niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/surf_localstat.py

@@ -0,0 +1,242 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SURF_LOCALSTAT_METADATA = Metadata(
+    id="5a51275b28d3b9824220c99fed994126246f2f36.boutiques",
+    name="SurfLocalstat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SurfLocalstatParameters = typing.TypedDict('SurfLocalstatParameters', {
+    "__STYX_TYPE__": typing.Literal["SurfLocalstat"],
+    "hood": typing.NotRequired[float | None],
+    "nbhd_rad": typing.NotRequired[float | None],
+    "prefix": str,
+    "stat": typing.Literal["mean", "mode", "num", "FWHM", "ALL"],
+    "input_dataset": InputPathType,
+    "surface": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "SurfLocalstat": surf_localstat_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 {
+        "SurfLocalstat": surf_localstat_outputs,
+    }.get(t)
+
+
+class SurfLocalstatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `surf_localstat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Computed local statistics dataset"""
+
+
+def surf_localstat_params(
+    prefix: str,
+    stat_: typing.Literal["mean", "mode", "num", "FWHM", "ALL"],
+    input_dataset: InputPathType,
+    surface: InputPathType,
+    hood: float | None = None,
+    nbhd_rad: float | None = None,
+) -> SurfLocalstatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Prefix of output data set.
+        stat_: Compute the specified statistic on the values extracted from the\
+            region around each voxel. Options: mean, mode, num, FWHM, ALL.
+        input_dataset: Input dataset.
+        surface: Input GIFTI surface file.
+        hood: Neighborhood of nodes within the specified radius R.
+        nbhd_rad: Distance from node n as measured by the shortest distance\
+            along the mesh.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SurfLocalstat",
+        "prefix": prefix,
+        "stat": stat_,
+        "input_dataset": input_dataset,
+        "surface": surface,
+    }
+    if hood is not None:
+        params["hood"] = hood
+    if nbhd_rad is not None:
+        params["nbhd_rad"] = nbhd_rad
+    return params
+
+
+def surf_localstat_cargs(
+    params: SurfLocalstatParameters,
+    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("SurfLocalstat")
+    if params.get("hood") is not None:
+        cargs.extend([
+            "-hood",
+            str(params.get("hood"))
+        ])
+    if params.get("nbhd_rad") is not None:
+        cargs.extend([
+            "-nbhd_rad",
+            str(params.get("nbhd_rad"))
+        ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    cargs.extend([
+        "-stat",
+        params.get("stat")
+    ])
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_dataset"))
+    ])
+    cargs.extend([
+        "-i_gii",
+        execution.input_file(params.get("surface"))
+    ])
+    return cargs
+
+
+def surf_localstat_outputs(
+    params: SurfLocalstatParameters,
+    execution: Execution,
+) -> SurfLocalstatOutputs:
+    """
+    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 = SurfLocalstatOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + ".niml.dset"),
+    )
+    return ret
+
+
+def surf_localstat_execute(
+    params: SurfLocalstatParameters,
+    execution: Execution,
+) -> SurfLocalstatOutputs:
+    """
+    Compute local statistics on a surface mesh.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SurfLocalstatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = surf_localstat_cargs(params, execution)
+    ret = surf_localstat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def surf_localstat(
+    prefix: str,
+    stat_: typing.Literal["mean", "mode", "num", "FWHM", "ALL"],
+    input_dataset: InputPathType,
+    surface: InputPathType,
+    hood: float | None = None,
+    nbhd_rad: float | None = None,
+    runner: Runner | None = None,
+) -> SurfLocalstatOutputs:
+    """
+    Compute local statistics on a surface mesh.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Prefix of output data set.
+        stat_: Compute the specified statistic on the values extracted from the\
+            region around each voxel. Options: mean, mode, num, FWHM, ALL.
+        input_dataset: Input dataset.
+        surface: Input GIFTI surface file.
+        hood: Neighborhood of nodes within the specified radius R.
