niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_lme.py

@@ -0,0 +1,524 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_LME_METADATA = Metadata(
+    id="e9a80d6729c55d33424066db0a326673e6b70516.boutiques",
+    name="3dLME",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dLmeParameters = typing.TypedDict('V3dLmeParameters', {
+    "__STYX_TYPE__": typing.Literal["3dLME"],
+    "PREFIX": str,
+    "MODEL": str,
+    "DATA_TABLE": str,
+    "BOUNDS": typing.NotRequired[list[float] | None],
+    "CIO_FLAG": bool,
+    "COR_STR": typing.NotRequired[str | None],
+    "CUTOFF": typing.NotRequired[float | None],
+    "DBG_ARGS_FLAG": bool,
+    "JOBS": typing.NotRequired[float | None],
+    "GLT_CODE": typing.NotRequired[str | None],
+    "GLT_LABEL": typing.NotRequired[str | None],
+    "GLF_LABEL": typing.NotRequired[str | None],
+    "GLF_CODE": typing.NotRequired[str | None],
+    "ICC_FLAG": bool,
+    "ICCB_FLAG": bool,
+    "LOG_LIK_FLAG": bool,
+    "LOGIT_FLAG": bool,
+    "ML_FLAG": bool,
+    "QVARS_CENTERS": typing.NotRequired[str | None],
+    "QVARS": typing.NotRequired[str | None],
+    "RANEFF": typing.NotRequired[str | None],
+    "MASK": typing.NotRequired[InputPathType | None],
+    "NUM_GLF": typing.NotRequired[float | None],
+    "NUM_GLT": typing.NotRequired[float | None],
+    "RESID": typing.NotRequired[str | None],
+    "RE": typing.NotRequired[str | None],
+    "REPREFIX": typing.NotRequired[str | None],
+    "RIO_FLAG": bool,
+    "SHOW_OPTIONS_FLAG": bool,
+    "SS_TYPE": 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 {
+        "3dLME": v_3d_lme_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 {
+        "3dLME": v_3d_lme_outputs,
+    }.get(t)
+
+
+class V3dLmeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_lme(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_nifti: OutputPathType
+    """Output file in NIfTI format"""
+
+
+def v_3d_lme_params(
+    prefix: str,
+    model: str,
+    data_table: str,
+    bounds: list[float] | None = None,
+    cio_flag: bool = False,
+    cor_str: str | None = None,
+    cutoff: float | None = None,
+    dbg_args_flag: bool = False,
+    jobs: float | None = None,
+    glt_code: str | None = None,
+    glt_label: str | None = None,
+    glf_label: str | None = None,
+    glf_code: str | None = None,
+    icc_flag: bool = False,
+    iccb_flag: bool = False,
+    log_lik_flag: bool = False,
+    logit_flag: bool = False,
+    ml_flag: bool = False,
+    qvars_centers: str | None = None,
+    qvars: str | None = None,
+    raneff: str | None = None,
+    mask: InputPathType | None = None,
+    num_glf: float | None = None,
+    num_glt: float | None = None,
+    resid: str | None = None,
+    re_: str | None = None,
+    reprefix: str | None = None,
+    rio_flag: bool = False,
+    show_options_flag: bool = False,
+    ss_type: float | None = None,
+) -> V3dLmeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Prefix for output files.
+        model: Model formula describing the fixed effects.
+        data_table: Data table description.
+        bounds: Lower and upper bounds for outlier removal.
+        cio_flag: Use AFNI's C io functions (default) or R's io functions with\
+            -Rio.
+        cor_str: Specify the correlation structure of the residuals.
+        cutoff: Specify the cutoff value for accuracy in logistic regression\
+            analysis.
+        dbg_args_flag: Enable saving parameters for debugging.
+        jobs: Number of jobs for parallel computing.
+        glt_code: General linear test coding.
+        glt_label: Label for general linear test.
+        glf_label: Label for general linear F-test.
