niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/surf_smooth.py

@@ -0,0 +1,388 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SURF_SMOOTH_METADATA = Metadata(
+    id="d12bfab32f106014ff3d8c52a7b720c737313260.boutiques",
+    name="SurfSmooth",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SurfSmoothParameters = typing.TypedDict('SurfSmoothParameters', {
+    "__STYX_TYPE__": typing.Literal["SurfSmooth"],
+    "surface": str,
+    "method": str,
+    "input_data": typing.NotRequired[InputPathType | None],
+    "target_fwhm": typing.NotRequired[float | None],
+    "fwhm": typing.NotRequired[float | None],
+    "number_iterations": typing.NotRequired[float | None],
+    "output_file": typing.NotRequired[str | None],
+    "band_pass_frequency": typing.NotRequired[float | None],
+    "lambda_mu": typing.NotRequired[str | None],
+    "interp_weights": typing.NotRequired[str | None],
+    "node_mask": typing.NotRequired[InputPathType | None],
+    "surface_output": typing.NotRequired[InputPathType | None],
+    "dbg_node": typing.NotRequired[float | None],
+    "use_neighbors_outside_mask": bool,
+    "talk_suma": bool,
+    "refresh_rate": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "SurfSmooth": surf_smooth_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 {
+        "SurfSmooth": surf_smooth_outputs,
+    }.get(t)
+
+
+class SurfSmoothOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `surf_smooth(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType | None
+    """Name of the output file."""
+
+
+def surf_smooth_params(
+    surface: str,
+    method: str,
+    input_data: InputPathType | None = None,
+    target_fwhm: float | None = None,
+    fwhm: float | None = None,
+    number_iterations: float | None = None,
+    output_file: str | None = None,
+    band_pass_frequency: float | None = None,
+    lambda_mu: str | None = None,
+    interp_weights: str | None = None,
+    node_mask: InputPathType | None = None,
+    surface_output: InputPathType | None = None,
+    dbg_node: float | None = None,
+    use_neighbors_outside_mask: bool = False,
+    talk_suma: bool = False,
+    refresh_rate: float | None = None,
+) -> SurfSmoothParameters:
+    """
+    Build parameters.
+    
+    Args:
+        surface: Option for specifying the surface to smooth or the domain over\
+            which DSET is defined.
+        method: Name of smoothing method to use. Choose from: HEAT_07, HEAT_05,\
+            LM, NN_geom.
+        input_data: File containing data (in 1D or NIML format). Required for\
+            HEAT_05 and HEAT_07 methods.
+        target_fwhm: Blur so that the final FWHM of the data is TF mm. Only for\
+            HEAT_07 method.
+        fwhm: Effective Full Width at Half Maximum for smoothing. Required for\
+            HEAT_05 and optional for HEAT_07 methods.
+        number_iterations: Number of smoothing iterations (default is 100 for\
+            LM and NN_geom, -1 for HEAT methods).
+        output_file: Name of output file. Default based on method being used.
+        band_pass_frequency: Bandpass frequency for LM method (0 < k < 10).
+        lambda_mu: Lambda and Mu parameters for LM method. Sample values are:\
+            0.6307 and -0.6732.
+        interp_weights: Set interpolation weights for LM method. Options:\
+            Equal, Fujiwara, Desbrun.
+        node_mask: Apply operations only to nodes listed in the given mask.
+        surface_output: Writes the surface with smoothed coordinates to disk.\
+            For LM and NN_geom methods.
+        dbg_node: Output debug information for node 'node'.
+        use_neighbors_outside_mask: Allow value from a node neighboring node n\
+            to contribute to the value at n even if the neighbor is not in the\
+            mask.
+        talk_suma: Send progress with each iteration to SUMA for real-time\
+            visualization.
