niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_lmer.py

@@ -0,0 +1,425 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_LMER_METADATA = Metadata(
+    id="02e68dcb59ede0c18ce18893dd5aa84a50513efe.boutiques",
+    name="3dLMEr",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dLmerParameters = typing.TypedDict('V3dLmerParameters', {
+    "__STYX_TYPE__": typing.Literal["3dLMEr"],
+    "bound_lower": typing.NotRequired[float | None],
+    "bound_upper": typing.NotRequired[float | None],
+    "cio": bool,
+    "data_table": InputPathType,
+    "debug_args": bool,
+    "glf_code": typing.NotRequired[str | None],
+    "glt_code": typing.NotRequired[str | None],
+    "help": bool,
+    "input_file_column": typing.NotRequired[str | None],
+    "jobs": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "model": str,
+    "prefix": str,
+    "qvar_centers": typing.NotRequired[str | None],
+    "qvars": typing.NotRequired[str | None],
+    "resid": typing.NotRequired[str | None],
+    "rio": bool,
+    "show_options": bool,
+    "ss_type": typing.NotRequired[float | None],
+    "trr": bool,
+    "vvar_centers": typing.NotRequired[str | None],
+    "vvars": typing.NotRequired[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 {
+        "3dLMEr": v_3d_lmer_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 {
+        "3dLMEr": v_3d_lmer_outputs,
+    }.get(t)
+
+
+class V3dLmerOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_lmer(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output file"""
+    residuals_file: OutputPathType | None
+    """Output residuals file"""
+
+
+def v_3d_lmer_params(
+    data_table: InputPathType,
+    model: str,
+    prefix: str,
+    bound_lower: float | None = None,
+    bound_upper: float | None = None,
+    cio: bool = False,
+    debug_args: bool = False,
+    glf_code: str | None = None,
+    glt_code: str | None = None,
+    help_: bool = False,
+    input_file_column: str | None = None,
+    jobs: float | None = None,
+    mask: InputPathType | None = None,
+    qvar_centers: str | None = None,
+    qvars: str | None = None,
+    resid: str | None = None,
+    rio: bool = False,
+    show_options: bool = False,
+    ss_type: float | None = None,
+    trr: bool = False,
+    vvar_centers: str | None = None,
+    vvars: str | None = None,
+) -> V3dLmerParameters:
+    """
+    Build parameters.
+    
+    Args:
+        data_table: List the data structure with a header as the first line.
+        model: Specify the model structure for all the variables.
+        prefix: Output file name.
+        bound_lower: Specify the lower and upper bounds for outlier removal.
+        bound_upper: Specify the lower and upper bounds for outlier removal.
+        cio: Use AFNI's C io functions.
+        debug_args: Enable R to save the parameters for debugging.
+        glf_code: Specify a general linear F-style (GLF) formulation.
+        glt_code: Specify the label and weights of interest in a general linear\
+            t-style (GLT) formulation.
+        help_: Display the help message.
+        input_file_column: Specify the column name for input files of effect\
+            estimate.
+        jobs: Number of jobs for parallel computing.
+        mask: Process voxels inside this mask only.
+        qvar_centers: Specify centering values for quantitative variables.
+        qvars: Identify quantitative variables (or covariates).
+        resid: Output file name for the residuals.
+        rio: Use R's io functions.
+        show_options: List of allowed options.
+        ss_type: Specify the type for sums of squares in the F-statistics.
+        trr: Perform test-retest reliability analysis.
+        vvar_centers: Specify centering values for voxel-wise covariates.