+        glf_code: General linear F-test coding.
+        icc_flag: Compute voxel-wise intra-class correlation.
+        iccb_flag: Compute voxel-wise intra-class correlation with Bayesian\
+            approach.
+        log_lik_flag: Include voxel-wise log likelihood in the output.
+        logit_flag: Perform voxel-wise logistic modeling.
+        ml_flag: Use Maximum Likelihood estimation instead of REML.
+        qvars_centers: Centering values for quantitative variables.
+        qvars: Identify quantitative variables (or covariates).
+        raneff: Specify the random effects.
+        mask: Mask file for voxel processing.
+        num_glf: Number of general linear F-tests.
+        num_glt: Number of general linear t-tests.
+        resid: Prefix for residuals output file.
+        re_: List of variables whose random effects are saved in the output.
+        reprefix: Prefix for random effects output file.
+        rio_flag: Use R's io functions instead of AFNI's C io functions.
+        show_options_flag: List of allowed options.
+        ss_type: Specify the type for sums of squares in the F-statistics.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dLME",
+        "PREFIX": prefix,
+        "MODEL": model,
+        "DATA_TABLE": data_table,
+        "CIO_FLAG": cio_flag,
+        "DBG_ARGS_FLAG": dbg_args_flag,
+        "ICC_FLAG": icc_flag,
+        "ICCB_FLAG": iccb_flag,
+        "LOG_LIK_FLAG": log_lik_flag,
+        "LOGIT_FLAG": logit_flag,
+        "ML_FLAG": ml_flag,
+        "RIO_FLAG": rio_flag,
+        "SHOW_OPTIONS_FLAG": show_options_flag,
+    }
+    if bounds is not None:
+        params["BOUNDS"] = bounds
+    if cor_str is not None:
+        params["COR_STR"] = cor_str
+    if cutoff is not None:
+        params["CUTOFF"] = cutoff
+    if jobs is not None:
+        params["JOBS"] = jobs
+    if glt_code is not None:
+        params["GLT_CODE"] = glt_code
+    if glt_label is not None:
+        params["GLT_LABEL"] = glt_label
+    if glf_label is not None:
+        params["GLF_LABEL"] = glf_label
+    if glf_code is not None:
+        params["GLF_CODE"] = glf_code
+    if qvars_centers is not None:
+        params["QVARS_CENTERS"] = qvars_centers
+    if qvars is not None:
+        params["QVARS"] = qvars
+    if raneff is not None:
+        params["RANEFF"] = raneff
+    if mask is not None:
+        params["MASK"] = mask
+    if num_glf is not None:
+        params["NUM_GLF"] = num_glf
+    if num_glt is not None:
+        params["NUM_GLT"] = num_glt
+    if resid is not None:
+        params["RESID"] = resid
+    if re_ is not None:
+        params["RE"] = re_
+    if reprefix is not None:
+        params["REPREFIX"] = reprefix
+    if ss_type is not None:
+        params["SS_TYPE"] = ss_type
+    return params
+
+
+def v_3d_lme_cargs(
+    params: V3dLmeParameters,
+    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("3dLME")
+    cargs.extend([
+        "-prefix",
+        params.get("PREFIX")
+    ])
+    cargs.extend([
+        "-model",
+        params.get("MODEL")
+    ])
+    cargs.extend([
+        "-dataTable",
+        params.get("DATA_TABLE")
+    ])
+    if params.get("BOUNDS") is not None:
+        cargs.extend([
+            "-bounds",
+            *map(str, params.get("BOUNDS"))
+        ])
+    if params.get("CIO_FLAG"):
+        cargs.append("-cio")
+    if params.get("COR_STR") is not None:
+        cargs.extend([
+            "-corStr",
+            params.get("COR_STR")
+        ])
+    if params.get("CUTOFF") is not None:
+        cargs.extend([
+            "-cutoff",
+            str(params.get("CUTOFF"))
+        ])
+    if params.get("DBG_ARGS_FLAG"):
+        cargs.append("-dbgArgs")
+    if params.get("JOBS") is not None:
+        cargs.extend([
+            "-jobs",
+            str(params.get("JOBS"))
+        ])
+    if params.get("GLT_CODE") is not None:
+        cargs.extend([
+            "-gltCode",
+            params.get("GLT_CODE")
+        ])
+    if params.get("GLT_LABEL") is not None:
+        cargs.extend([
+            "-gltLabel",
+            params.get("GLT_LABEL")
