niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/rba.py

@@ -0,0 +1,508 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+RBA_METADATA = Metadata(
+    id="787dd7e6ba494572a30d5b3c250d17d1a6fddc8c.boutiques",
+    name="RBA",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+RbaParameters = typing.TypedDict('RbaParameters', {
+    "__STYX_TYPE__": typing.Literal["RBA"],
+    "prefix": str,
+    "dataTable": InputPathType,
+    "chains": typing.NotRequired[float | None],
+    "iterations": typing.NotRequired[float | None],
+    "model": typing.NotRequired[str | None],
+    "eoi": typing.NotRequired[str | None],
+    "wcp": typing.NotRequired[float | None],
+    "tstat": typing.NotRequired[str | None],
+    "stdz": typing.NotRequired[str | None],
+    "cVars": typing.NotRequired[str | None],
+    "qVars": typing.NotRequired[str | None],
+    "distROI": typing.NotRequired[str | None],
+    "distSubj": typing.NotRequired[str | None],
+    "distY": typing.NotRequired[str | None],
+    "ridgePlot": typing.NotRequired[str | None],
+    "roi": typing.NotRequired[str | None],
+    "subj": typing.NotRequired[str | None],
+    "scale": typing.NotRequired[float | None],
+    "se": typing.NotRequired[str | None],
+    "pdp": typing.NotRequired[str | None],
+    "mean": typing.NotRequired[str | None],
+    "sigma": typing.NotRequired[str | None],
+    "debug": bool,
+    "verbose": typing.NotRequired[float | None],
+    "md": bool,
+    "r2z": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "RBA": rba_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 {
+        "RBA": rba_outputs,
+    }.get(t)
+
+
+class RbaOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `rba(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_txt: OutputPathType
+    """Main output text file with inference information for effects of
+    interest."""
+    output_rdata: OutputPathType
+    """Saved R data in binary format for post hoc processing."""
+
+
+def rba_params(
+    prefix: str,
+    data_table: InputPathType,
+    chains: float | None = None,
+    iterations: float | None = None,
+    model: str | None = None,
+    eoi: str | None = None,
+    wcp: float | None = None,
+    tstat: str | None = None,
+    stdz: str | None = None,
+    c_vars: str | None = None,
+    q_vars: str | None = None,
+    dist_roi: str | None = None,
+    dist_subj: str | None = None,
+    dist_y: str | None = None,
+    ridge_plot: str | None = None,
+    roi: str | None = None,
+    subj: str | None = None,
+    scale: float | None = None,
+    se: str | None = None,
+    pdp: str | None = None,
+    mean: str | None = None,
+    sigma: str | None = None,
+    debug: bool = False,
+    verbose: float | None = None,
+    md: bool = False,
+    r2z: bool = False,
+) -> RbaParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Prefix for output file names.
+        data_table: Data table in pure text format.
+        chains: Specify the number of Markov chains.
+        iterations: Specify the number of iterations per Markov chain.
+        model: Specify the model formula.
+        eoi: Identify effects of interest in the output.
+        wcp: Invoke within-chain parallelization.
+        tstat: Specify the column name that lists the t-statistic values.
+        stdz: Identify quantitative variables (or covariates) to be\
+            standardized.
+        c_vars: Identify categorical (qualitative) variables (or factors).
+        q_vars: Identify quantitative variables (or covariates).
+        dist_roi: Specify the distribution for the ROIs.
+        dist_subj: Specify the distribution for the subjects.
+        dist_y: Specify the distribution for the response variable.
+        ridge_plot: Plot the posterior distributions stacked together.
+        roi: Specify the column name that is designated as the region variable.
+        subj: Specify the column name that is designated as the measuring unit\
+            variable (usually subject).
+        scale: Specify a multiplier for the Y values.
+        se: This option indicates that standard error for the response variable\
+            is available as input.
+        pdp: Specify the layout of posterior distribution plot.
+        mean: Specify the formulation for the mean of the likelihood (sampling\
+            distribution).
+        sigma: Specify the formulation for the standard deviation (sigma) of\
+            the likelihood (sampling distribution).
+        debug: This option will enable R to save the parameters in a file for\
+            debugging.
+        verbose: Specify verbose level.
+        md: This option indicates that there are missing data in the input.