+        vvars: Identify voxel-wise covariates.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dLMEr",
+        "cio": cio,
+        "data_table": data_table,
+        "debug_args": debug_args,
+        "help": help_,
+        "model": model,
+        "prefix": prefix,
+        "rio": rio,
+        "show_options": show_options,
+        "trr": trr,
+    }
+    if bound_lower is not None:
+        params["bound_lower"] = bound_lower
+    if bound_upper is not None:
+        params["bound_upper"] = bound_upper
+    if glf_code is not None:
+        params["glf_code"] = glf_code
+    if glt_code is not None:
+        params["glt_code"] = glt_code
+    if input_file_column is not None:
+        params["input_file_column"] = input_file_column
+    if jobs is not None:
+        params["jobs"] = jobs
+    if mask is not None:
+        params["mask"] = mask
+    if qvar_centers is not None:
+        params["qvar_centers"] = qvar_centers
+    if qvars is not None:
+        params["qvars"] = qvars
+    if resid is not None:
+        params["resid"] = resid
+    if ss_type is not None:
+        params["ss_type"] = ss_type
+    if vvar_centers is not None:
+        params["vvar_centers"] = vvar_centers
+    if vvars is not None:
+        params["vvars"] = vvars
+    return params
+
+
+def v_3d_lmer_cargs(
+    params: V3dLmerParameters,
+    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("3dLMEr")
+    if params.get("bound_lower") is not None:
+        cargs.append(str(params.get("bound_lower")))
+    if params.get("bound_upper") is not None:
+        cargs.append(str(params.get("bound_upper")))
+    if params.get("cio"):
+        cargs.append("-cio")
+    cargs.extend([
+        "-dataTable",
+        execution.input_file(params.get("data_table"))
+    ])
+    if params.get("debug_args"):
+        cargs.append("-dbgArgs")
+    if params.get("glf_code") is not None:
+        cargs.extend([
+            "-glfCode",
+            params.get("glf_code")
+        ])
+    if params.get("glt_code") is not None:
+        cargs.extend([
+            "-gltCode",
+            params.get("glt_code")
+        ])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("input_file_column") is not None:
+        cargs.extend([
+            "-IF",
+            params.get("input_file_column")
+        ])
+    if params.get("jobs") is not None:
+        cargs.extend([
+            "-jobs",
+            str(params.get("jobs"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    cargs.extend([
+        "-model",
+        params.get("model")
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("qvar_centers") is not None:
+        cargs.extend([
+            "-qVarCenters",
+            params.get("qvar_centers")
+        ])
+    if params.get("qvars") is not None:
+        cargs.extend([
+            "-qVars",
+            params.get("qvars")
+        ])
+    if params.get("resid") is not None:
+        cargs.extend([
+            "-resid",
+            params.get("resid")
+        ])
+    if params.get("rio"):
+        cargs.append("-Rio")
+    if params.get("show_options"):
+        cargs.append("-show_allowed_options")
+    if params.get("ss_type") is not None:
+        cargs.extend([
+            "-SS_type",
+            str(params.get("ss_type"))
+        ])
+    if params.get("trr"):
+        cargs.append("-TRR")
+    if params.get("vvar_centers") is not None:
+        cargs.extend([
+            "-vVarCenters",
+            params.get("vvar_centers")
+        ])
+    if params.get("vvars") is not None:
+        cargs.extend([
+            "-vVars",
+            params.get("vvars")
+        ])
+    return cargs
+
+
+def v_3d_lmer_outputs(
+    params: V3dLmerParameters,
+    execution: Execution,
+) -> V3dLmerOutputs:
+    """
+    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 = V3dLmerOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + ".nii.gz"),
+        residuals_file=execution.output_file(params.get("resid") + ".nii.gz") if (params.get("resid") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_lmer_execute(
+    params: V3dLmerParameters,
+    execution: Execution,
+) -> V3dLmerOutputs:
+    """
+    Program for Voxelwise Linear Mixed-Effects (LME) Analysis.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dLmerOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_lmer_cargs(params, execution)
+    ret = v_3d_lmer_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_lmer(
+    data_table: InputPathType,
+    model: str,
+    prefix: str,
+    bound_lower: float | None = None,
+    bound_upper: float | None = None,
+    cio: bool = False,
+    debug_args: bool = False,
+    glf_code: str | None = None,
+    glt_code: str | None = None,
+    help_: bool = False,
+    input_file_column: str | None = None,
+    jobs: float | None = None,
+    mask: InputPathType | None = None,
+    qvar_centers: str | None = None,
+    qvars: str | None = None,
+    resid: str | None = None,
+    rio: bool = False,
+    show_options: bool = False,
+    ss_type: float | None = None,
+    trr: bool = False,
+    vvar_centers: str | None = None,
+    vvars: str | None = None,
+    runner: Runner | None = None,
+) -> V3dLmerOutputs:
+    """
+    Program for Voxelwise Linear Mixed-Effects (LME) Analysis.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        data_table: List the data structure with a header as the first line.
+        model: Specify the model structure for all the variables.
+        prefix: Output file name.
+        bound_lower: Specify the lower and upper bounds for outlier removal.
+        bound_upper: Specify the lower and upper bounds for outlier removal.
+        cio: Use AFNI's C io functions.
+        debug_args: Enable R to save the parameters for debugging.
+        glf_code: Specify a general linear F-style (GLF) formulation.
+        glt_code: Specify the label and weights of interest in a general linear\
+            t-style (GLT) formulation.
+        help_: Display the help message.
+        input_file_column: Specify the column name for input files of effect\
+            estimate.
+        jobs: Number of jobs for parallel computing.
+        mask: Process voxels inside this mask only.
+        qvar_centers: Specify centering values for quantitative variables.
+        qvars: Identify quantitative variables (or covariates).
+        resid: Output file name for the residuals.
+        rio: Use R's io functions.
+        show_options: List of allowed options.
+        ss_type: Specify the type for sums of squares in the F-statistics.
+        trr: Perform test-retest reliability analysis.
+        vvar_centers: Specify centering values for voxel-wise covariates.
