niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/slow_surf_clustsim_py.py

@@ -0,0 +1,285 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SLOW_SURF_CLUSTSIM_PY_METADATA = Metadata(
+    id="a7e11fd0c89e1ec778cc2b10b112e4d443b843ac.boutiques",
+    name="slow_surf_clustsim.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SlowSurfClustsimPyParameters = typing.TypedDict('SlowSurfClustsimPyParameters', {
+    "__STYX_TYPE__": typing.Literal["slow_surf_clustsim.py"],
+    "on_surface": typing.NotRequired[str | None],
+    "save_script": typing.NotRequired[str | None],
+    "print_script": bool,
+    "uvar": typing.NotRequired[list[str] | None],
+    "verbosity": typing.NotRequired[float | None],
+    "help": bool,
+    "hist": bool,
+    "show_default_cvars": bool,
+    "show_default_uvars": bool,
+    "show_valid_opts": bool,
+    "version": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "slow_surf_clustsim.py": slow_surf_clustsim_py_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 {
+    }.get(t)
+
+
+class SlowSurfClustsimPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `slow_surf_clustsim_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def slow_surf_clustsim_py_params(
+    on_surface: str | None = None,
+    save_script: str | None = None,
+    print_script: bool = False,
+    uvar: list[str] | None = None,
+    verbosity: float | None = None,
+    help_: bool = False,
+    hist: bool = False,
+    show_default_cvars: bool = False,
+    show_default_uvars: bool = False,
+    show_valid_opts: bool = False,
+    version: bool = False,
+) -> SlowSurfClustsimPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        on_surface: Start from noise on the surface (so no volume data is\
+            involved).
+        save_script: Save script to given file.
+        print_script: Print script to terminal.
+        uvar: Set the user variable (use -show_default_uvars to see user vars).\
+            Example usage: -uvar spec_file sb23_lh_141_std.spec -uvar surf_vol\
+            sb23_SurfVol_aligned+orig.
+        verbosity: Set the verbosity level.
+        help_: Show this help.
+        hist: Show module history.
+        show_default_cvars: List default control variables.
+        show_default_uvars: List default user variables.
+        show_valid_opts: List valid options.
+        version: Show current version.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "slow_surf_clustsim.py",
+        "print_script": print_script,
+        "help": help_,
+        "hist": hist,
+        "show_default_cvars": show_default_cvars,
+        "show_default_uvars": show_default_uvars,
+        "show_valid_opts": show_valid_opts,
+        "version": version,
+    }
+    if on_surface is not None:
+        params["on_surface"] = on_surface
+    if save_script is not None:
+        params["save_script"] = save_script
+    if uvar is not None:
+        params["uvar"] = uvar
+    if verbosity is not None:
+        params["verbosity"] = verbosity
+    return params
+
+
+def slow_surf_clustsim_py_cargs(
+    params: SlowSurfClustsimPyParameters,
+    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("slow_surf_clustsim.py")
+    if params.get("on_surface") is not None:
+        cargs.extend([
+            "-on_surface",
+            params.get("on_surface")
+        ])
+    if params.get("save_script") is not None:
+        cargs.extend([
+            "-save_script",
+            params.get("save_script")
+        ])
+    if params.get("print_script"):
+        cargs.append("-print_script")
+    if params.get("uvar") is not None:
+        cargs.extend([
+            "-uvar",
+            *params.get("uvar")
+        ])
+    if params.get("verbosity") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbosity"))
+        ])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("hist"):
+        cargs.append("-hist")
+    if params.get("show_default_cvars"):
+        cargs.append("-show_default_cvars")
+    if params.get("show_default_uvars"):
+        cargs.append("-show_default_uvars")
+    if params.get("show_valid_opts"):
+        cargs.append("-show_valid_opts")
+    if params.get("version"):
+        cargs.append("-ver")
+    return cargs
+
+
+def slow_surf_clustsim_py_outputs(
+    params: SlowSurfClustsimPyParameters,
+    execution: Execution,
+) -> SlowSurfClustsimPyOutputs:
+    """
+    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 = SlowSurfClustsimPyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def slow_surf_clustsim_py_execute(
+    params: SlowSurfClustsimPyParameters,
+    execution: Execution,
+) -> SlowSurfClustsimPyOutputs:
+    """
+    Generate a tcsh script to run clustsim on surface.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SlowSurfClustsimPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = slow_surf_clustsim_py_cargs(params, execution)
+    ret = slow_surf_clustsim_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def slow_surf_clustsim_py(
+    on_surface: str | None = None,
+    save_script: str | None = None,
+    print_script: bool = False,
+    uvar: list[str] | None = None,
+    verbosity: float | None = None,
+    help_: bool = False,
+    hist: bool = False,
+    show_default_cvars: bool = False,
+    show_default_uvars: bool = False,
+    show_valid_opts: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> SlowSurfClustsimPyOutputs:
+    """
+    Generate a tcsh script to run clustsim on surface.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        on_surface: Start from noise on the surface (so no volume data is\
+            involved).
