niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/tokens.py

@@ -0,0 +1,192 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TOKENS_METADATA = Metadata(
+    id="fa203a3c21c39761a0f8e237a33304c1ff4334e3.boutiques",
+    name="tokens",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+TokensParameters = typing.TypedDict('TokensParameters', {
+    "__STYX_TYPE__": typing.Literal["tokens"],
+    "infile": typing.NotRequired[InputPathType | None],
+    "extra_char": typing.NotRequired[list[str] | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "tokens": tokens_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 TokensOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `tokens(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def tokens_params(
+    infile: InputPathType | None = None,
+    extra_char: list[str] | None = None,
+) -> TokensParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Specify input file (stdin if none).
+        extra_char: Specify extra character to count as valid. Can be used more\
+            than once.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "tokens",
+    }
+    if infile is not None:
+        params["infile"] = infile
+    if extra_char is not None:
+        params["extra_char"] = extra_char
+    return params
+
+
+def tokens_cargs(
+    params: TokensParameters,
+    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("tokens")
+    if params.get("infile") is not None:
+        cargs.extend([
+            "-infile",
+            execution.input_file(params.get("infile"))
+        ])
+    if params.get("extra_char") is not None:
+        cargs.extend([
+            "-extra",
+            *params.get("extra_char")
+        ])
+    return cargs
+
+
+def tokens_outputs(
+    params: TokensParameters,
+    execution: Execution,
+) -> TokensOutputs:
+    """
+    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 = TokensOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def tokens_execute(
+    params: TokensParameters,
+    execution: Execution,
+) -> TokensOutputs:
+    """
+    Token counting tool.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `TokensOutputs`).
+    """
+    params = execution.params(params)
+    cargs = tokens_cargs(params, execution)
+    ret = tokens_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def tokens(
+    infile: InputPathType | None = None,
+    extra_char: list[str] | None = None,
+    runner: Runner | None = None,
+) -> TokensOutputs:
+    """
+    Token counting tool.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Specify input file (stdin if none).
+        extra_char: Specify extra character to count as valid. Can be used more\
+            than once.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `TokensOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TOKENS_METADATA)
+    params = tokens_params(
+        infile=infile,
+        extra_char=extra_char,
+    )
+    return tokens_execute(params, execution)
+
+
+__all__ = [
+    "TOKENS_METADATA",
+    "TokensOutputs",
+    "TokensParameters",
+    "tokens",
+    "tokens_params",
+]

niwrap_afni/afni/trr.py

@@ -0,0 +1,405 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TRR_METADATA = Metadata(
+    id="9675a33a650bccf2f38cabb937b9b11e9c6b765f.boutiques",
+    name="TRR",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+TrrParameters = typing.TypedDict('TrrParameters', {
+    "__STYX_TYPE__": typing.Literal["TRR"],
+    "prefix": str,
+    "chains": typing.NotRequired[float | None],
+    "iterations": typing.NotRequired[float | None],
+    "response_var": str,
+    "subject_var": str,
+    "repetition_var": typing.NotRequired[str | None],
+    "condition_var": typing.NotRequired[str | None],
+    "data_table": InputPathType,
+    "categorical_vars": typing.NotRequired[str | None],
+    "quantitative_vars": typing.NotRequired[str | None],
+    "response_dist": typing.NotRequired[str | None],
+    "model": typing.NotRequired[str | None],
+    "plot_size": typing.NotRequired[list[float] | None],
+    "standard_error": typing.NotRequired[str | None],
+    "t_stat": typing.NotRequired[str | None],
+    "within_chain_parallelization": typing.NotRequired[float | None],
+    "debug": bool,
+    "verbose": 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 {
+        "TRR": trr_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 {
+        "TRR": trr_outputs,
+    }.get(t)
+
+
+class TrrOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `trr(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file_txt: OutputPathType
+    """Main output file containing inference information for effects of
+    interest"""
+    output_file_pdf: OutputPathType
+    """Density plot of the TRR distribution"""
+    output_file_rdata: OutputPathType
+    """Saved R data in binary format for post hoc processing"""
+
+
+def trr_params(
+    prefix: str,
+    response_var: str,
+    subject_var: str,
+    data_table: InputPathType,
+    chains: float | None = None,
+    iterations: float | None = None,
+    repetition_var: str | None = None,
+    condition_var: str | None = None,
+    categorical_vars: str | None = None,
+    quantitative_vars: str | None = None,
+    response_dist: str | None = None,
+    model: str | None = None,
+    plot_size: list[float] | None = None,
+    standard_error: str | None = None,
+    t_stat: str | None = None,
+    within_chain_parallelization: float | None = None,
+    debug: bool = False,
+    verbose: float | None = None,
+) -> TrrParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Prefix for output file names.