+        vvars: Identify voxel-wise covariates.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dLmerOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LMER_METADATA)
+    params = v_3d_lmer_params(
+        bound_lower=bound_lower,
+        bound_upper=bound_upper,
+        cio=cio,
+        data_table=data_table,
+        debug_args=debug_args,
+        glf_code=glf_code,
+        glt_code=glt_code,
+        help_=help_,
+        input_file_column=input_file_column,
+        jobs=jobs,
+        mask=mask,
+        model=model,
+        prefix=prefix,
+        qvar_centers=qvar_centers,
+        qvars=qvars,
+        resid=resid,
+        rio=rio,
+        show_options=show_options,
+        ss_type=ss_type,
+        trr=trr,
+        vvar_centers=vvar_centers,
+        vvars=vvars,
+    )
+    return v_3d_lmer_execute(params, execution)
+
+
+__all__ = [
+    "V3dLmerOutputs",
+    "V3dLmerParameters",
+    "V_3D_LMER_METADATA",
+    "v_3d_lmer",
+    "v_3d_lmer_params",
+]

niwrap_afni/afni/v_3d_local_acf.py

@@ -0,0 +1,224 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_LOCAL_ACF_METADATA = Metadata(
+    id="f02de9f266ae864cf54889181b4c744098070407.boutiques",
+    name="3dLocalACF",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dLocalAcfParameters = typing.TypedDict('V3dLocalAcfParameters', {
+    "__STYX_TYPE__": typing.Literal["3dLocalACF"],
+    "prefix": str,
+    "input_file": InputPathType,
+    "neighborhood": typing.NotRequired[str | None],
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "auto_mask": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dLocalACF": v_3d_local_acf_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 {
+        "3dLocalACF": v_3d_local_acf_outputs,
+    }.get(t)
+
+
+class V3dLocalAcfOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_local_acf(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output dataset with ACF estimates"""
+
+
+def v_3d_local_acf_params(
+    prefix: str,
+    input_file: InputPathType,
+    neighborhood: str | None = None,
+    mask_file: InputPathType | None = None,
+    auto_mask: bool = False,
+) -> V3dLocalAcfParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Prefix for output dataset.
+        input_file: Input time series dataset.
+        neighborhood: Neighborhood specification (e.g., SPHERE(25)).
+        mask_file: Dataset to mask the analysis.
+        auto_mask: Automatically generate brain mask from input dataset.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dLocalACF",
+        "prefix": prefix,
+        "input_file": input_file,
+        "auto_mask": auto_mask,
+    }
+    if neighborhood is not None:
+        params["neighborhood"] = neighborhood
+    if mask_file is not None:
+        params["mask_file"] = mask_file
+    return params
+
+
+def v_3d_local_acf_cargs(
+    params: V3dLocalAcfParameters,
+    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("3dLocalACF")
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    cargs.append(execution.input_file(params.get("input_file")))
+    if params.get("neighborhood") is not None:
+        cargs.extend([
+            "-nbhd",
+            params.get("neighborhood")
+        ])
+    if params.get("mask_file") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_file"))
+        ])
+    if params.get("auto_mask"):
+        cargs.append("-automask")
+    return cargs
+
+
+def v_3d_local_acf_outputs(
+    params: V3dLocalAcfParameters,
+    execution: Execution,
+) -> V3dLocalAcfOutputs:
+    """
+    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 = V3dLocalAcfOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + ".nii.gz"),
+    )
+    return ret
+
+
+def v_3d_local_acf_execute(
+    params: V3dLocalAcfParameters,
+    execution: Execution,
+) -> V3dLocalAcfOutputs:
+    """
+    Estimate the spatial AutoCorrelation Function (ACF) locally in a neighborhood
+    around each voxel.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dLocalAcfOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_local_acf_cargs(params, execution)
+    ret = v_3d_local_acf_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_local_acf(
+    prefix: str,
+    input_file: InputPathType,
+    neighborhood: str | None = None,
+    mask_file: InputPathType | None = None,
+    auto_mask: bool = False,
+    runner: Runner | None = None,
+) -> V3dLocalAcfOutputs:
+    """
+    Estimate the spatial AutoCorrelation Function (ACF) locally in a neighborhood
+    around each voxel.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Prefix for output dataset.
+        input_file: Input time series dataset.
+        neighborhood: Neighborhood specification (e.g., SPHERE(25)).
+        mask_file: Dataset to mask the analysis.
+        auto_mask: Automatically generate brain mask from input dataset.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dLocalAcfOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LOCAL_ACF_METADATA)
+    params = v_3d_local_acf_params(
+        prefix=prefix,
+        input_file=input_file,
+        neighborhood=neighborhood,
+        mask_file=mask_file,
+        auto_mask=auto_mask,
+    )
+    return v_3d_local_acf_execute(params, execution)
+
+
+__all__ = [
+    "V3dLocalAcfOutputs",
+    "V3dLocalAcfParameters",
+    "V_3D_LOCAL_ACF_METADATA",
+    "v_3d_local_acf",
+    "v_3d_local_acf_params",
+]