+        ])
+    if params.get("GLF_LABEL") is not None:
+        cargs.extend([
+            "-glfLabel",
+            params.get("GLF_LABEL")
+        ])
+    if params.get("GLF_CODE") is not None:
+        cargs.extend([
+            "-glfCode",
+            params.get("GLF_CODE")
+        ])
+    if params.get("ICC_FLAG"):
+        cargs.append("-ICC")
+    if params.get("ICCB_FLAG"):
+        cargs.append("-ICCb")
+    if params.get("LOG_LIK_FLAG"):
+        cargs.append("-logLik")
+    if params.get("LOGIT_FLAG"):
+        cargs.append("-LOGIT")
+    cargs.append("-ml")
+    if params.get("ML_FLAG"):
+        cargs.append("-ML")
+    if params.get("QVARS_CENTERS") is not None:
+        cargs.extend([
+            "-qVarsCenters",
+            params.get("QVARS_CENTERS")
+        ])
+    if params.get("QVARS") is not None:
+        cargs.extend([
+            "-qVars",
+            params.get("QVARS")
+        ])
+    if params.get("RANEFF") is not None:
+        cargs.extend([
+            "-ranEff",
+            params.get("RANEFF")
+        ])
+    if params.get("MASK") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("MASK"))
+        ])
+    if params.get("NUM_GLF") is not None:
+        cargs.extend([
+            "-num_glf",
+            str(params.get("NUM_GLF"))
+        ])
+    if params.get("NUM_GLT") is not None:
+        cargs.extend([
+            "-num_glt",
+            str(params.get("NUM_GLT"))
+        ])
+    if params.get("RESID") is not None:
+        cargs.extend([
+            "-resid",
+            params.get("RESID")
+        ])
+    if params.get("RE") is not None:
+        cargs.extend([
+            "-RE",
+            params.get("RE")
+        ])
+    if params.get("REPREFIX") is not None:
+        cargs.extend([
+            "-REprefix",
+            params.get("REPREFIX")
+        ])
+    cargs.append("-RIO")
+    if params.get("RIO_FLAG"):
+        cargs.append("-Rio")
+    if params.get("SHOW_OPTIONS_FLAG"):
+        cargs.append("-show_allowed_options")
+    if params.get("SS_TYPE") is not None:
+        cargs.extend([
+            "-SS_type",
+            str(params.get("SS_TYPE"))
+        ])
+    return cargs
+
+
+def v_3d_lme_outputs(
+    params: V3dLmeParameters,
+    execution: Execution,
+) -> V3dLmeOutputs:
+    """
+    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 = V3dLmeOutputs(
+        root=execution.output_file("."),
+        output_nifti=execution.output_file(params.get("PREFIX") + ".nii"),
+    )
+    return ret
+
+
+def v_3d_lme_execute(
+    params: V3dLmeParameters,
+    execution: Execution,
+) -> V3dLmeOutputs:
+    """
+    AFNI Group Analysis Program with Linear Mixed-Effects Modeling Approach.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dLmeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_lme_cargs(params, execution)
+    ret = v_3d_lme_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_lme(
+    prefix: str,
+    model: str,
+    data_table: str,
+    bounds: list[float] | None = None,
+    cio_flag: bool = False,
+    cor_str: str | None = None,
+    cutoff: float | None = None,
+    dbg_args_flag: bool = False,
+    jobs: float | None = None,
+    glt_code: str | None = None,
+    glt_label: str | None = None,
+    glf_label: str | None = None,
+    glf_code: str | None = None,
+    icc_flag: bool = False,
+    iccb_flag: bool = False,
+    log_lik_flag: bool = False,
+    logit_flag: bool = False,
+    ml_flag: bool = False,
+    qvars_centers: str | None = None,
+    qvars: str | None = None,
+    raneff: str | None = None,
+    mask: InputPathType | None = None,
+    num_glf: float | None = None,
+    num_glt: float | None = None,
+    resid: str | None = None,
+    re_: str | None = None,
+    reprefix: str | None = None,
+    rio_flag: bool = False,
+    show_options_flag: bool = False,
+    ss_type: float | None = None,
+    runner: Runner | None = None,
+) -> V3dLmeOutputs:
+    """
+    AFNI Group Analysis Program with Linear Mixed-Effects Modeling Approach.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Prefix for output files.
