niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3dsvm.py

@@ -0,0 +1,518 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DSVM_METADATA = Metadata(
+    id="561addc870b41a8529b3ab4135131a6bc7b9089a.boutiques",
+    name="3dsvm",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dsvmParameters = typing.TypedDict('V3dsvmParameters', {
+    "__STYX_TYPE__": typing.Literal["3dsvm"],
+    "train_vol": typing.NotRequired[InputPathType | None],
+    "train_labels": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "no_model_mask": bool,
+    "model": str,
+    "alpha": typing.NotRequired[str | None],
+    "bucket": typing.NotRequired[str | None],
+    "type": typing.NotRequired[typing.Literal["classification", "regression"] | None],
+    "c_value": typing.NotRequired[float | None],
+    "epsilon": typing.NotRequired[float | None],
+    "kernel": typing.NotRequired[typing.Literal["linear", "polynomial", "rbf", "sigmoid"] | None],
+    "d_value": typing.NotRequired[float | None],
+    "gamma": typing.NotRequired[float | None],
+    "s_value": typing.NotRequired[float | None],
+    "r_value": typing.NotRequired[float | None],
+    "max_iterations": typing.NotRequired[float | None],
+    "wout": bool,
+    "test_vol": typing.NotRequired[InputPathType | None],
+    "predictions": typing.NotRequired[str | None],
+    "classout": bool,
+    "nopred_censored": bool,
+    "nodetrend": bool,
+    "nopred_scale": bool,
+    "test_labels": typing.NotRequired[InputPathType | None],
+    "multiclass": typing.NotRequired[typing.Literal["DAG", "vote"] | None],
+    "help": bool,
+    "version": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dsvm": v_3dsvm_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 {
+        "3dsvm": v_3dsvm_outputs,
+    }.get(t)
+
+
+class V3dsvmOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dsvm(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_model: OutputPathType
+    """Output model file in .1D format."""
+    out_alpha: OutputPathType
+    """Output alphas file in .1D format."""
+    out_bucket: OutputPathType
+    """Output bucket file in .1D format."""
+    out_predictions: OutputPathType
+    """Output predictions file in .1D format."""
+
+
+def v_3dsvm_params(
+    model: str,
+    train_vol: InputPathType | None = None,
+    train_labels: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    no_model_mask: bool = False,
+    alpha: str | None = None,
+    bucket: str | None = None,
+    type_: typing.Literal["classification", "regression"] | None = None,
+    c_value: float | None = None,
+    epsilon: float | None = None,
+    kernel: typing.Literal["linear", "polynomial", "rbf", "sigmoid"] | None = None,
+    d_value: float | None = None,
+    gamma: float | None = None,
+    s_value: float | None = None,
+    r_value: float | None = None,
+    max_iterations: float | None = None,
+    wout: bool = False,
+    test_vol: InputPathType | None = None,
+    predictions: str | None = None,
+    classout: bool = False,
+    nopred_censored: bool = False,
+    nodetrend: bool = False,
+    nopred_scale: bool = False,
+    test_labels: InputPathType | None = None,
+    multiclass: typing.Literal["DAG", "vote"] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> V3dsvmParameters:
+    """
+    Build parameters.
+    
+    Args:
+        model: The basename for the model brik containing the SVM model during\
+            training or testing.
+        train_vol: A 3D+t AFNI brik dataset to be used for training.
+        train_labels: Filename of class category .1D labels corresponding to\
+            the stimulus paradigm for the training data set.
+        mask: Specify a mask dataset to only perform the analysis on non-zero\
+            mask voxels.
+        no_model_mask: Flag to enable the omission of a mask file. Required if\
+            '-mask' is not used.
+        alpha: Write the alphas to a specified .1D file.
+        bucket: Outputs the sum of weighted linear support vectors written out\
+            to a functional (fim) brik file.
+        type_: Specify type: classification (default) or regression.
+        c_value: Control SVM model complexity (C value).
+        epsilon: Specify epsilon for regression.
+        kernel: Specify type of kernel function.
+        d_value: D parameter in polynomial kernel.
+        gamma: Gamma parameter in rbf kernel.
+        s_value: S parameter in sigmoid/poly kernel.
+        r_value: R parameter in sigmoid/poly kernel.
+        max_iterations: Specify the maximum number of iterations for the\
+            optimization. Default is 1 million.
+        wout: Flag to output sum of weighted linear support vectors to the\
+            bucket file.
+        test_vol: A 3D or 3D+t AFNI brik dataset to be used for testing.
+        predictions: Basename for .1D prediction files.
+        classout: Flag to specify that prediction files should be\
+            integer-valued, corresponding to class category decisions.
+        nopred_censored: Do not write predicted values for censored time-points\
+            to predictions file.
+        nodetrend: Flag to specify that prediction files should NOT be linearly\
+            detrended.
