niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/bayesian_group_ana_py.py

@@ -0,0 +1,342 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+BAYESIAN_GROUP_ANA_PY_METADATA = Metadata(
+    id="e49086bdbe64c248fa7b140fd8ae072e880fa9a7.boutiques",
+    name="BayesianGroupAna.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+BayesianGroupAnaPyParameters = typing.TypedDict('BayesianGroupAnaPyParameters', {
+    "__STYX_TYPE__": typing.Literal["BayesianGroupAna.py"],
+    "dataTable": InputPathType,
+    "y_variable": str,
+    "prefix": typing.NotRequired[str | None],
+    "x_variables": typing.NotRequired[list[str] | None],
+    "no_center": bool,
+    "iterations": typing.NotRequired[float | None],
+    "chains": typing.NotRequired[float | None],
+    "control_list": typing.NotRequired[str | None],
+    "plot": bool,
+    "more_plots": typing.NotRequired[list[str] | None],
+    "RData": bool,
+    "seed": typing.NotRequired[float | None],
+    "overwrite": bool,
+    "help": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "BayesianGroupAna.py": bayesian_group_ana_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 {
+        "BayesianGroupAna.py": bayesian_group_ana_py_outputs,
+    }.get(t)
+
+
+class BayesianGroupAnaPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `bayesian_group_ana_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    summary: OutputPathType | None
+    """Summary of the brmsfit object from R."""
+    rhats: OutputPathType | None
+    """Rhats for each effect and x variable combination."""
+    intercept_table: OutputPathType | None
+    """Table with the MedianEst, StdDev, 2.50%, 5%, 50%, 95%, and 97.50% of each
+    ROI for the Intercept term."""
+    x_var_table: OutputPathType | None
+    """The same table as the Intercept but for the specified x variable."""
+
+
+def bayesian_group_ana_py_params(
+    data_table: InputPathType,
+    y_variable: str,
+    prefix: str | None = None,
+    x_variables: list[str] | None = None,
+    no_center: bool = False,
+    iterations: float | None = None,
+    chains: float | None = None,
+    control_list: str | None = None,
+    plot: bool = False,
+    more_plots: list[str] | None = None,
+    rdata: bool = False,
+    seed: float | None = None,
+    overwrite: bool = False,
+    help_: bool = False,
+) -> BayesianGroupAnaPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        data_table: Input text file containing the data table.
+        y_variable: Column name for the y variable.
+        prefix: Name of the output file.
+        x_variables: Column name(s) for the x variables. If not specified, only\
+            the intercept will be added.
+        no_center: Disable centering on the x variables. Maybe useful if you\
+            centered manually.
+        iterations: Number of total iterations per chain including warmup.\
+            Default [1000].
+        chains: Number of Markov chains. Default [4].
+        control_list: Comma separated list of control parameters to pass to the\
+            brm function. Default is the brm function defaults.
+        plot: Output box, fit, and posterior prediction plots.
+        more_plots: Output 'stanplots' given different types of plot names.
+        rdata: Save the R session workspace and data.
+        seed: Seed to generate random number. Default [1234].
+        overwrite: Overwrites the output files.
+        help_: Show help message and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "BayesianGroupAna.py",
+        "dataTable": data_table,
+        "y_variable": y_variable,
+        "no_center": no_center,
+        "plot": plot,
+        "RData": rdata,
+        "overwrite": overwrite,
+        "help": help_,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if x_variables is not None:
+        params["x_variables"] = x_variables
+    if iterations is not None:
+        params["iterations"] = iterations
+    if chains is not None:
+        params["chains"] = chains
+    if control_list is not None:
+        params["control_list"] = control_list
+    if more_plots is not None:
+        params["more_plots"] = more_plots
+    if seed is not None:
+        params["seed"] = seed
+    return params
+
+
+def bayesian_group_ana_py_cargs(
+    params: BayesianGroupAnaPyParameters,
+    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("BayesianGroupAna.py")
+    cargs.append(execution.input_file(params.get("dataTable")))
+    cargs.append(params.get("y_variable"))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("x_variables") is not None:
+        cargs.extend([
+            "-x",
+            *params.get("x_variables")
+        ])
+    if params.get("no_center"):
+        cargs.append("-no_center")
+    if params.get("iterations") is not None:
+        cargs.extend([
+            "-iterations",
+            str(params.get("iterations"))
+        ])
+    if params.get("chains") is not None:
+        cargs.extend([
+            "-chains",
+            str(params.get("chains"))
+        ])
+    if params.get("control_list") is not None:
+        cargs.extend([
+            "-control_list",
+            params.get("control_list")
+        ])
+    if params.get("plot"):
+        cargs.append("-plot")
+    if params.get("more_plots") is not None:
+        cargs.extend([
+            "-more_plots",
+            *params.get("more_plots")
+        ])
+    if params.get("RData"):
+        cargs.append("-RData")
+    if params.get("seed") is not None:
+        cargs.extend([
+            "-seed",
+            str(params.get("seed"))
