j: bool = False,
+    skip_col_k: bool = False,
+    skip_col_vals: bool = False,
+    no_headers: bool = False,
+    save_seg_coords: str | None = None,
+    cmask: str | None = None,
+    gp_index: float | None = None,
+    oob_index: float | None = None,
+    oob_value: float | None = None,
+    oom_value: float | None = None,
+    outcols_afni_nsd: bool = False,
+    outcols_1_result: bool = False,
+    outcols_results: bool = False,
+    outcols_nsd_format: bool = False,
+    help_: bool = False,
+    hist: bool = False,
+    version: bool = False,
+    keep_norm_dir: bool = False,
+    reverse_norm_dir: bool = False,
+    runner: Runner | None = None,
+) -> V3dVol2SurfOutputs:
+    """
+    Map data from a volume domain to a surface domain.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        spec_file: SUMA spec file.
+        sv: AFNI volume dataset mapped by the surface.
+        grid_parent: AFNI volume dataset used as a grid and orientation master\
+            for output.
+        map_func: Filter for values along the segment.
+        surf_a: Name of surface A from the spec file.
+        surf_b: Name of surface B from the spec file.
+        out_1_d: Specify a 1D file for the output.
+        out_niml: Specify a niml file for the output.
+        use_norms: Use normals for second surface.
+        norm_len: Length for node normals.
+        first_node: Skip all previous nodes.
+        last_node: Skip all following nodes.
+        debug_level: Verbose output level.
+        dnode: Node for debug.
+        f_steps: Number of steps along each segment (defines the number of\
+            evenly spaced points along each segment).
+        f_index: Whether to use all segment point values or only those\
+            corresponding to unique volume voxels.
+        f_p1_mm: Distance in millimeters to add to the first point of each line\
+            segment.
+        f_pn_mm: Distance in millimeters to add to the second point of each\
+            line segment.
+        f_p1_fr: Fractional distance to add to the first point of each line\
+            segment.
+        f_pn_fr: Fractional distance to add to the second point of each line\
+            segment.
+        skip_col_nodes: Do not output node column.
+        skip_col_1dindex: Do not output 1dindex column.
+        skip_col_i: Do not output i column.
+        skip_col_j: Do not output j column.
+        skip_col_k: Do not output k column.
+        skip_col_vals: Do not output vals column.
+        no_headers: Do not output column headers.
+        save_seg_coords: Save segment coordinates to a file.
+        cmask: Command for dataset mask.
+        gp_index: Choose grid_parent sub-brick.
+        oob_index: Specify default index for out of bounds nodes.
+        oob_value: Specify default value for out of bounds nodes.
+        oom_value: Specify default value for out of mask nodes.
+        outcols_afni_nsd: Output nodes and one result column.
+        outcols_1_result: Output only one result column.
+        outcols_results: Output only all result columns.
+        outcols_nsd_format: Output nodes and all results (NI_SURF_DSET format).
+        help_: Show this help.
+        hist: Show revision history.
+        version: Show version information.
+        keep_norm_dir: Keep the direction of the normals.
+        reverse_norm_dir: Reverse the normal directions.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dVol2SurfOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_VOL2_SURF_METADATA)
+    params = v_3d_vol2_surf_params(
+        spec_file=spec_file,
+        sv=sv,
+        grid_parent=grid_parent,
+        map_func=map_func,
+        surf_a=surf_a,
+        surf_b=surf_b,
+        out_1_d=out_1_d,
+        out_niml=out_niml,
+        use_norms=use_norms,
+        norm_len=norm_len,
+        first_node=first_node,
+        last_node=last_node,
+        debug_level=debug_level,
+        dnode=dnode,
+        f_steps=f_steps,
+        f_index=f_index,
+        f_p1_mm=f_p1_mm,
+        f_pn_mm=f_pn_mm,
+        f_p1_fr=f_p1_fr,
+        f_pn_fr=f_pn_fr,
+        skip_col_nodes=skip_col_nodes,
+        skip_col_1dindex=skip_col_1dindex,
+        skip_col_i=skip_col_i,
+        skip_col_j=skip_col_j,
+        skip_col_k=skip_col_k,
+        skip_col_vals=skip_col_vals,
+        no_headers=no_headers,
+        save_seg_coords=save_seg_coords,
+        cmask=cmask,
+        gp_index=gp_index,
+        oob_index=oob_index,
+        oob_value=oob_value,
+        oom_value=oom_value,
+        outcols_afni_nsd=outcols_afni_nsd,
+        outcols_1_result=outcols_1_result,
+        outcols_results=outcols_results,
+        outcols_nsd_format=outcols_nsd_format,
+        help_=help_,
+        hist=hist,
+        version=version,
+        keep_norm_dir=keep_norm_dir,
+        reverse_norm_dir=reverse_norm_dir,
+    )
+    return v_3d_vol2_surf_execute(params, execution)
+
+
+__all__ = [
+    "V3dVol2SurfOutputs",
+    "V3dVol2SurfParameters",
+    "V_3D_VOL2_SURF_METADATA",
+    "v_3d_vol2_surf",
+    "v_3d_vol2_surf_params",
+]