niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_gen_priors.py

@@ -0,0 +1,487 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_GEN_PRIORS_METADATA = Metadata(
+    id="845d9172d4ae6f1eca3fec82fab483b9e0b7907b.boutiques",
+    name="3dGenPriors",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dGenPriorsParameters = typing.TypedDict('V3dGenPriorsParameters', {
+    "__STYX_TYPE__": typing.Literal["3dGenPriors"],
+    "sigs": InputPathType,
+    "tdist": InputPathType,
+    "cprefix": str,
+    "pprefix": str,
+    "labeltable": InputPathType,
+    "do": str,
+    "prefix": typing.NotRequired[str | None],
+    "cmask": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[str | None],
+    "mrange": typing.NotRequired[list[float] | None],
+    "debug": typing.NotRequired[float | None],
+    "vox_debug": typing.NotRequired[str | None],
+    "vox_debug_file": typing.NotRequired[str | None],
+    "uid": typing.NotRequired[str | None],
+    "use_tmp": bool,
+    "no_tmp": bool,
+    "pset": typing.NotRequired[str | None],
+    "cset": typing.NotRequired[str | None],
+    "regroup_classes": typing.NotRequired[str | None],
+    "classes": typing.NotRequired[str | None],
+    "features": typing.NotRequired[str | None],
+    "strict_feature_match": bool,
+    "featgroups": typing.NotRequired[str | None],
+    "show_this_dist": typing.NotRequired[str | None],
+    "fast": bool,
+    "slow": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dGenPriors": v_3d_gen_priors_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 {
+        "3dGenPriors": v_3d_gen_priors_outputs,
+    }.get(t)
+
+
+class V3dGenPriorsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_gen_priors(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_cprefix: OutputPathType
+    """Main classification output"""
+    out_pprefix: OutputPathType
+    """Main probability output"""
+
+
+def v_3d_gen_priors_params(
+    sigs: InputPathType,
+    tdist: InputPathType,
+    cprefix: str,
+    pprefix: str,
+    labeltable: InputPathType,
+    do: str,
+    prefix: str | None = None,
+    cmask: str | None = None,
+    mask: str | None = None,
+    mrange: list[float] | None = None,
+    debug: float | None = None,
+    vox_debug: str | None = None,
+    vox_debug_file: str | None = None,
+    uid: str | None = None,
+    use_tmp: bool = False,
+    no_tmp: bool = False,
+    pset: str | None = None,
+    cset: str | None = None,
+    regroup_classes: str | None = None,
+    classes: str | None = None,
+    features: str | None = None,
+    strict_feature_match: bool = False,
+    featgroups: str | None = None,
+    show_this_dist: str | None = None,
+    fast: bool = False,
+    slow: bool = False,
+) -> V3dGenPriorsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        sigs: Signatures dataset. A dataset with F features per voxel.
+        tdist: Training results. This file is generated by 3dSignatures.
+        cprefix: Prefix for class dataset.
+        pprefix: Prefix for probability dataset.
+        labeltable: Labeltable to attach to output dataset.
+        do: Specify the output that this program should create.
+        prefix: Specify root prefix for output volumes.
+        cmask: Provide cmask expression. Voxels where expression is 0 are\
+            excluded from computations.
+        mask: Provide mask dataset.
+        mrange: Consider MASK only for values between M0 and M1, inclusive.
+        debug: Set debug level.
+        vox_debug: 1D index or 3D indices (I J K) of voxel to debug.
+        vox_debug_file: File in which debug information is output.
+        uid: User identifier string. Used to generate names for temporary\
+            files.
+        use_tmp: Use temporary storage to speed up the program.
+        no_tmp: Do not use temporary storage.
+        pset: Reuse probability output from an earlier run.
+        cset: Reuse classification output from an earlier run.
+        regroup_classes: Regroup classes into parent classes. Requires naming\
+            the original classes as C1.*, C2.*, etc.
+        classes: Classify into these classes only.
+        features: Use these features only. Otherwise, all features in the\
+            signature file will be used.
+        strict_feature_match: Use strict feature name matching.
+        featgroups: Feature groups.
+        show_this_dist: Show information obtained from the training data about\
+            the distribution of DIST. Set DIST to ALL to see all distributions.
+        fast: Use OpenMPized routines for faster performance.