+        r2z: Perform Fisher transformation on the response variable if it is a\
+            correlation coefficient.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "RBA",
+        "prefix": prefix,
+        "dataTable": data_table,
+        "debug": debug,
+        "md": md,
+        "r2z": r2z,
+    }
+    if chains is not None:
+        params["chains"] = chains
+    if iterations is not None:
+        params["iterations"] = iterations
+    if model is not None:
+        params["model"] = model
+    if eoi is not None:
+        params["eoi"] = eoi
+    if wcp is not None:
+        params["wcp"] = wcp
+    if tstat is not None:
+        params["tstat"] = tstat
+    if stdz is not None:
+        params["stdz"] = stdz
+    if c_vars is not None:
+        params["cVars"] = c_vars
+    if q_vars is not None:
+        params["qVars"] = q_vars
+    if dist_roi is not None:
+        params["distROI"] = dist_roi
+    if dist_subj is not None:
+        params["distSubj"] = dist_subj
+    if dist_y is not None:
+        params["distY"] = dist_y
+    if ridge_plot is not None:
+        params["ridgePlot"] = ridge_plot
+    if roi is not None:
+        params["roi"] = roi
+    if subj is not None:
+        params["subj"] = subj
+    if scale is not None:
+        params["scale"] = scale
+    if se is not None:
+        params["se"] = se
+    if pdp is not None:
+        params["pdp"] = pdp
+    if mean is not None:
+        params["mean"] = mean
+    if sigma is not None:
+        params["sigma"] = sigma
+    if verbose is not None:
+        params["verbose"] = verbose
+    return params
+
+
+def rba_cargs(
+    params: RbaParameters,
+    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("RBA")
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    cargs.extend([
+        "-dataTable",
+        execution.input_file(params.get("dataTable"))
+    ])
+    if params.get("chains") is not None:
+        cargs.extend([
+            "-chains",
+            str(params.get("chains"))
+        ])
+    if params.get("iterations") is not None:
+        cargs.extend([
+            "-iterations",
+            str(params.get("iterations"))
+        ])
+    if params.get("model") is not None:
+        cargs.extend([
+            "-model",
+            params.get("model")
+        ])
+    if params.get("eoi") is not None:
+        cargs.extend([
+            "-EOI",
+            params.get("eoi")
+        ])
+    if params.get("wcp") is not None:
+        cargs.extend([
+            "-WCP",
+            str(params.get("wcp"))
+        ])
+    if params.get("tstat") is not None:
+        cargs.extend([
+            "-tstat",
+            params.get("tstat")
+        ])
+    if params.get("stdz") is not None:
+        cargs.extend([
+            "-stdz",
+            params.get("stdz")
+        ])
+    if params.get("cVars") is not None:
+        cargs.extend([
+            "-cVars",
+            params.get("cVars")
+        ])
+    if params.get("qVars") is not None:
+        cargs.extend([
+            "-qVars",
+            params.get("qVars")
+        ])
+    if params.get("distROI") is not None:
+        cargs.extend([
+            "-distROI",
+            params.get("distROI")
+        ])
+    if params.get("distSubj") is not None:
+        cargs.extend([
+            "-distSubj",
+            params.get("distSubj")
+        ])
+    if params.get("distY") is not None:
+        cargs.extend([
+            "-distY",
+            params.get("distY")
+        ])
+    if params.get("ridgePlot") is not None:
+        cargs.extend([
+            "-ridgePlot",
+            params.get("ridgePlot")
+        ])
+    if params.get("roi") is not None:
+        cargs.extend([
+            "-ROI",
+            params.get("roi")
+        ])
+    if params.get("subj") is not None:
+        cargs.extend([
+            "-Subj",
+            params.get("subj")
+        ])
+    if params.get("scale") is not None:
+        cargs.extend([
+            "-scale",
+            str(params.get("scale"))
+        ])
+    if params.get("se") is not None:
+        cargs.extend([
+            "-se",
+            params.get("se")
+        ])
+    if params.get("pdp") is not None:
+        cargs.extend([
+            "-PDP",
+            params.get("pdp")
+        ])
+    if params.get("mean") is not None:
+        cargs.extend([
+            "-mean",
+            params.get("mean")
+        ])
+    if params.get("sigma") is not None:
+        cargs.extend([
+            "-sigma",
+            params.get("sigma")
+        ])
+    if params.get("debug"):
+        cargs.append("-dbgArgs")
+    if params.get("verbose") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbose"))
+        ])
+    if params.get("md"):
+        cargs.append("-MD")
+    if params.get("r2z"):
+        cargs.append("-r2z")
+    return cargs
+
+
+def rba_outputs(
+    params: RbaParameters,
+    execution: Execution,
+) -> RbaOutputs:
+    """
+    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 = RbaOutputs(
+        root=execution.output_file("."),
+        output_txt=execution.output_file(params.get("prefix") + ".txt"),
+        output_rdata=execution.output_file(params.get("prefix") + ".RData"),
+    )
+    return ret
+
+
+def rba_execute(
+    params: RbaParameters,
+    execution: Execution,
+) -> RbaOutputs:
+    """
+    Region-Based Analysis Program through Bayesian Multilevel Modeling.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `RbaOutputs`).