+        refresh_rate: Maximum number of updates to SUMA per second.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SurfSmooth",
+        "surface": surface,
+        "method": method,
+        "use_neighbors_outside_mask": use_neighbors_outside_mask,
+        "talk_suma": talk_suma,
+    }
+    if input_data is not None:
+        params["input_data"] = input_data
+    if target_fwhm is not None:
+        params["target_fwhm"] = target_fwhm
+    if fwhm is not None:
+        params["fwhm"] = fwhm
+    if number_iterations is not None:
+        params["number_iterations"] = number_iterations
+    if output_file is not None:
+        params["output_file"] = output_file
+    if band_pass_frequency is not None:
+        params["band_pass_frequency"] = band_pass_frequency
+    if lambda_mu is not None:
+        params["lambda_mu"] = lambda_mu
+    if interp_weights is not None:
+        params["interp_weights"] = interp_weights
+    if node_mask is not None:
+        params["node_mask"] = node_mask
+    if surface_output is not None:
+        params["surface_output"] = surface_output
+    if dbg_node is not None:
+        params["dbg_node"] = dbg_node
+    if refresh_rate is not None:
+        params["refresh_rate"] = refresh_rate
+    return params
+
+
+def surf_smooth_cargs(
+    params: SurfSmoothParameters,
+    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("SurfSmooth")
+    cargs.extend([
+        "-SURF_1",
+        params.get("surface")
+    ])
+    cargs.extend([
+        "-met",
+        params.get("method")
+    ])
+    if params.get("input_data") is not None:
+        cargs.extend([
+            "-input",
+            execution.input_file(params.get("input_data"))
+        ])
+    if params.get("target_fwhm") is not None:
+        cargs.extend([
+            "-target_fwhm",
+            str(params.get("target_fwhm"))
+        ])
+    if params.get("fwhm") is not None:
+        cargs.extend([
+            "-fwhm",
+            str(params.get("fwhm"))
+        ])
+    if params.get("number_iterations") is not None:
+        cargs.extend([
+            "-Niter",
+            str(params.get("number_iterations"))
+        ])
+    if params.get("output_file") is not None:
+        cargs.extend([
+            "-output",
+            params.get("output_file")
+        ])
+    if params.get("band_pass_frequency") is not None:
+        cargs.extend([
+            "-kpb",
+            str(params.get("band_pass_frequency"))
+        ])
+    if params.get("lambda_mu") is not None:
+        cargs.extend([
+            "-lm",
+            params.get("lambda_mu")
+        ])
+    if params.get("interp_weights") is not None:
+        cargs.extend([
+            "-iw",
+            params.get("interp_weights")
+        ])
+    if params.get("node_mask") is not None:
+        cargs.extend([
+            "-MASK",
+            execution.input_file(params.get("node_mask"))
+        ])
+    if params.get("surface_output") is not None:
+        cargs.extend([
+            "-surf_out",
+            execution.input_file(params.get("surface_output"))
+        ])
+    if params.get("dbg_node") is not None:
+        cargs.extend([
+            "-dbg_n",
+            str(params.get("dbg_node"))
+        ])
+    if params.get("use_neighbors_outside_mask"):
+        cargs.append("-use_neighbors_outside_mask")
+    if params.get("talk_suma"):
+        cargs.append("-talk_suma")
+    if params.get("refresh_rate") is not None:
+        cargs.extend([
+            "-refresh_rate",
+            str(params.get("refresh_rate"))
+        ])
+    return cargs
+
+
+def surf_smooth_outputs(
+    params: SurfSmoothParameters,
+    execution: Execution,
+) -> SurfSmoothOutputs:
+    """
+    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 = SurfSmoothOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(params.get("output_file")) if (params.get("output_file") is not None) else None,
+    )
+    return ret
+
+
+def surf_smooth_execute(
+    params: SurfSmoothParameters,
+    execution: Execution,
+) -> SurfSmoothOutputs:
+    """
+    Tool for smoothing data on surfaces using various methods.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SurfSmoothOutputs`).
+    """
+    params = execution.params(params)
+    cargs = surf_smooth_cargs(params, execution)
+    ret = surf_smooth_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def surf_smooth(
+    surface: str,
+    method: str,
+    input_data: InputPathType | None = None,
+    target_fwhm: float | None = None,
+    fwhm: float | None = None,
+    number_iterations: float | None = None,
+    output_file: str | None = None,
+    band_pass_frequency: float | None = None,
+    lambda_mu: str | None = None,
+    interp_weights: str | None = None,
+    node_mask: InputPathType | None = None,
+    surface_output: InputPathType | None = None,
+    dbg_node: float | None = None,
+    use_neighbors_outside_mask: bool = False,
+    talk_suma: bool = False,
+    refresh_rate: float | None = None,
+    runner: Runner | None = None,
+) -> SurfSmoothOutputs:
+    """
+    Tool for smoothing data on surfaces using various methods.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        surface: Option for specifying the surface to smooth or the domain over\
+            which DSET is defined.
+        method: Name of smoothing method to use. Choose from: HEAT_07, HEAT_05,\
+            LM, NN_geom.
+        input_data: File containing data (in 1D or NIML format). Required for\
+            HEAT_05 and HEAT_07 methods.
+        target_fwhm: Blur so that the final FWHM of the data is TF mm. Only for\
+            HEAT_07 method.
+        fwhm: Effective Full Width at Half Maximum for smoothing. Required for\
+            HEAT_05 and optional for HEAT_07 methods.
+        number_iterations: Number of smoothing iterations (default is 100 for\
+            LM and NN_geom, -1 for HEAT methods).
+        output_file: Name of output file. Default based on method being used.
+        band_pass_frequency: Bandpass frequency for LM method (0 < k < 10).
