niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_isc.py

@@ -0,0 +1,298 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_ISC_METADATA = Metadata(
+    id="d937806e40a345507430d710b195292450cd9998.boutiques",
+    name="3dISC",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dIscParameters = typing.TypedDict('V3dIscParameters', {
+    "__STYX_TYPE__": typing.Literal["3dISC"],
+    "outfile_prefix": str,
+    "num_jobs": typing.NotRequired[float | None],
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "model_structure": str,
+    "qvar_centers": typing.NotRequired[str | None],
+    "quantitative_vars": typing.NotRequired[str | None],
+    "fisher_transform": bool,
+    "io_functions": typing.NotRequired[typing.Literal["AFNI", "R"] | None],
+    "data_table": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dISC": v_3d_isc_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 {
+        "3dISC": v_3d_isc_outputs,
+    }.get(t)
+
+
+class V3dIscOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_isc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    isc_output: OutputPathType
+    """Main output ISC file"""
+    tstat_output: OutputPathType
+    """T-statistic of ISC"""
+
+
+def v_3d_isc_params(
+    outfile_prefix: str,
+    model_structure: str,
+    data_table: str,
+    num_jobs: float | None = None,
+    mask_file: InputPathType | None = None,
+    qvar_centers: str | None = None,
+    quantitative_vars: str | None = None,
+    fisher_transform: bool = False,
+    io_functions: typing.Literal["AFNI", "R"] | None = None,
+) -> V3dIscParameters:
+    """
+    Build parameters.
+    
+    Args:
+        outfile_prefix: Output file name. For AFNI format, provide prefix only,\
+            with no view+suffix needed.
+        model_structure: Specify the model structure for all the variables. The\
+            expression FORMULA with more than one variable has to be surrounded\
+            within quotes.
+        data_table: List the data structure with a header as the first line.\
+            Has to occur last in the script.
+        num_jobs: Specify the number of jobs to run concurrently. Choose 1 for\
+            a single-processor computer.
+        mask_file: Process voxels inside this mask only. Default is no masking.
+        qvar_centers: Specify centering values for quantitative variables\
+            identified under -qVars. Multiple centers are separated by commas\
+            without spaces and should be within quotes.
+        quantitative_vars: Identify quantitative variables (or covariates). The\
+            list should be comma-separated and within quotes.
+        fisher_transform: Perform Fisher transformation on the response\
+            variable (input files) if it is a correlation value.
+        io_functions: Use AFNI's C io functions (default) or R's io functions.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dISC",
+        "outfile_prefix": outfile_prefix,
+        "model_structure": model_structure,
+        "fisher_transform": fisher_transform,
+        "data_table": data_table,
+    }
+    if num_jobs is not None:
+        params["num_jobs"] = num_jobs
+    if mask_file is not None:
+        params["mask_file"] = mask_file
+    if qvar_centers is not None:
+        params["qvar_centers"] = qvar_centers
+    if quantitative_vars is not None:
+        params["quantitative_vars"] = quantitative_vars
+    if io_functions is not None:
+        params["io_functions"] = io_functions
+    return params
+
+
+def v_3d_isc_cargs(
+    params: V3dIscParameters,
+    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("3dISC")
+    cargs.extend([
+        "-prefix",
+        params.get("outfile_prefix")
+    ])
+    if params.get("num_jobs") is not None:
+        cargs.extend([
+            "-jobs",
+            str(params.get("num_jobs"))
+        ])
+    if params.get("mask_file") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_file"))
+        ])
+    cargs.extend([
+        "-model",
+        params.get("model_structure")
+    ])
+    if params.get("qvar_centers") is not None:
+        cargs.extend([
+            "-qVarCenters",
+            params.get("qvar_centers")
+        ])
+    if params.get("quantitative_vars") is not None:
+        cargs.extend([
+            "-qVars",
+            params.get("quantitative_vars")
+        ])
+    if params.get("fisher_transform"):
+        cargs.append("-r2z")
+    if params.get("io_functions") is not None:
+        cargs.extend([
+            "-cio",
+            params.get("io_functions")
+        ])
+    cargs.extend([
+        "-dataTable",