+    """
+    params = execution.params(params)
+    cargs = rba_cargs(params, execution)
+    ret = rba_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def rba(
+    prefix: str,
+    data_table: InputPathType,
+    chains: float | None = None,
+    iterations: float | None = None,
+    model: str | None = None,
+    eoi: str | None = None,
+    wcp: float | None = None,
+    tstat: str | None = None,
+    stdz: str | None = None,
+    c_vars: str | None = None,
+    q_vars: str | None = None,
+    dist_roi: str | None = None,
+    dist_subj: str | None = None,
+    dist_y: str | None = None,
+    ridge_plot: str | None = None,
+    roi: str | None = None,
+    subj: str | None = None,
+    scale: float | None = None,
+    se: str | None = None,
+    pdp: str | None = None,
+    mean: str | None = None,
+    sigma: str | None = None,
+    debug: bool = False,
+    verbose: float | None = None,
+    md: bool = False,
+    r2z: bool = False,
+    runner: Runner | None = None,
+) -> RbaOutputs:
+    """
+    Region-Based Analysis Program through Bayesian Multilevel Modeling.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Prefix for output file names.
+        data_table: Data table in pure text format.
+        chains: Specify the number of Markov chains.
+        iterations: Specify the number of iterations per Markov chain.
+        model: Specify the model formula.
+        eoi: Identify effects of interest in the output.
+        wcp: Invoke within-chain parallelization.
+        tstat: Specify the column name that lists the t-statistic values.
+        stdz: Identify quantitative variables (or covariates) to be\
+            standardized.
+        c_vars: Identify categorical (qualitative) variables (or factors).
+        q_vars: Identify quantitative variables (or covariates).
+        dist_roi: Specify the distribution for the ROIs.
+        dist_subj: Specify the distribution for the subjects.
+        dist_y: Specify the distribution for the response variable.
+        ridge_plot: Plot the posterior distributions stacked together.
+        roi: Specify the column name that is designated as the region variable.
+        subj: Specify the column name that is designated as the measuring unit\
+            variable (usually subject).
+        scale: Specify a multiplier for the Y values.
+        se: This option indicates that standard error for the response variable\
+            is available as input.
+        pdp: Specify the layout of posterior distribution plot.
+        mean: Specify the formulation for the mean of the likelihood (sampling\
+            distribution).
+        sigma: Specify the formulation for the standard deviation (sigma) of\
+            the likelihood (sampling distribution).
+        debug: This option will enable R to save the parameters in a file for\
+            debugging.
+        verbose: Specify verbose level.
+        md: This option indicates that there are missing data in the input.
+        r2z: Perform Fisher transformation on the response variable if it is a\
+            correlation coefficient.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `RbaOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RBA_METADATA)
+    params = rba_params(
+        prefix=prefix,
+        data_table=data_table,
+        chains=chains,
+        iterations=iterations,
+        model=model,
+        eoi=eoi,
+        wcp=wcp,
+        tstat=tstat,
+        stdz=stdz,
+        c_vars=c_vars,
+        q_vars=q_vars,
+        dist_roi=dist_roi,
+        dist_subj=dist_subj,
+        dist_y=dist_y,
+        ridge_plot=ridge_plot,
+        roi=roi,
+        subj=subj,
+        scale=scale,
+        se=se,
+        pdp=pdp,
+        mean=mean,
+        sigma=sigma,
+        debug=debug,
+        verbose=verbose,
+        md=md,
+        r2z=r2z,
+    )
+    return rba_execute(params, execution)
+
+
+__all__ = [
+    "RBA_METADATA",
+    "RbaOutputs",
+    "RbaParameters",
+    "rba",
+    "rba_params",
+]