+        lambda_mu: Lambda and Mu parameters for LM method. Sample values are:\
+            0.6307 and -0.6732.
+        interp_weights: Set interpolation weights for LM method. Options:\
+            Equal, Fujiwara, Desbrun.
+        node_mask: Apply operations only to nodes listed in the given mask.
+        surface_output: Writes the surface with smoothed coordinates to disk.\
+            For LM and NN_geom methods.
+        dbg_node: Output debug information for node 'node'.
+        use_neighbors_outside_mask: Allow value from a node neighboring node n\
+            to contribute to the value at n even if the neighbor is not in the\
+            mask.
+        talk_suma: Send progress with each iteration to SUMA for real-time\
+            visualization.
+        refresh_rate: Maximum number of updates to SUMA per second.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SurfSmoothOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_SMOOTH_METADATA)
+    params = surf_smooth_params(
+        surface=surface,
+        method=method,
+        input_data=input_data,
+        target_fwhm=target_fwhm,
+        fwhm=fwhm,
+        number_iterations=number_iterations,
+        output_file=output_file,
+        band_pass_frequency=band_pass_frequency,
+        lambda_mu=lambda_mu,
+        interp_weights=interp_weights,
+        node_mask=node_mask,
+        surface_output=surface_output,
+        dbg_node=dbg_node,
+        use_neighbors_outside_mask=use_neighbors_outside_mask,
+        talk_suma=talk_suma,
+        refresh_rate=refresh_rate,
+    )
+    return surf_smooth_execute(params, execution)
+
+
+__all__ = [
+    "SURF_SMOOTH_METADATA",
+    "SurfSmoothOutputs",
+    "SurfSmoothParameters",
+    "surf_smooth",
+    "surf_smooth_params",
+]

niwrap_afni/afni/surf_to_surf.py

@@ -0,0 +1,327 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SURF_TO_SURF_METADATA = Metadata(
+    id="a2c971cd7bb0ee914e8be7cd7e5159482c16cc13.boutiques",
+    name="SurfToSurf",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SurfToSurfParameters = typing.TypedDict('SurfToSurfParameters', {
+    "__STYX_TYPE__": typing.Literal["SurfToSurf"],
+    "input_surface_1": InputPathType,
+    "input_surface_2": InputPathType,
+    "surface_volume": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "output_params": typing.NotRequired[str | None],
+    "node_indices": typing.NotRequired[InputPathType | None],
+    "proj_dir": typing.NotRequired[InputPathType | None],
+    "data": typing.NotRequired[InputPathType | None],
+    "node_debug": typing.NotRequired[float | None],
+    "debug_level": typing.NotRequired[float | None],
+    "make_consistent": bool,
+    "dset": typing.NotRequired[InputPathType | None],
+    "mapfile": typing.NotRequired[InputPathType | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "SurfToSurf": surf_to_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 {
+        "SurfToSurf": surf_to_surf_outputs,
+    }.get(t)
+
+
+class SurfToSurfOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `surf_to_surf(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """Output file in 1D format"""
+
+
+def surf_to_surf_params(
+    input_surface_1: InputPathType,
+    input_surface_2: InputPathType,
+    surface_volume: InputPathType | None = None,
+    prefix: str | None = None,
+    output_params: str | None = None,
+    node_indices: InputPathType | None = None,
+    proj_dir: InputPathType | None = None,
+    data: InputPathType | None = None,
+    node_debug: float | None = None,
+    debug_level: float | None = None,
+    make_consistent: bool = False,
+    dset: InputPathType | None = None,
+    mapfile: InputPathType | None = None,
+) -> SurfToSurfParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_surface_1: First input surface file (S1).
+        input_surface_2: Second input surface file (S2).
+        surface_volume: Specify the surface volume (SV1).
+        prefix: Specify prefix for the output file.
+        output_params: List of mapping parameters to include in output.
+        node_indices: 1D file containing node indices of S1 to consider.
+        proj_dir: 1D file containing projection directions.
+        data: 1D file containing data to be interpolated.
+        node_debug: Node index for debugging purposes.
+        debug_level: Debugging level.
+        make_consistent: Force a consistency check and correct triangle\
+            orientation.
+        dset: Dataset file for data interpolation; mutually exclusive with\
+            -data.