+        response_var: Specify the column name for the response variable.
+        subject_var: Specify the column name for the subject variable.
+        data_table: Specify the path to the data table in pure text format.
+        chains: Specify the number of Markov chains.
+        iterations: Specify the number of iterations per Markov chain.
+        repetition_var: Specify the column name for the repetition variable.
+        condition_var: Specify the column name for the condition variable.
+        categorical_vars: Identify categorical (qualitative) variables.
+        quantitative_vars: Identify quantitative (covariate) variables.
+        response_dist: Specify the distribution for the response variable\
+            (e.g., 'gaussian', 'student', 'exgaussian').
+        model: Specify the effects associated with explanatory variables.
+        plot_size: Specify the layout of posterior distribution plot (PDP) with\
+            width and height in inches.
+        standard_error: Include standard error for the response variable as\
+            input.
+        t_stat: Specify the column name for the t-statistic values.
+        within_chain_parallelization: Invoke within-chain parallelization;\
+            specify number of threads per chain.
+        debug: Enable R to save the parameters for debugging.
+        verbose: Specify verbose level.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "TRR",
+        "prefix": prefix,
+        "response_var": response_var,
+        "subject_var": subject_var,
+        "data_table": data_table,
+        "debug": debug,
+    }
+    if chains is not None:
+        params["chains"] = chains
+    if iterations is not None:
+        params["iterations"] = iterations
+    if repetition_var is not None:
+        params["repetition_var"] = repetition_var
+    if condition_var is not None:
+        params["condition_var"] = condition_var
+    if categorical_vars is not None:
+        params["categorical_vars"] = categorical_vars
+    if quantitative_vars is not None:
+        params["quantitative_vars"] = quantitative_vars
+    if response_dist is not None:
+        params["response_dist"] = response_dist
+    if model is not None:
+        params["model"] = model
+    if plot_size is not None:
+        params["plot_size"] = plot_size
+    if standard_error is not None:
+        params["standard_error"] = standard_error
+    if t_stat is not None:
+        params["t_stat"] = t_stat
+    if within_chain_parallelization is not None:
+        params["within_chain_parallelization"] = within_chain_parallelization
+    if verbose is not None:
+        params["verbose"] = verbose
+    return params
+
+
+def trr_cargs(
+    params: TrrParameters,
+    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("TRR")
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    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"))
+        ])
+    cargs.extend([
+        "-Y",
+        params.get("response_var")
+    ])
+    cargs.extend([
+        "-subject",
+        params.get("subject_var")
+    ])
+    if params.get("repetition_var") is not None:
+        cargs.extend([
+            "-repetition",
+            params.get("repetition_var")
+        ])
+    if params.get("condition_var") is not None:
+        cargs.extend([
+            "-condition",
+            params.get("condition_var")
+        ])
+    cargs.extend([
+        "-dataTable",
+        execution.input_file(params.get("data_table"))
+    ])
+    if params.get("categorical_vars") is not None:
+        cargs.extend([
+            "-cVars",
+            params.get("categorical_vars")
+        ])
+    if params.get("quantitative_vars") is not None:
+        cargs.extend([
+            "-qVars",
+            params.get("quantitative_vars")
+        ])
+    if params.get("response_dist") is not None:
+        cargs.extend([
+            "-distY",
+            params.get("response_dist")
+        ])
+    if params.get("model") is not None:
+        cargs.extend([
+            "-model",
+            params.get("model")
+        ])
+    if params.get("plot_size") is not None:
+        cargs.extend([
+            "-PDP",
+            *map(str, params.get("plot_size"))
+        ])
+    if params.get("standard_error") is not None:
+        cargs.extend([
+            "-se",
+            params.get("standard_error")
+        ])
+    if params.get("t_stat") is not None:
+        cargs.extend([