+        nbhd_rad: Distance from node n as measured by the shortest distance\
+            along the mesh.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SurfLocalstatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_LOCALSTAT_METADATA)
+    params = surf_localstat_params(
+        hood=hood,
+        nbhd_rad=nbhd_rad,
+        prefix=prefix,
+        stat_=stat_,
+        input_dataset=input_dataset,
+        surface=surface,
+    )
+    return surf_localstat_execute(params, execution)
+
+
+__all__ = [
+    "SURF_LOCALSTAT_METADATA",
+    "SurfLocalstatOutputs",
+    "SurfLocalstatParameters",
+    "surf_localstat",
+    "surf_localstat_params",
+]

niwrap_afni/afni/surf_measures.py

@@ -0,0 +1,373 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SURF_MEASURES_METADATA = Metadata(
+    id="21378ea7d8b0e920275d5e4fab477aa23c434ab4.boutiques",
+    name="SurfMeasures",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SurfMeasuresParameters = typing.TypedDict('SurfMeasuresParameters', {
+    "__STYX_TYPE__": typing.Literal["SurfMeasures"],
+    "spec_file": InputPathType,
+    "surf_A": str,
+    "surf_B": typing.NotRequired[str | None],
+    "out_1D": typing.NotRequired[str | None],
+    "out_dset": str,
+    "func": typing.NotRequired[list[str] | None],
+    "surf_volume": typing.NotRequired[InputPathType | None],
+    "cmask": typing.NotRequired[str | None],
+    "debug": typing.NotRequired[int | None],
+    "dnode": typing.NotRequired[float | None],
+    "nodes_1D": typing.NotRequired[InputPathType | None],
+    "info_all": bool,
+    "info_area": bool,
+    "info_norms": bool,
+    "info_thick": bool,
+    "info_vol": bool,
+    "info_volg": bool,
+    "ver": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "SurfMeasures": surf_measures_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 {
+        "SurfMeasures": surf_measures_outputs,
+    }.get(t)
+
+
+class SurfMeasuresOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `surf_measures(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_1_d: OutputPathType | None
+    """Output in 1D format"""
+    output_dset: OutputPathType
+    """Output in specified dataset format"""
+
+
+def surf_measures_params(
+    spec_file: InputPathType,
+    surf_a: str,
+    out_dset: str,
+    surf_b: str | None = None,
+    out_1_d: str | None = None,
+    func: list[str] | None = None,
+    surf_volume: InputPathType | None = None,
+    cmask: str | None = None,
+    debug: int | None = None,
+    dnode: float | None = None,
+    nodes_1_d: InputPathType | None = None,
+    info_all: bool = False,
+    info_area: bool = False,
+    info_norms: bool = False,
+    info_thick: bool = False,
+    info_vol: bool = False,
+    info_volg: bool = False,
+    ver: bool = False,
+) -> SurfMeasuresParameters:
+    """
+    Build parameters.
+    
+    Args:
+        spec_file: SUMA spec file containing a list of related surfaces.
+        surf_a: Surface name (in spec file) for the first surface.
+        out_dset: Output filename with dataset format.
+        surf_b: Surface name (in spec file) for the second surface.
+        out_1_d: Output filename in 1D format.
+        func: Measure function to be applied.
+        surf_volume: AFNI volume dataset associated with the surface.
+        cmask: Restrict nodes with a mask.
+        debug: Display extra run-time information with specified debug level\
+            (0-5).
+        dnode: Display extra information for specified node.
+        nodes_1_d: Restrict output to specific nodes listed in a file.
+        info_all: Display all final info.
+        info_area: Display total area of each triangulated surface.
+        info_norms: Display info about the normals.
+        info_thick: Display minimum and maximum thickness between surfaces.
+        info_vol: Display total computed volume between surfaces.
+        info_volg: Display total computed volume estimated via Gauss' theorem.
