niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_anova2.py

@@ -0,0 +1,515 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_ANOVA2_METADATA = Metadata(
+    id="ebf600e872cacd3686c204e18def40bac83877e7.boutiques",
+    name="3dANOVA2",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dAnova2Parameters = typing.TypedDict('V3dAnova2Parameters', {
+    "__STYX_TYPE__": typing.Literal["3dANOVA2"],
+    "type": int,
+    "alevels": int,
+    "blevels": int,
+    "dataset": typing.NotRequired[list[str] | None],
+    "voxel": typing.NotRequired[int | None],
+    "diskspace": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "ftr": typing.NotRequired[str | None],
+    "fa": typing.NotRequired[str | None],
+    "fb": typing.NotRequired[str | None],
+    "fab": typing.NotRequired[str | None],
+    "amean": typing.NotRequired[str | None],
+    "bmean": typing.NotRequired[str | None],
+    "xmean": typing.NotRequired[str | None],
+    "adiff": typing.NotRequired[str | None],
+    "bdiff": typing.NotRequired[str | None],
+    "xdiff": typing.NotRequired[str | None],
+    "acontr": typing.NotRequired[str | None],
+    "bcontr": typing.NotRequired[str | None],
+    "xcontr": typing.NotRequired[str | None],
+    "bucket": typing.NotRequired[str | None],
+    "old_method": bool,
+    "ok": bool,
+    "assume_sph": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dANOVA2": v_3d_anova2_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 {
+        "3dANOVA2": v_3d_anova2_outputs,
+    }.get(t)
+
+
+class V3dAnova2Outputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_anova2(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_ftr: OutputPathType | None
+    """F-statistic for treatment effect output file"""
+    output_fa: OutputPathType | None
+    """F-statistic for factor A effect output file"""
+    output_fb: OutputPathType | None
+    """F-statistic for factor B effect output file"""
+    output_fab: OutputPathType | None
+    """F-statistic for interaction output file"""
+    output_amean: OutputPathType | None
+    """Estimate mean of factor A level output file"""
+    output_bmean: OutputPathType | None
+    """Estimate mean of factor B level output file"""
+    output_xmean: OutputPathType | None
+    """Estimate mean of cell at level i of factor A and level j of factor B
+    output file"""
+    output_adiff: OutputPathType | None
+    """Difference between levels i and j of factor A output file"""
+    output_bdiff: OutputPathType | None
+    """Difference between levels i and j of factor B output file"""
+    output_xdiff: OutputPathType | None
+    """Difference between cell mean at A=i, B=j and cell mean at A=k, B=l output
+    file"""
+    output_acontr: OutputPathType | None
+    """Contrast in factor A levels output file"""
+    output_bcontr: OutputPathType | None
+    """Contrast in factor B levels output file"""
+    output_xcontr: OutputPathType | None
+    """Contrast in cell means output file"""
+    output_bucket: OutputPathType | None
+    """Create one AFNI 'bucket' dataset file"""
+
+
+def v_3d_anova2_params(
+    type_: int,
+    alevels: int,
+    blevels: int,
+    dataset: list[str] | None = None,
+    voxel: int | None = None,
+    diskspace: bool = False,
+    mask: InputPathType | None = None,
+    ftr: str | None = None,
+    fa: str | None = None,
+    fb: str | None = None,
+    fab: str | None = None,
+    amean: str | None = None,
+    bmean: str | None = None,
+    xmean: str | None = None,
+    adiff: str | None = None,
+    bdiff: str | None = None,
+    xdiff: str | None = None,
+    acontr: str | None = None,
+    bcontr: str | None = None,
+    xcontr: str | None = None,
+    bucket: str | None = None,
+    old_method: bool = False,
+    ok: bool = False,
+    assume_sph: bool = False,
+) -> V3dAnova2Parameters:
+    """
+    Build parameters.
+    
+    Args:
+        type_: Type of ANOVA model to be used: 1=fixed, 2=random, 3=mixed.