+        params.get("data_table")
+    ])
+    return cargs
+
+
+def v_3d_isc_outputs(
+    params: V3dIscParameters,
+    execution: Execution,
+) -> V3dIscOutputs:
+    """
+    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 = V3dIscOutputs(
+        root=execution.output_file("."),
+        isc_output=execution.output_file(params.get("outfile_prefix") + "_ISC.nii"),
+        tstat_output=execution.output_file(params.get("outfile_prefix") + "_tstat.nii"),
+    )
+    return ret
+
+
+def v_3d_isc_execute(
+    params: V3dIscParameters,
+    execution: Execution,
+) -> V3dIscOutputs:
+    """
+    Program for Voxelwise Inter-Subject Correlation (ISC) Analysis using linear
+    mixed-effects modeling.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dIscOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_isc_cargs(params, execution)
+    ret = v_3d_isc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_isc(
+    outfile_prefix: str,
+    model_structure: str,
+    data_table: str,
+    num_jobs: float | None = None,
+    mask_file: InputPathType | None = None,
+    qvar_centers: str | None = None,
+    quantitative_vars: str | None = None,
+    fisher_transform: bool = False,
+    io_functions: typing.Literal["AFNI", "R"] | None = None,
+    runner: Runner | None = None,
+) -> V3dIscOutputs:
+    """
+    Program for Voxelwise Inter-Subject Correlation (ISC) Analysis using linear
+    mixed-effects modeling.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        outfile_prefix: Output file name. For AFNI format, provide prefix only,\
+            with no view+suffix needed.
+        model_structure: Specify the model structure for all the variables. The\
+            expression FORMULA with more than one variable has to be surrounded\
+            within quotes.
+        data_table: List the data structure with a header as the first line.\
+            Has to occur last in the script.
+        num_jobs: Specify the number of jobs to run concurrently. Choose 1 for\
+            a single-processor computer.
+        mask_file: Process voxels inside this mask only. Default is no masking.
+        qvar_centers: Specify centering values for quantitative variables\
+            identified under -qVars. Multiple centers are separated by commas\
+            without spaces and should be within quotes.
+        quantitative_vars: Identify quantitative variables (or covariates). The\
+            list should be comma-separated and within quotes.
+        fisher_transform: Perform Fisher transformation on the response\
+            variable (input files) if it is a correlation value.
+        io_functions: Use AFNI's C io functions (default) or R's io functions.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dIscOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ISC_METADATA)
+    params = v_3d_isc_params(
+        outfile_prefix=outfile_prefix,
+        num_jobs=num_jobs,
+        mask_file=mask_file,
+        model_structure=model_structure,
+        qvar_centers=qvar_centers,
+        quantitative_vars=quantitative_vars,
+        fisher_transform=fisher_transform,
+        io_functions=io_functions,
+        data_table=data_table,
+    )
+    return v_3d_isc_execute(params, execution)
+
+
+__all__ = [
+    "V3dIscOutputs",
+    "V3dIscParameters",
+    "V_3D_ISC_METADATA",
+    "v_3d_isc",
+    "v_3d_isc_params",
+]

niwrap_afni/afni/v_3d_kruskal_wallis.py

@@ -0,0 +1,231 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_KRUSKAL_WALLIS_METADATA = Metadata(
+    id="d8f52138ea0ac2f25d27a21c1fd03e57b216b428.boutiques",
+    name="3dKruskalWallis",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dKruskalWallisParameters = typing.TypedDict('V3dKruskalWallisParameters', {
+    "__STYX_TYPE__": typing.Literal["3dKruskalWallis"],
+    "levels": int,
+    "datasets": list[str],
+    "workmem": typing.NotRequired[int | None],
+    "voxel": typing.NotRequired[int | None],
+    "output": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dKruskalWallis": v_3d_kruskal_wallis_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 {
+        "3dKruskalWallis": v_3d_kruskal_wallis_outputs,
+    }.get(t)
+
+
+class V3dKruskalWallisOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_kruskal_wallis(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile_prefix: OutputPathType
+    """Output file containing Kruskal-Wallis statistics"""
+
+
+def v_3d_kruskal_wallis_params(
+    levels: int,
+    datasets: list[str],
+    output: str,
+    workmem: int | None = None,
+    voxel: int | None = None,
+) -> V3dKruskalWallisParameters:
+    """
+    Build parameters.