+        slow: Do not use OpenMPized routines.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dGenPriors",
+        "sigs": sigs,
+        "tdist": tdist,
+        "cprefix": cprefix,
+        "pprefix": pprefix,
+        "labeltable": labeltable,
+        "do": do,
+        "use_tmp": use_tmp,
+        "no_tmp": no_tmp,
+        "strict_feature_match": strict_feature_match,
+        "fast": fast,
+        "slow": slow,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if cmask is not None:
+        params["cmask"] = cmask
+    if mask is not None:
+        params["mask"] = mask
+    if mrange is not None:
+        params["mrange"] = mrange
+    if debug is not None:
+        params["debug"] = debug
+    if vox_debug is not None:
+        params["vox_debug"] = vox_debug
+    if vox_debug_file is not None:
+        params["vox_debug_file"] = vox_debug_file
+    if uid is not None:
+        params["uid"] = uid
+    if pset is not None:
+        params["pset"] = pset
+    if cset is not None:
+        params["cset"] = cset
+    if regroup_classes is not None:
+        params["regroup_classes"] = regroup_classes
+    if classes is not None:
+        params["classes"] = classes
+    if features is not None:
+        params["features"] = features
+    if featgroups is not None:
+        params["featgroups"] = featgroups
+    if show_this_dist is not None:
+        params["show_this_dist"] = show_this_dist
+    return params
+
+
+def v_3d_gen_priors_cargs(
+    params: V3dGenPriorsParameters,
+    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("3dGenPriors")
+    cargs.extend([
+        "-sig",
+        execution.input_file(params.get("sigs"))
+    ])
+    cargs.extend([
+        "-tdist",
+        execution.input_file(params.get("tdist"))
+    ])
+    cargs.extend([
+        "-cprefix",
+        params.get("cprefix")
+    ])
+    cargs.extend([
+        "-pprefix",
+        params.get("pprefix")
+    ])
+    cargs.extend([
+        "-labeltable",
+        execution.input_file(params.get("labeltable"))
+    ])
+    cargs.extend([
+        "-do",
+        params.get("do")
+    ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("cmask") is not None:
+        cargs.extend([
+            "-cmask",
+            params.get("cmask")
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            params.get("mask")
+        ])
+    if params.get("mrange") is not None:
+        cargs.extend([
+            "-mrange",
+            *map(str, params.get("mrange"))
+        ])
+    if params.get("debug") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug"))
+        ])
+    if params.get("vox_debug") is not None:
+        cargs.extend([
+            "-vox_debug",
+            params.get("vox_debug")
+        ])
+    if params.get("vox_debug_file") is not None:
+        cargs.extend([
+            "-vox_debug_file",
+            params.get("vox_debug_file")
+        ])
+    if params.get("uid") is not None:
+        cargs.extend([
+            "-uid",
+            params.get("uid")
+        ])
+    if params.get("use_tmp"):
+        cargs.append("-use_tmp")
+    if params.get("no_tmp"):
+        cargs.append("-no_tmp")
+    if params.get("pset") is not None:
+        cargs.extend([
+            "-pset",
+            params.get("pset")
+        ])
+    if params.get("cset") is not None:
+        cargs.extend([
+            "-cset",
+            params.get("cset")
+        ])
+    if params.get("regroup_classes") is not None:
+        cargs.extend([
+            "-regroup_classes",
+            params.get("regroup_classes")
+        ])
+    if params.get("classes") is not None:
+        cargs.extend([
+            "-classes",
+            params.get("classes")
+        ])
+    if params.get("features") is not None:
+        cargs.extend([
+            "-features",
+            params.get("features")
+        ])
+    if params.get("strict_feature_match"):
+        cargs.append("-strict_feature_match")
+    if params.get("featgroups") is not None:
+        cargs.extend([
+            "-featgroups",
+            params.get("featgroups")
+        ])
+    if params.get("show_this_dist") is not None:
+        cargs.extend([
+            "-ShowThisDist",
+            params.get("show_this_dist")
+        ])
+    if params.get("fast"):
+        cargs.append("-fast")
+    if params.get("slow"):
+        cargs.append("-slow")
+    return cargs
+
+
+def v_3d_gen_priors_outputs(
+    params: V3dGenPriorsParameters,
+    execution: Execution,
+) -> V3dGenPriorsOutputs:
+    """