+        nopred_scale: Do not scale predictions. Values below 0.0 correspond to\
+            (class A) and values above 0.0 to (class B).
+        test_labels: Filename of 'true' class category .1D labels for the test\
+            dataset.
+        multiclass: Specify the multiclass algorithm for classification.
+        help_: Print help message.
+        version: Print version history.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dsvm",
+        "no_model_mask": no_model_mask,
+        "model": model,
+        "wout": wout,
+        "classout": classout,
+        "nopred_censored": nopred_censored,
+        "nodetrend": nodetrend,
+        "nopred_scale": nopred_scale,
+        "help": help_,
+        "version": version,
+    }
+    if train_vol is not None:
+        params["train_vol"] = train_vol
+    if train_labels is not None:
+        params["train_labels"] = train_labels
+    if mask is not None:
+        params["mask"] = mask
+    if alpha is not None:
+        params["alpha"] = alpha
+    if bucket is not None:
+        params["bucket"] = bucket
+    if type_ is not None:
+        params["type"] = type_
+    if c_value is not None:
+        params["c_value"] = c_value
+    if epsilon is not None:
+        params["epsilon"] = epsilon
+    if kernel is not None:
+        params["kernel"] = kernel
+    if d_value is not None:
+        params["d_value"] = d_value
+    if gamma is not None:
+        params["gamma"] = gamma
+    if s_value is not None:
+        params["s_value"] = s_value
+    if r_value is not None:
+        params["r_value"] = r_value
+    if max_iterations is not None:
+        params["max_iterations"] = max_iterations
+    if test_vol is not None:
+        params["test_vol"] = test_vol
+    if predictions is not None:
+        params["predictions"] = predictions
+    if test_labels is not None:
+        params["test_labels"] = test_labels
+    if multiclass is not None:
+        params["multiclass"] = multiclass
+    return params
+
+
+def v_3dsvm_cargs(
+    params: V3dsvmParameters,
+    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("3dsvm")
+    if params.get("train_vol") is not None:
+        cargs.extend([
+            "-trainvol",
+            execution.input_file(params.get("train_vol"))
+        ])
+    if params.get("train_labels") is not None:
+        cargs.extend([
+            "-trainlabels",
+            execution.input_file(params.get("train_labels"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("no_model_mask"):
+        cargs.append("-nomodelmask")
+    cargs.extend([
+        "-model",
+        params.get("model")
+    ])
+    if params.get("alpha") is not None:
+        cargs.extend([
+            "-alpha",
+            params.get("alpha")
+        ])
+    if params.get("bucket") is not None:
+        cargs.extend([
+            "-bucket",
+            params.get("bucket")
+        ])
+    if params.get("type") is not None:
+        cargs.extend([
+            "-type",
+            params.get("type")
+        ])
+    if params.get("c_value") is not None:
+        cargs.extend([
+            "-c",
+            str(params.get("c_value"))
+        ])
+    if params.get("epsilon") is not None:
+        cargs.extend([
+            "-e",
+            str(params.get("epsilon"))
+        ])
+    if params.get("kernel") is not None:
+        cargs.extend([
+            "-kernel",
+            params.get("kernel")
+        ])
+    if params.get("d_value") is not None:
+        cargs.extend([
+            "-d",
+            str(params.get("d_value"))
+        ])
+    if params.get("gamma") is not None:
+        cargs.extend([
+            "-g",
+            str(params.get("gamma"))
+        ])
+    if params.get("s_value") is not None:
+        cargs.extend([
+            "-s",
+            str(params.get("s_value"))
+        ])
+    if params.get("r_value") is not None:
+        cargs.extend([
+            "-r",
+            str(params.get("r_value"))
+        ])
+    if params.get("max_iterations") is not None:
+        cargs.extend([
+            "-max_iterations",
+            str(params.get("max_iterations"))
+        ])
+    if params.get("wout"):
+        cargs.append("-wout")
+    if params.get("test_vol") is not None:
+        cargs.extend([
+            "-testvol",
+            execution.input_file(params.get("test_vol"))
+        ])
+    if params.get("predictions") is not None:
+        cargs.extend([
+            "-predictions",
+            params.get("predictions")
+        ])
+    if params.get("classout"):
+        cargs.append("-classout")
+    if params.get("nopred_censored"):
+        cargs.append("-nopredcensored")
+    if params.get("nodetrend"):
+        cargs.append("-nodetrend")
+    if params.get("nopred_scale"):
+        cargs.append("-nopredscale")
+    if params.get("test_labels") is not None:
+        cargs.extend([
+            "-testlabels",
+            execution.input_file(params.get("test_labels"))
+        ])
+    if params.get("multiclass") is not None:
+        cargs.extend([
+            "-multiclass",
+            params.get("multiclass")
+        ])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-version")
+    return cargs
+
+
+def v_3dsvm_outputs(
+    params: V3dsvmParameters,
+    execution: Execution,
+) -> V3dsvmOutputs:
+    """