+        alevels: Number of levels of factor A.
+        blevels: Number of levels of factor B.
+        dataset: Data set for levels of factor A and factor B.
+        voxel: Screen output for voxel number.
+        diskspace: Print out disk space required for program execution.
+        mask: Use sub-brick #0 of dataset 'mset' to define which voxels to\
+            process.
+        ftr: F-statistic for treatment effect.
+        fa: F-statistic for factor A effect.
+        fb: F-statistic for factor B effect.
+        fab: F-statistic for interaction.
+        amean: Estimate mean of factor A level.
+        bmean: Estimate mean of factor B level.
+        xmean: Estimate mean of cell at level i of factor A and level j of\
+            factor B.
+        adiff: Difference between levels i and j of factor A.
+        bdiff: Difference between levels i and j of factor B.
+        xdiff: Difference between cell mean at A=i, B=j and cell mean at A=k,\
+            B=l.
+        acontr: Contrast in factor A levels.
+        bcontr: Contrast in factor B levels.
+        xcontr: Contrast in cell means.
+        bucket: Create one AFNI 'bucket' dataset whose sub-bricks are obtained\
+            by concatenating the above output files.
+        old_method: Request to perform ANOVA using the previous functionality\
+            (requires -OK, also).
+        ok: Confirm understanding that contrasts that do not sum to zero have\
+            inflated t-stats, and contrasts that do sum to zero assume sphericity\
+            (to be used with -old_method).
+        assume_sph: Assume sphericity (zero-sum contrasts, only). This allows\
+            use of the old_method for computing contrasts which sum to zero.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dANOVA2",
+        "type": type_,
+        "alevels": alevels,
+        "blevels": blevels,
+        "diskspace": diskspace,
+        "old_method": old_method,
+        "ok": ok,
+        "assume_sph": assume_sph,
+    }
+    if dataset is not None:
+        params["dataset"] = dataset
+    if voxel is not None:
+        params["voxel"] = voxel
+    if mask is not None:
+        params["mask"] = mask
+    if ftr is not None:
+        params["ftr"] = ftr
+    if fa is not None:
+        params["fa"] = fa
+    if fb is not None:
+        params["fb"] = fb
+    if fab is not None:
+        params["fab"] = fab
+    if amean is not None:
+        params["amean"] = amean
+    if bmean is not None:
+        params["bmean"] = bmean
+    if xmean is not None:
+        params["xmean"] = xmean
+    if adiff is not None:
+        params["adiff"] = adiff
+    if bdiff is not None:
+        params["bdiff"] = bdiff
+    if xdiff is not None:
+        params["xdiff"] = xdiff
+    if acontr is not None:
+        params["acontr"] = acontr
+    if bcontr is not None:
+        params["bcontr"] = bcontr
+    if xcontr is not None:
+        params["xcontr"] = xcontr
+    if bucket is not None:
+        params["bucket"] = bucket
+    return params
+
+
+def v_3d_anova2_cargs(
+    params: V3dAnova2Parameters,
+    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("3dANOVA2")
+    cargs.extend([
+        "-type",
+        str(params.get("type"))
+    ])
+    cargs.extend([
+        "-alevels",
+        str(params.get("alevels"))
+    ])
+    cargs.extend([
+        "-blevels",
+        str(params.get("blevels"))
+    ])
+    if params.get("dataset") is not None:
+        cargs.extend([
+            "-dset",
+            *params.get("dataset")
+        ])
+    if params.get("voxel") is not None:
+        cargs.extend([
+            "-voxel",
+            str(params.get("voxel"))
+        ])
+    if params.get("diskspace"):
+        cargs.append("-diskspace")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("ftr") is not None:
+        cargs.extend([
+            "-ftr",
+            params.get("ftr")
+        ])
+    if params.get("fa") is not None:
+        cargs.extend([