+        mapfile: File containing mapping parameters between surfaces S2 and S1.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SurfToSurf",
+        "input_surface_1": input_surface_1,
+        "input_surface_2": input_surface_2,
+        "make_consistent": make_consistent,
+    }
+    if surface_volume is not None:
+        params["surface_volume"] = surface_volume
+    if prefix is not None:
+        params["prefix"] = prefix
+    if output_params is not None:
+        params["output_params"] = output_params
+    if node_indices is not None:
+        params["node_indices"] = node_indices
+    if proj_dir is not None:
+        params["proj_dir"] = proj_dir
+    if data is not None:
+        params["data"] = data
+    if node_debug is not None:
+        params["node_debug"] = node_debug
+    if debug_level is not None:
+        params["debug_level"] = debug_level
+    if dset is not None:
+        params["dset"] = dset
+    if mapfile is not None:
+        params["mapfile"] = mapfile
+    return params
+
+
+def surf_to_surf_cargs(
+    params: SurfToSurfParameters,
+    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("SurfToSurf")
+    cargs.append(execution.input_file(params.get("input_surface_1")))
+    cargs.append(execution.input_file(params.get("input_surface_2")))
+    if params.get("surface_volume") is not None:
+        cargs.extend([
+            "-sv",
+            execution.input_file(params.get("surface_volume"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("output_params") is not None:
+        cargs.extend([
+            "-output_params",
+            params.get("output_params")
+        ])
+    if params.get("node_indices") is not None:
+        cargs.extend([
+            "-node_indices",
+            execution.input_file(params.get("node_indices"))
+        ])
+    if params.get("proj_dir") is not None:
+        cargs.extend([
+            "-proj_dir",
+            execution.input_file(params.get("proj_dir"))
+        ])
+    if params.get("data") is not None:
+        cargs.extend([
+            "-data",
+            execution.input_file(params.get("data"))
+        ])
+    if params.get("node_debug") is not None:
+        cargs.extend([
+            "-node_debug",
+            str(params.get("node_debug"))
+        ])
+    if params.get("debug_level") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug_level"))
+        ])
+    if params.get("make_consistent"):
+        cargs.append("-make_consistent")
+    if params.get("dset") is not None:
+        cargs.extend([
+            "-dset",
+            execution.input_file(params.get("dset"))
+        ])
+    if params.get("mapfile") is not None:
+        cargs.extend([
+            "-mapfile",
+            execution.input_file(params.get("mapfile"))
+        ])
+    return cargs
+
+
+def surf_to_surf_outputs(
+    params: SurfToSurfParameters,
+    execution: Execution,
+) -> SurfToSurfOutputs:
+    """
+    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 = SurfToSurfOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + ".1D") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def surf_to_surf_execute(
+    params: SurfToSurfParameters,
+    execution: Execution,
+) -> SurfToSurfOutputs:
+    """
+    Interpolate data from one surface to another.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SurfToSurfOutputs`).
+    """
+    params = execution.params(params)
+    cargs = surf_to_surf_cargs(params, execution)
+    ret = surf_to_surf_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def surf_to_surf(
+    input_surface_1: InputPathType,
+    input_surface_2: InputPathType,
+    surface_volume: InputPathType | None = None,
+    prefix: str | None = None,
+    output_params: str | None = None,
+    node_indices: InputPathType | None = None,
+    proj_dir: InputPathType | None = None,
+    data: InputPathType | None = None,
+    node_debug: float | None = None,
+    debug_level: float | None = None,
+    make_consistent: bool = False,
+    dset: InputPathType | None = None,
+    mapfile: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> SurfToSurfOutputs:
+    """
+    Interpolate data from one surface to another.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_surface_1: First input surface file (S1).
+        input_surface_2: Second input surface file (S2).
+        surface_volume: Specify the surface volume (SV1).
+        prefix: Specify prefix for the output file.
+        output_params: List of mapping parameters to include in output.
+        node_indices: 1D file containing node indices of S1 to consider.
+        proj_dir: 1D file containing projection directions.
+        data: 1D file containing data to be interpolated.
+        node_debug: Node index for debugging purposes.
+        debug_level: Debugging level.
+        make_consistent: Force a consistency check and correct triangle\
+            orientation.
+        dset: Dataset file for data interpolation; mutually exclusive with\
+            -data.
+        mapfile: File containing mapping parameters between surfaces S2 and S1.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SurfToSurfOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_TO_SURF_METADATA)
+    params = surf_to_surf_params(
+        input_surface_1=input_surface_1,
+        input_surface_2=input_surface_2,
+        surface_volume=surface_volume,
+        prefix=prefix,
+        output_params=output_params,
+        node_indices=node_indices,
+        proj_dir=proj_dir,
+        data=data,
+        node_debug=node_debug,
+        debug_level=debug_level,
+        make_consistent=make_consistent,
+        dset=dset,
+        mapfile=mapfile,
+    )
+    return surf_to_surf_execute(params, execution)
+
+
+__all__ = [
+    "SURF_TO_SURF_METADATA",
+    "SurfToSurfOutputs",
+    "SurfToSurfParameters",
+    "surf_to_surf",
+    "surf_to_surf_params",
+]