niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3dttest__.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DTTEST___METADATA = Metadata(
+    id="9816ba0be883f397c48e16a5a699629ad3d438ae.boutiques",
+    name="3dttest++",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dttestParameters = typing.TypedDict('V3dttestParameters', {
+    "__STYX_TYPE__": typing.Literal["3dttest++"],
+    "setA": list[str],
+    "setB": typing.NotRequired[list[str] | None],
+    "setA_long": typing.NotRequired[list[str] | None],
+    "setB_long": typing.NotRequired[list[str] | None],
+    "covariates": typing.NotRequired[InputPathType | None],
+    "labelA": typing.NotRequired[str | None],
+    "labelB": typing.NotRequired[str | None],
+    "setweightA": typing.NotRequired[InputPathType | None],
+    "setweightB": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "resid": typing.NotRequired[str | None],
+    "paired": bool,
+    "unpooled": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "exblur": typing.NotRequired[int | None],
+    "randomsign": bool,
+    "permute": bool,
+    "ETAC": bool,
+    "ETAC_blur": typing.NotRequired[list[float] | None],
+    "ETAC_opt": typing.NotRequired[list[str] | None],
+    "seed": 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 {
+        "3dttest++": v_3dttest___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 {
+        "3dttest++": v_3dttest___outputs,
+    }.get(t)
+
+
+class V3dttestOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dttest__(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType | None
+    """Main output dataset"""
+    residuals: OutputPathType | None
+    """Output residuals dataset"""
+
+
+def v_3dttest___params(
+    set_a: list[str],
+    set_b: list[str] | None = None,
+    set_a_long: list[str] | None = None,
+    set_b_long: list[str] | None = None,
+    covariates: InputPathType | None = None,
+    label_a: str | None = None,
+    label_b: str | None = None,
+    setweight_a: InputPathType | None = None,
+    setweight_b: InputPathType | None = None,
+    prefix: str | None = None,
+    resid: str | None = None,
+    paired: bool = False,
+    unpooled: bool = False,
+    mask: InputPathType | None = None,
+    exblur: int | None = None,
+    randomsign: bool = False,
+    permute: bool = False,
+    etac: bool = False,
+    etac_blur: list[float] | None = None,
+    etac_opt: list[str] | None = None,
+    seed: float | None = None,
+) -> V3dttestParameters:
+    """
+    Build parameters.
+    
+    Args:
+        set_a: Set A in short form, e.g., 'a+tlrc[3]' b+tlrc[3] ...'.
+        set_b: Set B in short form, e.g., 'x+tlrc[3]' y+tlrc[3] ...'.
+        set_a_long: Specify an overall name for the set of datasets (Long\
+            form). Example: -setA Green sub001 a+tlrc[3] sub002 b+tlrc[3] ...
+        set_b_long: Specify an overall name for the set of datasets (Long\
+            form). Example: -setB Blue sub001 x+tlrc[3] sub002 y+tlrc[3] ...
+        covariates: File containing covariates.
+        label_a: Label for the set (for Set A). Limited to 12 characters.
+        label_b: Label for the set (for Set B). Limited to 12 characters.
+        setweight_a: File with voxel-wise weights for -setA datasets.
+        setweight_b: File with voxel-wise weights for -setB datasets.
+        prefix: Output the prefix name of the dataset result. For surface-based\
+            datasets, use -prefix p.niml.dset or -prefix p.gii.dset.
+        resid: Residuals will be output into a dataset with the given prefix.
+        paired: Specify to use a paired-sample t-test to compare setA and setB.\
+            Both sets must have the same cardinality.
+        unpooled: Specify separate variance estimates for setA and setB (not\
+            pooled together).
+        mask: Set mask for dataset analysis.
+        exblur: Add extra Gaussian blurring kernel FWHM (mm). Example: -exblur\
+            6.
+        randomsign: Randomize signs of datasets. Used with output from -resid\
+            to generate null hypothesis statistics.
+        permute: With -randomsign, adds inter-set permutation to randomization\
+            when both sets are used.
+        etac: Apply the Equitable Thresholding And Clustering (ETAC) method for\
+            thresholding results.
+        etac_blur: List of multiple levels of spatial blurring for ETAC.\
+            Example: -ETAC_blur 4 6.