+        model: Model formula describing the fixed effects.
+        data_table: Data table description.
+        bounds: Lower and upper bounds for outlier removal.
+        cio_flag: Use AFNI's C io functions (default) or R's io functions with\
+            -Rio.
+        cor_str: Specify the correlation structure of the residuals.
+        cutoff: Specify the cutoff value for accuracy in logistic regression\
+            analysis.
+        dbg_args_flag: Enable saving parameters for debugging.
+        jobs: Number of jobs for parallel computing.
+        glt_code: General linear test coding.
+        glt_label: Label for general linear test.
+        glf_label: Label for general linear F-test.
+        glf_code: General linear F-test coding.
+        icc_flag: Compute voxel-wise intra-class correlation.
+        iccb_flag: Compute voxel-wise intra-class correlation with Bayesian\
+            approach.
+        log_lik_flag: Include voxel-wise log likelihood in the output.
+        logit_flag: Perform voxel-wise logistic modeling.
+        ml_flag: Use Maximum Likelihood estimation instead of REML.
+        qvars_centers: Centering values for quantitative variables.
+        qvars: Identify quantitative variables (or covariates).
+        raneff: Specify the random effects.
+        mask: Mask file for voxel processing.
+        num_glf: Number of general linear F-tests.
+        num_glt: Number of general linear t-tests.
+        resid: Prefix for residuals output file.
+        re_: List of variables whose random effects are saved in the output.
+        reprefix: Prefix for random effects output file.
+        rio_flag: Use R's io functions instead of AFNI's C io functions.
+        show_options_flag: List of allowed options.
+        ss_type: Specify the type for sums of squares in the F-statistics.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dLmeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LME_METADATA)
+    params = v_3d_lme_params(
+        prefix=prefix,
+        model=model,
+        data_table=data_table,
+        bounds=bounds,
+        cio_flag=cio_flag,
+        cor_str=cor_str,
+        cutoff=cutoff,
+        dbg_args_flag=dbg_args_flag,
+        jobs=jobs,
+        glt_code=glt_code,
+        glt_label=glt_label,
+        glf_label=glf_label,
+        glf_code=glf_code,
+        icc_flag=icc_flag,
+        iccb_flag=iccb_flag,
+        log_lik_flag=log_lik_flag,
+        logit_flag=logit_flag,
+        ml_flag=ml_flag,
+        qvars_centers=qvars_centers,
+        qvars=qvars,
+        raneff=raneff,
+        mask=mask,
+        num_glf=num_glf,
+        num_glt=num_glt,
+        resid=resid,
+        re_=re_,
+        reprefix=reprefix,
+        rio_flag=rio_flag,
+        show_options_flag=show_options_flag,
+        ss_type=ss_type,
+    )
+    return v_3d_lme_execute(params, execution)
+
+
+__all__ = [
+    "V3dLmeOutputs",
+    "V3dLmeParameters",
+    "V_3D_LME_METADATA",
+    "v_3d_lme",
+    "v_3d_lme_params",
+]