+        ])
+    if params.get("overwrite"):
+        cargs.append("-overwrite")
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def bayesian_group_ana_py_outputs(
+    params: BayesianGroupAnaPyParameters,
+    execution: Execution,
+) -> BayesianGroupAnaPyOutputs:
+    """
+    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 = BayesianGroupAnaPyOutputs(
+        root=execution.output_file("."),
+        summary=execution.output_file(params.get("prefix") + "_summary.txt") if (params.get("prefix") is not None) else None,
+        rhats=execution.output_file(params.get("prefix") + "_rhats.csv") if (params.get("prefix") is not None) else None,
+        intercept_table=execution.output_file(params.get("prefix") + "_Intercept_table.csv") if (params.get("prefix") is not None) else None,
+        x_var_table=execution.output_file(params.get("prefix") + "_table.csv") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def bayesian_group_ana_py_execute(
+    params: BayesianGroupAnaPyParameters,
+    execution: Execution,
+) -> BayesianGroupAnaPyOutputs:
+    """
+    This program conducts Bayesian Group Analysis (BGA) on a list of regions of
+    interest (ROIs). Compared to the conventional univariate GLM, BGA pools and
+    shares the information across the ROIs in a multilevel system.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `BayesianGroupAnaPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = bayesian_group_ana_py_cargs(params, execution)
+    ret = bayesian_group_ana_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def bayesian_group_ana_py(
+    data_table: InputPathType,
+    y_variable: str,
+    prefix: str | None = None,
+    x_variables: list[str] | None = None,
+    no_center: bool = False,
+    iterations: float | None = None,
+    chains: float | None = None,
+    control_list: str | None = None,
+    plot: bool = False,
+    more_plots: list[str] | None = None,
+    rdata: bool = False,
+    seed: float | None = None,
+    overwrite: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> BayesianGroupAnaPyOutputs:
+    """
+    This program conducts Bayesian Group Analysis (BGA) on a list of regions of
+    interest (ROIs). Compared to the conventional univariate GLM, BGA pools and
+    shares the information across the ROIs in a multilevel system.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        data_table: Input text file containing the data table.
+        y_variable: Column name for the y variable.
+        prefix: Name of the output file.
+        x_variables: Column name(s) for the x variables. If not specified, only\
+            the intercept will be added.
+        no_center: Disable centering on the x variables. Maybe useful if you\
+            centered manually.
+        iterations: Number of total iterations per chain including warmup.\
+            Default [1000].
+        chains: Number of Markov chains. Default [4].
+        control_list: Comma separated list of control parameters to pass to the\
+            brm function. Default is the brm function defaults.
+        plot: Output box, fit, and posterior prediction plots.
+        more_plots: Output 'stanplots' given different types of plot names.
+        rdata: Save the R session workspace and data.
+        seed: Seed to generate random number. Default [1234].
+        overwrite: Overwrites the output files.
+        help_: Show help message and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `BayesianGroupAnaPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BAYESIAN_GROUP_ANA_PY_METADATA)
+    params = bayesian_group_ana_py_params(
+        data_table=data_table,
+        y_variable=y_variable,
+        prefix=prefix,
+        x_variables=x_variables,
+        no_center=no_center,
+        iterations=iterations,
+        chains=chains,
+        control_list=control_list,
+        plot=plot,
+        more_plots=more_plots,
+        rdata=rdata,
+        seed=seed,
+        overwrite=overwrite,
+        help_=help_,
+    )
+    return bayesian_group_ana_py_execute(params, execution)
+
+
+__all__ = [
+    "BAYESIAN_GROUP_ANA_PY_METADATA",
+    "BayesianGroupAnaPyOutputs",
+    "BayesianGroupAnaPyParameters",
+    "bayesian_group_ana_py",
+    "bayesian_group_ana_py_params",
+]

niwrap_afni/afni/brain_skin.py

@@ -0,0 +1,358 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+BRAIN_SKIN_METADATA = Metadata(
+    id="4f110568466cb173a0801348ecaabe46ca587148.boutiques",
+    name="BrainSkin",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+BrainSkinParameters = typing.TypedDict('BrainSkinParameters', {
+    "__STYX_TYPE__": typing.Literal["BrainSkin"],
+    "surface": str,
+    "skingrid_volume": InputPathType,
+    "prefix": str,
+    "plimit": typing.NotRequired[float | None],
+    "dlimit": typing.NotRequired[float | None],
+    "segdo": typing.NotRequired[str | None],
+    "voxelize": typing.NotRequired[str | None],
+    "infill": typing.NotRequired[str | None],
+    "out_file": typing.NotRequired[InputPathType | None],
+    "vol_hull": typing.NotRequired[InputPathType | None],
+    "no_zero_attraction": bool,
+    "node_dbg": 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 {
+        "BrainSkin": brain_skin_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 {
+        "BrainSkin": brain_skin_outputs,
+    }.get(t)
+
+
+class BrainSkinOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `brain_skin(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    stitch_surface: OutputPathType
+    """A bunch of triangles for closing the surface."""