+        etac_opt: Specify options for ETAC. Example: -ETAC_opt\
+            NN=2:sid=2:hpow=0,2:pthr=0.01,0.005,0.002,0.01:name=Fred.
+        seed: Random number seed for -randomsign and -permute/ETAC.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dttest++",
+        "setA": set_a,
+        "paired": paired,
+        "unpooled": unpooled,
+        "randomsign": randomsign,
+        "permute": permute,
+        "ETAC": etac,
+    }
+    if set_b is not None:
+        params["setB"] = set_b
+    if set_a_long is not None:
+        params["setA_long"] = set_a_long
+    if set_b_long is not None:
+        params["setB_long"] = set_b_long
+    if covariates is not None:
+        params["covariates"] = covariates
+    if label_a is not None:
+        params["labelA"] = label_a
+    if label_b is not None:
+        params["labelB"] = label_b
+    if setweight_a is not None:
+        params["setweightA"] = setweight_a
+    if setweight_b is not None:
+        params["setweightB"] = setweight_b
+    if prefix is not None:
+        params["prefix"] = prefix
+    if resid is not None:
+        params["resid"] = resid
+    if mask is not None:
+        params["mask"] = mask
+    if exblur is not None:
+        params["exblur"] = exblur
+    if etac_blur is not None:
+        params["ETAC_blur"] = etac_blur
+    if etac_opt is not None:
+        params["ETAC_opt"] = etac_opt
+    if seed is not None:
+        params["seed"] = seed
+    return params
+
+
+def v_3dttest___cargs(
+    params: V3dttestParameters,
+    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("3dttest++")
+    cargs.extend([
+        "-setA",
+        *params.get("setA")
+    ])
+    if params.get("setB") is not None:
+        cargs.extend([
+            "-setB",
+            *params.get("setB")
+        ])
+    if params.get("setA_long") is not None:
+        cargs.extend([
+            "-setA",
+            *params.get("setA_long")
+        ])
+    if params.get("setB_long") is not None:
+        cargs.extend([
+            "-setB",
+            *params.get("setB_long")
+        ])
+    if params.get("covariates") is not None:
+        cargs.extend([
+            "-covariates",
+            execution.input_file(params.get("covariates"))
+        ])
+    if params.get("labelA") is not None:
+        cargs.extend([
+            "-labelA",
+            params.get("labelA")
+        ])
+    if params.get("labelB") is not None:
+        cargs.extend([
+            "-labelB",
+            params.get("labelB")
+        ])
+    if params.get("setweightA") is not None:
+        cargs.extend([
+            "-setweightA",
+            execution.input_file(params.get("setweightA"))
+        ])
+    if params.get("setweightB") is not None:
+        cargs.extend([
+            "-setweightB",
+            execution.input_file(params.get("setweightB"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("resid") is not None:
+        cargs.extend([
+            "-resid",
+            params.get("resid")
+        ])
+    if params.get("paired"):
+        cargs.append("-paired")
+    if params.get("unpooled"):
+        cargs.append("-unpooled")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("exblur") is not None:
+        cargs.extend([
+            "-exblur",
+            str(params.get("exblur"))
+        ])
+    if params.get("randomsign"):
+        cargs.append("-randomsign")
+    if params.get("permute"):
+        cargs.append("-permute")
+    if params.get("ETAC"):
+        cargs.append("-ETAC")
+    if params.get("ETAC_blur") is not None:
+        cargs.extend([
+            "-ETAC_blur",
+            *map(str, params.get("ETAC_blur"))
+        ])
+    if params.get("ETAC_opt") is not None:
+        cargs.extend([
+            "-ETAC_opt",
+            *params.get("ETAC_opt")
+        ])
+    if params.get("seed") is not None:
+        cargs.extend([
+            "-seed",
+            str(params.get("seed"))
+        ])
+    return cargs
+
+
+def v_3dttest___outputs(
+    params: V3dttestParameters,
+    execution: Execution,
+) -> V3dttestOutputs:
+    """
+    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 = V3dttestOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+        residuals=execution.output_file(params.get("resid") + ".nii.gz") if (params.get("resid") is not None) else None,
+    )
+    return ret
+
+
+def v_3dttest___execute(
+    params: V3dttestParameters,
+    execution: Execution,
+) -> V3dttestOutputs:
+    """
+    Gosset (Student) t-test of sets of 3D datasets in AFNI.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dttestOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dttest___cargs(params, execution)
+    ret = v_3dttest___outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dttest__(
+    set_a: list[str],
+    set_b: list[str] | None = None,
+    set_a_long: list[str] | None = None,
+    set_b_long: list[str] | None = None,
+    covariates: InputPathType | None = None,
+    label_a: str | None = None,
+    label_b: str | None = None,
+    setweight_a: InputPathType | None = None,
+    setweight_b: InputPathType | None = None,
+    prefix: str | None = None,
+    resid: str | None = None,
+    paired: bool = False,
+    unpooled: bool = False,
+    mask: InputPathType | None = None,
+    exblur: int | None = None,
+    randomsign: bool = False,
+    permute: bool = False,
+    etac: bool = False,
+    etac_blur: list[float] | None = None,
+    etac_opt: list[str] | None = None,
+    seed: float | None = None,
+    runner: Runner | None = None,
+) -> V3dttestOutputs:
+    """
+    Gosset (Student) t-test of sets of 3D datasets in AFNI.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        set_a: Set A in short form, e.g., 'a+tlrc[3]' b+tlrc[3] ...'.