+    
+    Args:
+        levels: Number of treatments.
+        datasets: Data set for treatment #1 through to treatment #s. Specify\
+            sub-brick if more than one present.
+        output: Kruskal-Wallis statistics are written to file prefixname.
+        workmem: Number of megabytes of RAM to use for statistical workspace.
+        voxel: Screen output for voxel # num.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dKruskalWallis",
+        "levels": levels,
+        "datasets": datasets,
+        "output": output,
+    }
+    if workmem is not None:
+        params["workmem"] = workmem
+    if voxel is not None:
+        params["voxel"] = voxel
+    return params
+
+
+def v_3d_kruskal_wallis_cargs(
+    params: V3dKruskalWallisParameters,
+    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("3dKruskalWallis")
+    cargs.extend([
+        "-levels",
+        str(params.get("levels"))
+    ])
+    cargs.extend([
+        "-dset",
+        *params.get("datasets")
+    ])
+    if params.get("workmem") is not None:
+        cargs.extend([
+            "-workmem",
+            str(params.get("workmem"))
+        ])
+    if params.get("voxel") is not None:
+        cargs.extend([
+            "-voxel",
+            str(params.get("voxel"))
+        ])
+    cargs.extend([
+        "-out",
+        params.get("output")
+    ])
+    return cargs
+
+
+def v_3d_kruskal_wallis_outputs(
+    params: V3dKruskalWallisParameters,
+    execution: Execution,
+) -> V3dKruskalWallisOutputs:
+    """
+    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 = V3dKruskalWallisOutputs(
+        root=execution.output_file("."),
+        outfile_prefix=execution.output_file(params.get("output") + "+tlrc"),
+    )
+    return ret
+
+
+def v_3d_kruskal_wallis_execute(
+    params: V3dKruskalWallisParameters,
+    execution: Execution,
+) -> V3dKruskalWallisOutputs:
+    """
+    This program performs nonparametric Kruskal-Wallis test for comparison of
+    multiple treatments.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dKruskalWallisOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_kruskal_wallis_cargs(params, execution)
+    ret = v_3d_kruskal_wallis_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_kruskal_wallis(
+    levels: int,
+    datasets: list[str],
+    output: str,
+    workmem: int | None = None,
+    voxel: int | None = None,
+    runner: Runner | None = None,
+) -> V3dKruskalWallisOutputs:
+    """
+    This program performs nonparametric Kruskal-Wallis test for comparison of
+    multiple treatments.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        levels: Number of treatments.
+        datasets: Data set for treatment #1 through to treatment #s. Specify\
+            sub-brick if more than one present.
+        output: Kruskal-Wallis statistics are written to file prefixname.
+        workmem: Number of megabytes of RAM to use for statistical workspace.
+        voxel: Screen output for voxel # num.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dKruskalWallisOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_KRUSKAL_WALLIS_METADATA)
+    params = v_3d_kruskal_wallis_params(
+        levels=levels,
+        datasets=datasets,
+        workmem=workmem,
+        voxel=voxel,
+        output=output,
+    )
+    return v_3d_kruskal_wallis_execute(params, execution)
+
+
+__all__ = [
+    "V3dKruskalWallisOutputs",
+    "V3dKruskalWallisParameters",
+    "V_3D_KRUSKAL_WALLIS_METADATA",
+    "v_3d_kruskal_wallis",
+    "v_3d_kruskal_wallis_params",
+]