+    initial_skin_surface: OutputPathType
+    """Initial skin surface"""
+    reduced_skin_surface: OutputPathType
+    """Reduced mesh version of initial skin surface."""
+    inflated_skin_surface: OutputPathType
+    """Original surface inflated inside skin surface."""
+    patching_voxels: OutputPathType
+    """Surface patching voxels."""
+    surf_voxels: OutputPathType
+    """Voxels inside original surface"""
+    skin_voxels: OutputPathType
+    """Mix of ptchvox and surfvox."""
+    infilled_voxels: OutputPathType
+    """Skin vox dataset filled in."""
+    node_pairs_results: OutputPathType
+    """Results of computations for finding node pairs that span sulci."""
+    inflating_surface_results: OutputPathType
+    """Results of computations for inflating initial surface inside skin
+    surface."""
+    segments_display: OutputPathType
+    """Segments between node pairs spanning sulci."""
+
+
+def brain_skin_params(
+    surface: str,
+    skingrid_volume: InputPathType,
+    prefix: str,
+    plimit: float | None = None,
+    dlimit: float | None = None,
+    segdo: str | None = None,
+    voxelize: str | None = None,
+    infill: str | None = None,
+    out_file: InputPathType | None = None,
+    vol_hull: InputPathType | None = None,
+    no_zero_attraction: bool = False,
+    node_dbg: float | None = None,
+) -> BrainSkinParameters:
+    """
+    Build parameters.
+    
+    Args:
+        surface: Surface to smooth or the domain over which DSET is defined.
+        skingrid_volume: A high-res volume to provide a grid for voxelization\
+            steps.
+        prefix: Prefix to use for variety of output files.
+        plimit: Maximum length of path along surface in mm for node pairing.
+        dlimit: Maximum length of Euclidean distance in mm for node pairing.
+        segdo: Output a displayable object file that contains segments between\
+            paired nodes.
+        voxelize: Voxelization method. Choose from: slow: Sure footed but slow,\
+            fast: Faster and works OK, mask: Fastest and works OK too (default).
+        infill: Infill method. Choose from: slow: proper infill, but not\
+            needed, fast: brutish infill, all we need (default).
+        out_file: Output intermediary results from skin forming step.
+        vol_hull: Deform an Icosahedron to match the convex hull of a mask\
+            volume.
+        no_zero_attraction: With vol_skin, the surface will try to shrink\
+            aggressively, even if there is no promise of non-zero values below.
+        node_dbg: Output debugging information for node N for -vol_skin and\
+            -vol_hull options.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "BrainSkin",
+        "surface": surface,
+        "skingrid_volume": skingrid_volume,
+        "prefix": prefix,
+        "no_zero_attraction": no_zero_attraction,
+    }
+    if plimit is not None:
+        params["plimit"] = plimit
+    if dlimit is not None:
+        params["dlimit"] = dlimit
+    if segdo is not None:
+        params["segdo"] = segdo
+    if voxelize is not None:
+        params["voxelize"] = voxelize
+    if infill is not None:
+        params["infill"] = infill
+    if out_file is not None:
+        params["out_file"] = out_file
+    if vol_hull is not None:
+        params["vol_hull"] = vol_hull
+    if node_dbg is not None:
+        params["node_dbg"] = node_dbg
+    return params
+
+
+def brain_skin_cargs(
+    params: BrainSkinParameters,
+    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("BrainSkin")
+    cargs.append(params.get("surface"))
+    cargs.extend([
+        "-skingrid",
+        execution.input_file(params.get("skingrid_volume"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("plimit") is not None:
+        cargs.extend([
+            "-plimit",
+            str(params.get("plimit"))
+        ])
+    if params.get("dlimit") is not None:
+        cargs.extend([
+            "-dlimit",
+            str(params.get("dlimit"))
+        ])
+    if params.get("segdo") is not None:
+        cargs.extend([
+            "-segdo",
+            params.get("segdo")
+        ])
+    if params.get("voxelize") is not None:
+        cargs.extend([
+            "-voxelize",
+            params.get("voxelize")
+        ])
+    if params.get("infill") is not None:
+        cargs.extend([
+            "-infill",
+            params.get("infill")
+        ])
+    if params.get("out_file") is not None:
+        cargs.extend([
+            "-out",
+            execution.input_file(params.get("out_file"))
+        ])
+    if params.get("vol_hull") is not None:
+        cargs.extend([