+            "-tstat",
+            params.get("t_stat")
+        ])
+    if params.get("within_chain_parallelization") is not None:
+        cargs.extend([
+            "-WCP",
+            str(params.get("within_chain_parallelization"))
+        ])
+    if params.get("debug"):
+        cargs.append("-dbgArgs")
+    if params.get("verbose") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbose"))
+        ])
+    return cargs
+
+
+def trr_outputs(
+    params: TrrParameters,
+    execution: Execution,
+) -> TrrOutputs:
+    """
+    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 = TrrOutputs(
+        root=execution.output_file("."),
+        output_file_txt=execution.output_file(params.get("prefix") + ".txt"),
+        output_file_pdf=execution.output_file(params.get("prefix") + ".pdf"),
+        output_file_rdata=execution.output_file(params.get("prefix") + ".RData"),
+    )
+    return ret
+
+
+def trr_execute(
+    params: TrrParameters,
+    execution: Execution,
+) -> TrrOutputs:
+    """
+    Test-Retest Reliability 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 `TrrOutputs`).
+    """
+    params = execution.params(params)
+    cargs = trr_cargs(params, execution)
+    ret = trr_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def trr(
+    prefix: str,
+    response_var: str,
+    subject_var: str,
+    data_table: InputPathType,
+    chains: float | None = None,
+    iterations: float | None = None,
+    repetition_var: str | None = None,
+    condition_var: str | None = None,
+    categorical_vars: str | None = None,
+    quantitative_vars: str | None = None,
+    response_dist: str | None = None,
+    model: str | None = None,
+    plot_size: list[float] | None = None,
+    standard_error: str | None = None,
+    t_stat: str | None = None,
+    within_chain_parallelization: float | None = None,
+    debug: bool = False,
+    verbose: float | None = None,
+    runner: Runner | None = None,
+) -> TrrOutputs:
+    """
+    Test-Retest Reliability Program through Bayesian Multilevel Modeling.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Prefix for output file names.
+        response_var: Specify the column name for the response variable.
+        subject_var: Specify the column name for the subject variable.
+        data_table: Specify the path to the data table in pure text format.
+        chains: Specify the number of Markov chains.
+        iterations: Specify the number of iterations per Markov chain.
+        repetition_var: Specify the column name for the repetition variable.
+        condition_var: Specify the column name for the condition variable.
+        categorical_vars: Identify categorical (qualitative) variables.
+        quantitative_vars: Identify quantitative (covariate) variables.
+        response_dist: Specify the distribution for the response variable\
+            (e.g., 'gaussian', 'student', 'exgaussian').
+        model: Specify the effects associated with explanatory variables.
+        plot_size: Specify the layout of posterior distribution plot (PDP) with\
+            width and height in inches.
+        standard_error: Include standard error for the response variable as\
+            input.
+        t_stat: Specify the column name for the t-statistic values.
+        within_chain_parallelization: Invoke within-chain parallelization;\
+            specify number of threads per chain.
+        debug: Enable R to save the parameters for debugging.
+        verbose: Specify verbose level.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `TrrOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TRR_METADATA)
+    params = trr_params(
+        prefix=prefix,
+        chains=chains,
+        iterations=iterations,
+        response_var=response_var,
+        subject_var=subject_var,
+        repetition_var=repetition_var,
+        condition_var=condition_var,
+        data_table=data_table,
+        categorical_vars=categorical_vars,
+        quantitative_vars=quantitative_vars,
+        response_dist=response_dist,
+        model=model,
+        plot_size=plot_size,
+        standard_error=standard_error,
+        t_stat=t_stat,
+        within_chain_parallelization=within_chain_parallelization,
+        debug=debug,
+        verbose=verbose,
+    )
+    return trr_execute(params, execution)
+
+
+__all__ = [
+    "TRR_METADATA",
+    "TrrOutputs",
+    "TrrParameters",
+    "trr",
+    "trr_params",
+]