+        save_script: Save script to given file.
+        print_script: Print script to terminal.
+        uvar: Set the user variable (use -show_default_uvars to see user vars).\
+            Example usage: -uvar spec_file sb23_lh_141_std.spec -uvar surf_vol\
+            sb23_SurfVol_aligned+orig.
+        verbosity: Set the verbosity level.
+        help_: Show this help.
+        hist: Show module history.
+        show_default_cvars: List default control variables.
+        show_default_uvars: List default user variables.
+        show_valid_opts: List valid options.
+        version: Show current version.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SlowSurfClustsimPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SLOW_SURF_CLUSTSIM_PY_METADATA)
+    params = slow_surf_clustsim_py_params(
+        on_surface=on_surface,
+        save_script=save_script,
+        print_script=print_script,
+        uvar=uvar,
+        verbosity=verbosity,
+        help_=help_,
+        hist=hist,
+        show_default_cvars=show_default_cvars,
+        show_default_uvars=show_default_uvars,
+        show_valid_opts=show_valid_opts,
+        version=version,
+    )
+    return slow_surf_clustsim_py_execute(params, execution)
+
+
+__all__ = [
+    "SLOW_SURF_CLUSTSIM_PY_METADATA",
+    "SlowSurfClustsimPyOutputs",
+    "SlowSurfClustsimPyParameters",
+    "slow_surf_clustsim_py",
+    "slow_surf_clustsim_py_params",
+]

niwrap_afni/afni/spharm_deco.py

@@ -0,0 +1,284 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SPHARM_DECO_METADATA = Metadata(
+    id="6c5408eda75c3fcbee3c137d9a99cb7b538fb149.boutiques",
+    name="SpharmDeco",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SpharmDecoParameters = typing.TypedDict('SpharmDecoParameters', {
+    "__STYX_TYPE__": typing.Literal["SpharmDeco"],
+    "i_type_s": InputPathType,
+    "unit_sph_label": str,
+    "order_l": float,
+    "i_type_sd": typing.NotRequired[list[InputPathType] | None],
+    "data_d": typing.NotRequired[InputPathType | None],
+    "bases_prefix": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "o_type_sdr": typing.NotRequired[list[InputPathType] | None],
+    "debug": typing.NotRequired[float | None],
+    "sigma": 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 {
+        "SpharmDeco": spharm_deco_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 {
+        "SpharmDeco": spharm_deco_outputs,
+    }.get(t)
+
+
+class SpharmDecoOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `spharm_deco(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    harmonics_file: OutputPathType
+    """File for harmonics of each order l."""
+    beta_coefficients: OutputPathType
+    """Beta coefficients for each data column."""
+    reconstructed_data: OutputPathType
+    """Reconstructed data or surface files named based on PREFIX."""
+
+
+def spharm_deco_params(
+    i_type_s: InputPathType,
+    unit_sph_label: str,
+    order_l: float,
+    i_type_sd: list[InputPathType] | None = None,
+    data_d: InputPathType | None = None,
+    bases_prefix: str | None = None,
+    prefix: str | None = None,
+    o_type_sdr: list[InputPathType] | None = None,
+    debug: float | None = None,
+    sigma: float | None = None,
+) -> SpharmDecoParameters:
+    """
+    Build parameters.
+    
+    Args:
+        i_type_s: Unit sphere, isotopic to the surface domain over which the\
+            data to be decomposed is defined.
+        unit_sph_label: Label of the unit sphere.
+        order_l: Decomposition order.
+        i_type_sd: A surface whose node coordinates provide data vectors (X, Y,\
+            Z) to be decomposed or a dataset whose columns are to be individually\
+            decomposed. You can specify multiple surfaces to be processed.
+        data_d: Data vectors to be decomposed.
+        bases_prefix: Save the basis functions under the prefix BASES_PREFIX.
+        prefix: Write out the reconstructed data into dataset PREFIX and write\
+            the beta coefficients for each processed data column.
+        o_type_sdr: Write out a new surface with reconstructed coordinates.
+        debug: Debug levels (1-3).