+            "-vol_hull",
+            execution.input_file(params.get("vol_hull"))
+        ])
+    if params.get("no_zero_attraction"):
+        cargs.append("-no_zero_attraction")
+    if params.get("node_dbg") is not None:
+        cargs.extend([
+            "-node_dbg",
+            str(params.get("node_dbg"))
+        ])
+    return cargs
+
+
+def brain_skin_outputs(
+    params: BrainSkinParameters,
+    execution: Execution,
+) -> BrainSkinOutputs:
+    """
+    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 = BrainSkinOutputs(
+        root=execution.output_file("."),
+        stitch_surface=execution.output_file(params.get("prefix") + ".stitch.gii"),
+        initial_skin_surface=execution.output_file(params.get("prefix") + ".skin.gii"),
+        reduced_skin_surface=execution.output_file(params.get("prefix") + ".skin_simp.gii"),
+        inflated_skin_surface=execution.output_file(params.get("prefix") + ".skin.isotopic.gii"),
+        patching_voxels=execution.output_file(params.get("prefix") + ".ptchvox+orig"),
+        surf_voxels=execution.output_file(params.get("prefix") + ".surfvox+orig"),
+        skin_voxels=execution.output_file(params.get("prefix") + ".skinvox+orig"),
+        infilled_voxels=execution.output_file(params.get("prefix") + ".infilled+orig"),
+        node_pairs_results=execution.output_file(params.get("prefix") + ".niml.dset"),
+        inflating_surface_results=execution.output_file(params.get("prefix") + ".areas.niml.dset"),
+        segments_display=execution.output_file(params.get("prefix") + ".1D.do"),
+    )
+    return ret
+
+
+def brain_skin_execute(
+    params: BrainSkinParameters,
+    execution: Execution,
+) -> BrainSkinOutputs:
+    """
+    A program to create an unfolded surface that wraps the brain (skin) and
+    Gyrification Indices.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `BrainSkinOutputs`).
+    """
+    params = execution.params(params)
+    cargs = brain_skin_cargs(params, execution)
+    ret = brain_skin_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def brain_skin(
+    surface: str,
+    skingrid_volume: InputPathType,
+    prefix: str,
+    plimit: float | None = None,
+    dlimit: float | None = None,
+    segdo: str | None = None,
+    voxelize: str | None = None,
+    infill: str | None = None,
+    out_file: InputPathType | None = None,
+    vol_hull: InputPathType | None = None,
+    no_zero_attraction: bool = False,
+    node_dbg: float | None = None,
+    runner: Runner | None = None,
+) -> BrainSkinOutputs:
+    """
+    A program to create an unfolded surface that wraps the brain (skin) and
+    Gyrification Indices.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        surface: Surface to smooth or the domain over which DSET is defined.
+        skingrid_volume: A high-res volume to provide a grid for voxelization\
+            steps.
+        prefix: Prefix to use for variety of output files.
+        plimit: Maximum length of path along surface in mm for node pairing.
+        dlimit: Maximum length of Euclidean distance in mm for node pairing.
+        segdo: Output a displayable object file that contains segments between\
+            paired nodes.
+        voxelize: Voxelization method. Choose from: slow: Sure footed but slow,\
+            fast: Faster and works OK, mask: Fastest and works OK too (default).
+        infill: Infill method. Choose from: slow: proper infill, but not\
+            needed, fast: brutish infill, all we need (default).
+        out_file: Output intermediary results from skin forming step.
+        vol_hull: Deform an Icosahedron to match the convex hull of a mask\
+            volume.
+        no_zero_attraction: With vol_skin, the surface will try to shrink\
+            aggressively, even if there is no promise of non-zero values below.
+        node_dbg: Output debugging information for node N for -vol_skin and\
+            -vol_hull options.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `BrainSkinOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BRAIN_SKIN_METADATA)
+    params = brain_skin_params(
+        surface=surface,
+        skingrid_volume=skingrid_volume,
+        prefix=prefix,
+        plimit=plimit,
+        dlimit=dlimit,
+        segdo=segdo,
+        voxelize=voxelize,
+        infill=infill,
+        out_file=out_file,
+        vol_hull=vol_hull,
+        no_zero_attraction=no_zero_attraction,
+        node_dbg=node_dbg,
+    )
+    return brain_skin_execute(params, execution)
+
+
+__all__ = [
+    "BRAIN_SKIN_METADATA",
+    "BrainSkinOutputs",
+    "BrainSkinParameters",
+    "brain_skin",
+    "brain_skin_params",
+]