+    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 = V3dsvmOutputs(
+        root=execution.output_file("."),
+        out_model=execution.output_file("model_{output}.1D"),
+        out_alpha=execution.output_file("alpha_{output}.1D"),
+        out_bucket=execution.output_file("bucket_{output}.1D"),
+        out_predictions=execution.output_file("predictions_{output}.1D"),
+    )
+    return ret
+
+
+def v_3dsvm_execute(
+    params: V3dsvmParameters,
+    execution: Execution,
+) -> V3dsvmOutputs:
+    """
+    Support vector machine analysis of brain data using the SVM-light package.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dsvmOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dsvm_cargs(params, execution)
+    ret = v_3dsvm_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dsvm(
+    model: str,
+    train_vol: InputPathType | None = None,
+    train_labels: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    no_model_mask: bool = False,
+    alpha: str | None = None,
+    bucket: str | None = None,
+    type_: typing.Literal["classification", "regression"] | None = None,
+    c_value: float | None = None,
+    epsilon: float | None = None,
+    kernel: typing.Literal["linear", "polynomial", "rbf", "sigmoid"] | None = None,
+    d_value: float | None = None,
+    gamma: float | None = None,
+    s_value: float | None = None,
+    r_value: float | None = None,
+    max_iterations: float | None = None,
+    wout: bool = False,
+    test_vol: InputPathType | None = None,
+    predictions: str | None = None,
+    classout: bool = False,
+    nopred_censored: bool = False,
+    nodetrend: bool = False,
+    nopred_scale: bool = False,
+    test_labels: InputPathType | None = None,
+    multiclass: typing.Literal["DAG", "vote"] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> V3dsvmOutputs:
+    """
+    Support vector machine analysis of brain data using the SVM-light package.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        model: The basename for the model brik containing the SVM model during\
+            training or testing.
+        train_vol: A 3D+t AFNI brik dataset to be used for training.
+        train_labels: Filename of class category .1D labels corresponding to\
+            the stimulus paradigm for the training data set.
+        mask: Specify a mask dataset to only perform the analysis on non-zero\
+            mask voxels.
+        no_model_mask: Flag to enable the omission of a mask file. Required if\
+            '-mask' is not used.
+        alpha: Write the alphas to a specified .1D file.
+        bucket: Outputs the sum of weighted linear support vectors written out\
+            to a functional (fim) brik file.
+        type_: Specify type: classification (default) or regression.
+        c_value: Control SVM model complexity (C value).
+        epsilon: Specify epsilon for regression.
+        kernel: Specify type of kernel function.
+        d_value: D parameter in polynomial kernel.
+        gamma: Gamma parameter in rbf kernel.
+        s_value: S parameter in sigmoid/poly kernel.
+        r_value: R parameter in sigmoid/poly kernel.
+        max_iterations: Specify the maximum number of iterations for the\
+            optimization. Default is 1 million.
+        wout: Flag to output sum of weighted linear support vectors to the\
+            bucket file.
+        test_vol: A 3D or 3D+t AFNI brik dataset to be used for testing.
+        predictions: Basename for .1D prediction files.
+        classout: Flag to specify that prediction files should be\
+            integer-valued, corresponding to class category decisions.
+        nopred_censored: Do not write predicted values for censored time-points\
+            to predictions file.
+        nodetrend: Flag to specify that prediction files should NOT be linearly\
+            detrended.
+        nopred_scale: Do not scale predictions. Values below 0.0 correspond to\
+            (class A) and values above 0.0 to (class B).
+        test_labels: Filename of 'true' class category .1D labels for the test\
+            dataset.
+        multiclass: Specify the multiclass algorithm for classification.
+        help_: Print help message.
+        version: Print version history.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dsvmOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DSVM_METADATA)
+    params = v_3dsvm_params(
+        train_vol=train_vol,
+        train_labels=train_labels,
+        mask=mask,
+        no_model_mask=no_model_mask,
+        model=model,
+        alpha=alpha,
+        bucket=bucket,
+        type_=type_,
+        c_value=c_value,
+        epsilon=epsilon,
+        kernel=kernel,
+        d_value=d_value,
+        gamma=gamma,
+        s_value=s_value,
+        r_value=r_value,
+        max_iterations=max_iterations,
+        wout=wout,
+        test_vol=test_vol,
+        predictions=predictions,
+        classout=classout,
+        nopred_censored=nopred_censored,
+        nodetrend=nodetrend,
+        nopred_scale=nopred_scale,
+        test_labels=test_labels,
+        multiclass=multiclass,
+        help_=help_,
+        version=version,
+    )
+    return v_3dsvm_execute(params, execution)
+
+
+__all__ = [
+    "V3dsvmOutputs",
+    "V3dsvmParameters",
+    "V_3DSVM_METADATA",
+    "v_3dsvm",
+    "v_3dsvm_params",
+]