+        ver: Show program version and compile date.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SurfMeasures",
+        "spec_file": spec_file,
+        "surf_A": surf_a,
+        "out_dset": out_dset,
+        "info_all": info_all,
+        "info_area": info_area,
+        "info_norms": info_norms,
+        "info_thick": info_thick,
+        "info_vol": info_vol,
+        "info_volg": info_volg,
+        "ver": ver,
+    }
+    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 func is not None:
+        params["func"] = func
+    if surf_volume is not None:
+        params["surf_volume"] = surf_volume
+    if cmask is not None:
+        params["cmask"] = cmask
+    if debug is not None:
+        params["debug"] = debug
+    if dnode is not None:
+        params["dnode"] = dnode
+    if nodes_1_d is not None:
+        params["nodes_1D"] = nodes_1_d
+    return params
+
+
+def surf_measures_cargs(
+    params: SurfMeasuresParameters,
+    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("SurfMeasures")
+    cargs.extend([
+        "-spec",
+        execution.input_file(params.get("spec_file"))
+    ])
+    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")
+        ])
+    cargs.extend([
+        "-out",
+        params.get("out_dset")
+    ])
+    if params.get("func") is not None:
+        cargs.extend([
+            "-func",
+            *params.get("func")
+        ])
+    if params.get("surf_volume") is not None:
+        cargs.extend([
+            "-sv",
+            execution.input_file(params.get("surf_volume"))
+        ])
+    if params.get("cmask") is not None:
+        cargs.extend([
+            "-cmask",
+            params.get("cmask")
+        ])
+    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("nodes_1D") is not None:
+        cargs.extend([
+            "-nodes_1D",
+            execution.input_file(params.get("nodes_1D"))
+        ])
+    if params.get("info_all"):
+        cargs.append("-info_all")
+    if params.get("info_area"):
+        cargs.append("-info_area")
+    if params.get("info_norms"):
+        cargs.append("-info_norms")
+    if params.get("info_thick"):
+        cargs.append("-info_thick")
+    if params.get("info_vol"):
+        cargs.append("-info_vol")
+    if params.get("info_volg"):
+        cargs.append("-info_volg")
+    if params.get("ver"):
+        cargs.append("-ver")
+    return cargs
+
+
+def surf_measures_outputs(
+    params: SurfMeasuresParameters,
+    execution: Execution,
+) -> SurfMeasuresOutputs:
+    """
+    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 = SurfMeasuresOutputs(
+        root=execution.output_file("."),
+        output_1_d=execution.output_file(params.get("out_1D") + ".1D") if (params.get("out_1D") is not None) else None,
+        output_dset=execution.output_file(params.get("out_dset")),
+    )
+    return ret
+
+
+def surf_measures_execute(
+    params: SurfMeasuresParameters,
+    execution: Execution,
+) -> SurfMeasuresOutputs:
+    """
+    Compute measures from surface dataset(s).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SurfMeasuresOutputs`).
+    """
+    params = execution.params(params)
+    cargs = surf_measures_cargs(params, execution)
+    ret = surf_measures_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def surf_measures(
+    spec_file: InputPathType,
+    surf_a: str,
+    out_dset: str,
+    surf_b: str | None = None,
+    out_1_d: str | None = None,
+    func: list[str] | None = None,
+    surf_volume: InputPathType | None = None,
+    cmask: str | None = None,
+    debug: int | None = None,
+    dnode: float | None = None,
+    nodes_1_d: InputPathType | None = None,
+    info_all: bool = False,
+    info_area: bool = False,
+    info_norms: bool = False,
+    info_thick: bool = False,
+    info_vol: bool = False,
+    info_volg: bool = False,
+    ver: bool = False,
+    runner: Runner | None = None,
+) -> SurfMeasuresOutputs:
+    """
+    Compute measures from surface dataset(s).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        spec_file: SUMA spec file containing a list of related surfaces.
+        surf_a: Surface name (in spec file) for the first surface.
+        out_dset: Output filename with dataset format.
+        surf_b: Surface name (in spec file) for the second surface.
+        out_1_d: Output filename in 1D format.
+        func: Measure function to be applied.
+        surf_volume: AFNI volume dataset associated with the surface.
+        cmask: Restrict nodes with a mask.
+        debug: Display extra run-time information with specified debug level\
+            (0-5).
+        dnode: Display extra information for specified node.
+        nodes_1_d: Restrict output to specific nodes listed in a file.
+        info_all: Display all final info.
+        info_area: Display total area of each triangulated surface.
+        info_norms: Display info about the normals.
+        info_thick: Display minimum and maximum thickness between surfaces.
+        info_vol: Display total computed volume between surfaces.
+        info_volg: Display total computed volume estimated via Gauss' theorem.
+        ver: Show program version and compile date.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SurfMeasuresOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_MEASURES_METADATA)
+    params = surf_measures_params(
+        spec_file=spec_file,
+        surf_a=surf_a,
+        surf_b=surf_b,
+        out_1_d=out_1_d,
+        out_dset=out_dset,
+        func=func,
+        surf_volume=surf_volume,
+        cmask=cmask,
+        debug=debug,
+        dnode=dnode,
+        nodes_1_d=nodes_1_d,
+        info_all=info_all,
+        info_area=info_area,
+        info_norms=info_norms,
+        info_thick=info_thick,
+        info_vol=info_vol,
+        info_volg=info_volg,
+        ver=ver,
+    )
+    return surf_measures_execute(params, execution)
+
+
+__all__ = [
+    "SURF_MEASURES_METADATA",
+    "SurfMeasuresOutputs",
+    "SurfMeasuresParameters",
+    "surf_measures",
+    "surf_measures_params",
+]