+            "-fa",
+            params.get("fa")
+        ])
+    if params.get("fb") is not None:
+        cargs.extend([
+            "-fb",
+            params.get("fb")
+        ])
+    if params.get("fab") is not None:
+        cargs.extend([
+            "-fab",
+            params.get("fab")
+        ])
+    if params.get("amean") is not None:
+        cargs.extend([
+            "-amean",
+            params.get("amean")
+        ])
+    if params.get("bmean") is not None:
+        cargs.extend([
+            "-bmean",
+            params.get("bmean")
+        ])
+    if params.get("xmean") is not None:
+        cargs.extend([
+            "-xmean",
+            params.get("xmean")
+        ])
+    if params.get("adiff") is not None:
+        cargs.extend([
+            "-adiff",
+            params.get("adiff")
+        ])
+    if params.get("bdiff") is not None:
+        cargs.extend([
+            "-bdiff",
+            params.get("bdiff")
+        ])
+    if params.get("xdiff") is not None:
+        cargs.extend([
+            "-xdiff",
+            params.get("xdiff")
+        ])
+    if params.get("acontr") is not None:
+        cargs.extend([
+            "-acontr",
+            params.get("acontr")
+        ])
+    if params.get("bcontr") is not None:
+        cargs.extend([
+            "-bcontr",
+            params.get("bcontr")
+        ])
+    if params.get("xcontr") is not None:
+        cargs.extend([
+            "-xcontr",
+            params.get("xcontr")
+        ])
+    if params.get("bucket") is not None:
+        cargs.extend([
+            "-bucket",
+            params.get("bucket")
+        ])
+    if params.get("old_method"):
+        cargs.append("-old_method")
+    if params.get("ok"):
+        cargs.append("-OK")
+    if params.get("assume_sph"):
+        cargs.append("-assume_sph")
+    return cargs
+
+
+def v_3d_anova2_outputs(
+    params: V3dAnova2Parameters,
+    execution: Execution,
+) -> V3dAnova2Outputs:
+    """
+    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 = V3dAnova2Outputs(
+        root=execution.output_file("."),
+        output_ftr=execution.output_file(params.get("ftr") + ".+tlrc") if (params.get("ftr") is not None) else None,
+        output_fa=execution.output_file(params.get("fa") + ".+tlrc") if (params.get("fa") is not None) else None,
+        output_fb=execution.output_file(params.get("fb") + ".+tlrc") if (params.get("fb") is not None) else None,
+        output_fab=execution.output_file(params.get("fab") + ".+tlrc") if (params.get("fab") is not None) else None,
+        output_amean=execution.output_file(params.get("amean") + ".+tlrc") if (params.get("amean") is not None) else None,
+        output_bmean=execution.output_file(params.get("bmean") + ".+tlrc") if (params.get("bmean") is not None) else None,
+        output_xmean=execution.output_file(params.get("xmean") + ".+tlrc") if (params.get("xmean") is not None) else None,
+        output_adiff=execution.output_file(params.get("adiff") + ".+tlrc") if (params.get("adiff") is not None) else None,
+        output_bdiff=execution.output_file(params.get("bdiff") + ".+tlrc") if (params.get("bdiff") is not None) else None,
+        output_xdiff=execution.output_file(params.get("xdiff") + ".+tlrc") if (params.get("xdiff") is not None) else None,
+        output_acontr=execution.output_file(params.get("acontr") + ".+tlrc") if (params.get("acontr") is not None) else None,
+        output_bcontr=execution.output_file(params.get("bcontr") + ".+tlrc") if (params.get("bcontr") is not None) else None,
+        output_xcontr=execution.output_file(params.get("xcontr") + ".+tlrc") if (params.get("xcontr") is not None) else None,
+        output_bucket=execution.output_file(params.get("bucket") + ".+tlrc") if (params.get("bucket") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_anova2_execute(
+    params: V3dAnova2Parameters,
+    execution: Execution,
+) -> V3dAnova2Outputs:
+    """
+    This program performs a two-factor Analysis of Variance (ANOVA) on 3D datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dAnova2Outputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_anova2_cargs(params, execution)
+    ret = v_3d_anova2_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_anova2(
+    type_: int,
+    alevels: int,
+    blevels: int,
+    dataset: list[str] | None = None,
+    voxel: int | None = None,
+    diskspace: bool = False,
+    mask: InputPathType | None = None,
+    ftr: str | None = None,
+    fa: str | None = None,
+    fb: str | None = None,
+    fab: str | None = None,
+    amean: str | None = None,
+    bmean: str | None = None,
+    xmean: str | None = None,
+    adiff: str | None = None,
+    bdiff: str | None = None,
+    xdiff: str | None = None,
+    acontr: str | None = None,
+    bcontr: str | None = None,
+    xcontr: str | None = None,
+    bucket: str | None = None,
+    old_method: bool = False,
+    ok: bool = False,
+    assume_sph: bool = False,
+    runner: Runner | None = None,
+) -> V3dAnova2Outputs:
+    """
+    This program performs a two-factor Analysis of Variance (ANOVA) on 3D datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        type_: Type of ANOVA model to be used: 1=fixed, 2=random, 3=mixed.
+        alevels: Number of levels of factor A.
+        blevels: Number of levels of factor B.
+        dataset: Data set for levels of factor A and factor B.
+        voxel: Screen output for voxel number.
+        diskspace: Print out disk space required for program execution.
+        mask: Use sub-brick #0 of dataset 'mset' to define which voxels to\
+            process.
+        ftr: F-statistic for treatment effect.
+        fa: F-statistic for factor A effect.
+        fb: F-statistic for factor B effect.
+        fab: F-statistic for interaction.
+        amean: Estimate mean of factor A level.
+        bmean: Estimate mean of factor B level.
+        xmean: Estimate mean of cell at level i of factor A and level j of\
+            factor B.
+        adiff: Difference between levels i and j of factor A.
+        bdiff: Difference between levels i and j of factor B.
+        xdiff: Difference between cell mean at A=i, B=j and cell mean at A=k,\
+            B=l.
+        acontr: Contrast in factor A levels.
+        bcontr: Contrast in factor B levels.
+        xcontr: Contrast in cell means.
+        bucket: Create one AFNI 'bucket' dataset whose sub-bricks are obtained\
+            by concatenating the above output files.
+        old_method: Request to perform ANOVA using the previous functionality\
+            (requires -OK, also).
+        ok: Confirm understanding that contrasts that do not sum to zero have\
+            inflated t-stats, and contrasts that do sum to zero assume sphericity\
+            (to be used with -old_method).
+        assume_sph: Assume sphericity (zero-sum contrasts, only). This allows\
+            use of the old_method for computing contrasts which sum to zero.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dAnova2Outputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ANOVA2_METADATA)
+    params = v_3d_anova2_params(
+        type_=type_,
+        alevels=alevels,
+        blevels=blevels,
+        dataset=dataset,
+        voxel=voxel,
+        diskspace=diskspace,
+        mask=mask,
+        ftr=ftr,
+        fa=fa,
+        fb=fb,
+        fab=fab,
+        amean=amean,
+        bmean=bmean,
+        xmean=xmean,
+        adiff=adiff,
+        bdiff=bdiff,
+        xdiff=xdiff,
+        acontr=acontr,
+        bcontr=bcontr,
+        xcontr=xcontr,
+        bucket=bucket,
+        old_method=old_method,
+        ok=ok,
+        assume_sph=assume_sph,
+    )
+    return v_3d_anova2_execute(params, execution)
+
+
+__all__ = [
+    "V3dAnova2Outputs",
+    "V3dAnova2Parameters",
+    "V_3D_ANOVA2_METADATA",
+    "v_3d_anova2",
+    "v_3d_anova2_params",
+]