+        set_b: Set B in short form, e.g., 'x+tlrc[3]' y+tlrc[3] ...'.
+        set_a_long: Specify an overall name for the set of datasets (Long\
+            form). Example: -setA Green sub001 a+tlrc[3] sub002 b+tlrc[3] ...
+        set_b_long: Specify an overall name for the set of datasets (Long\
+            form). Example: -setB Blue sub001 x+tlrc[3] sub002 y+tlrc[3] ...
+        covariates: File containing covariates.
+        label_a: Label for the set (for Set A). Limited to 12 characters.
+        label_b: Label for the set (for Set B). Limited to 12 characters.
+        setweight_a: File with voxel-wise weights for -setA datasets.
+        setweight_b: File with voxel-wise weights for -setB datasets.
+        prefix: Output the prefix name of the dataset result. For surface-based\
+            datasets, use -prefix p.niml.dset or -prefix p.gii.dset.
+        resid: Residuals will be output into a dataset with the given prefix.
+        paired: Specify to use a paired-sample t-test to compare setA and setB.\
+            Both sets must have the same cardinality.
+        unpooled: Specify separate variance estimates for setA and setB (not\
+            pooled together).
+        mask: Set mask for dataset analysis.
+        exblur: Add extra Gaussian blurring kernel FWHM (mm). Example: -exblur\
+            6.
+        randomsign: Randomize signs of datasets. Used with output from -resid\
+            to generate null hypothesis statistics.
+        permute: With -randomsign, adds inter-set permutation to randomization\
+            when both sets are used.
+        etac: Apply the Equitable Thresholding And Clustering (ETAC) method for\
+            thresholding results.
+        etac_blur: List of multiple levels of spatial blurring for ETAC.\
+            Example: -ETAC_blur 4 6.
+        etac_opt: Specify options for ETAC. Example: -ETAC_opt\
+            NN=2:sid=2:hpow=0,2:pthr=0.01,0.005,0.002,0.01:name=Fred.
+        seed: Random number seed for -randomsign and -permute/ETAC.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dttestOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DTTEST___METADATA)
+    params = v_3dttest___params(
+        set_a=set_a,
+        set_b=set_b,
+        set_a_long=set_a_long,
+        set_b_long=set_b_long,
+        covariates=covariates,
+        label_a=label_a,
+        label_b=label_b,
+        setweight_a=setweight_a,
+        setweight_b=setweight_b,
+        prefix=prefix,
+        resid=resid,
+        paired=paired,
+        unpooled=unpooled,
+        mask=mask,
+        exblur=exblur,
+        randomsign=randomsign,
+        permute=permute,
+        etac=etac,
+        etac_blur=etac_blur,
+        etac_opt=etac_opt,
+        seed=seed,
+    )
+    return v_3dttest___execute(params, execution)
+
+
+__all__ = [
+    "V3dttestOutputs",
+    "V3dttestParameters",
+    "V_3DTTEST___METADATA",
+    "v_3dttest__",
+    "v_3dttest___params",
+]