+        sigma: Smoothing parameter (0 .. 0.001) which weighs down the\
+            contribution of higher order harmonics.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SpharmDeco",
+        "i_type_s": i_type_s,
+        "unit_sph_label": unit_sph_label,
+        "order_l": order_l,
+    }
+    if i_type_sd is not None:
+        params["i_type_sd"] = i_type_sd
+    if data_d is not None:
+        params["data_d"] = data_d
+    if bases_prefix is not None:
+        params["bases_prefix"] = bases_prefix
+    if prefix is not None:
+        params["prefix"] = prefix
+    if o_type_sdr is not None:
+        params["o_type_sdr"] = o_type_sdr
+    if debug is not None:
+        params["debug"] = debug
+    if sigma is not None:
+        params["sigma"] = sigma
+    return params
+
+
+def spharm_deco_cargs(
+    params: SpharmDecoParameters,
+    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("SpharmDeco")
+    cargs.append(execution.input_file(params.get("i_type_s")))
+    cargs.append(params.get("unit_sph_label"))
+    cargs.append(str(params.get("order_l")))
+    if params.get("i_type_sd") is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("i_type_sd")])
+    if params.get("data_d") is not None:
+        cargs.append(execution.input_file(params.get("data_d")))
+    if params.get("bases_prefix") is not None:
+        cargs.append(params.get("bases_prefix"))
+    if params.get("prefix") is not None:
+        cargs.append(params.get("prefix"))
+    if params.get("o_type_sdr") is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("o_type_sdr")])
+    if params.get("debug") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug"))
+        ])
+    if params.get("sigma") is not None:
+        cargs.extend([
+            "-sigma",
+            str(params.get("sigma"))
+        ])
+    return cargs
+
+
+def spharm_deco_outputs(
+    params: SpharmDecoParameters,
+    execution: Execution,
+) -> SpharmDecoOutputs:
+    """
+    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 = SpharmDecoOutputs(
+        root=execution.output_file("."),
+        harmonics_file=execution.output_file("BASES_PREFIX.sph*.1D"),
+        beta_coefficients=execution.output_file("PREFIX.beta.col*.1D.dset"),
+        reconstructed_data=execution.output_file("<PREFIX>_reconstructed"),
+    )
+    return ret
+
+
+def spharm_deco_execute(
+    params: SpharmDecoParameters,
+    execution: Execution,
+) -> SpharmDecoOutputs:
+    """
+    Spherical Harmonics Decomposition of a surface's coordinates or data.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SpharmDecoOutputs`).
+    """
+    params = execution.params(params)
+    cargs = spharm_deco_cargs(params, execution)
+    ret = spharm_deco_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def spharm_deco(
+    i_type_s: InputPathType,
+    unit_sph_label: str,
+    order_l: float,
+    i_type_sd: list[InputPathType] | None = None,
+    data_d: InputPathType | None = None,
+    bases_prefix: str | None = None,
+    prefix: str | None = None,
+    o_type_sdr: list[InputPathType] | None = None,
+    debug: float | None = None,
+    sigma: float | None = None,
+    runner: Runner | None = None,
+) -> SpharmDecoOutputs:
+    """
+    Spherical Harmonics Decomposition of a surface's coordinates or data.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        i_type_s: Unit sphere, isotopic to the surface domain over which the\
+            data to be decomposed is defined.
+        unit_sph_label: Label of the unit sphere.
+        order_l: Decomposition order.
+        i_type_sd: A surface whose node coordinates provide data vectors (X, Y,\
+            Z) to be decomposed or a dataset whose columns are to be individually\
+            decomposed. You can specify multiple surfaces to be processed.
+        data_d: Data vectors to be decomposed.
+        bases_prefix: Save the basis functions under the prefix BASES_PREFIX.
+        prefix: Write out the reconstructed data into dataset PREFIX and write\
+            the beta coefficients for each processed data column.
+        o_type_sdr: Write out a new surface with reconstructed coordinates.
+        debug: Debug levels (1-3).
+        sigma: Smoothing parameter (0 .. 0.001) which weighs down the\
+            contribution of higher order harmonics.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SpharmDecoOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SPHARM_DECO_METADATA)
+    params = spharm_deco_params(
+        i_type_s=i_type_s,
+        unit_sph_label=unit_sph_label,
+        order_l=order_l,
+        i_type_sd=i_type_sd,
+        data_d=data_d,
+        bases_prefix=bases_prefix,
+        prefix=prefix,
+        o_type_sdr=o_type_sdr,
+        debug=debug,
+        sigma=sigma,
+    )
+    return spharm_deco_execute(params, execution)
+
+
+__all__ = [
+    "SPHARM_DECO_METADATA",
+    "SpharmDecoOutputs",
+    "SpharmDecoParameters",
+    "spharm_deco",
+    "spharm_deco_params",
+]