+    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 = V3dGenPriorsOutputs(
+        root=execution.output_file("."),
+        out_cprefix=execution.output_file(params.get("cprefix") + ".nii.gz"),
+        out_pprefix=execution.output_file(params.get("pprefix") + ".nii.gz"),
+    )
+    return ret
+
+
+def v_3d_gen_priors_execute(
+    params: V3dGenPriorsParameters,
+    execution: Execution,
+) -> V3dGenPriorsOutputs:
+    """
+    Produces classification priors based on voxel signatures.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dGenPriorsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_gen_priors_cargs(params, execution)
+    ret = v_3d_gen_priors_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_gen_priors(
+    sigs: InputPathType,
+    tdist: InputPathType,
+    cprefix: str,
+    pprefix: str,
+    labeltable: InputPathType,
+    do: str,
+    prefix: str | None = None,
+    cmask: str | None = None,
+    mask: str | None = None,
+    mrange: list[float] | None = None,
+    debug: float | None = None,
+    vox_debug: str | None = None,
+    vox_debug_file: str | None = None,
+    uid: str | None = None,
+    use_tmp: bool = False,
+    no_tmp: bool = False,
+    pset: str | None = None,
+    cset: str | None = None,
+    regroup_classes: str | None = None,
+    classes: str | None = None,
+    features: str | None = None,
+    strict_feature_match: bool = False,
+    featgroups: str | None = None,
+    show_this_dist: str | None = None,
+    fast: bool = False,
+    slow: bool = False,
+    runner: Runner | None = None,
+) -> V3dGenPriorsOutputs:
+    """
+    Produces classification priors based on voxel signatures.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        sigs: Signatures dataset. A dataset with F features per voxel.
+        tdist: Training results. This file is generated by 3dSignatures.
+        cprefix: Prefix for class dataset.
+        pprefix: Prefix for probability dataset.
+        labeltable: Labeltable to attach to output dataset.
+        do: Specify the output that this program should create.
+        prefix: Specify root prefix for output volumes.
+        cmask: Provide cmask expression. Voxels where expression is 0 are\
+            excluded from computations.
+        mask: Provide mask dataset.
+        mrange: Consider MASK only for values between M0 and M1, inclusive.
+        debug: Set debug level.
+        vox_debug: 1D index or 3D indices (I J K) of voxel to debug.
+        vox_debug_file: File in which debug information is output.
+        uid: User identifier string. Used to generate names for temporary\
+            files.
+        use_tmp: Use temporary storage to speed up the program.
+        no_tmp: Do not use temporary storage.
+        pset: Reuse probability output from an earlier run.
+        cset: Reuse classification output from an earlier run.
+        regroup_classes: Regroup classes into parent classes. Requires naming\
+            the original classes as C1.*, C2.*, etc.
+        classes: Classify into these classes only.
+        features: Use these features only. Otherwise, all features in the\
+            signature file will be used.
+        strict_feature_match: Use strict feature name matching.
+        featgroups: Feature groups.
+        show_this_dist: Show information obtained from the training data about\
+            the distribution of DIST. Set DIST to ALL to see all distributions.
+        fast: Use OpenMPized routines for faster performance.
+        slow: Do not use OpenMPized routines.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dGenPriorsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_GEN_PRIORS_METADATA)
+    params = v_3d_gen_priors_params(
+        sigs=sigs,
+        tdist=tdist,
+        cprefix=cprefix,
+        pprefix=pprefix,
+        labeltable=labeltable,
+        do=do,
+        prefix=prefix,
+        cmask=cmask,
+        mask=mask,
+        mrange=mrange,
+        debug=debug,
+        vox_debug=vox_debug,
+        vox_debug_file=vox_debug_file,
+        uid=uid,
+        use_tmp=use_tmp,
+        no_tmp=no_tmp,
+        pset=pset,
+        cset=cset,
+        regroup_classes=regroup_classes,
+        classes=classes,
+        features=features,
+        strict_feature_match=strict_feature_match,
+        featgroups=featgroups,
+        show_this_dist=show_this_dist,
+        fast=fast,
+        slow=slow,
+    )
+    return v_3d_gen_priors_execute(params, execution)
+
+
+__all__ = [
+    "V3dGenPriorsOutputs",
+    "V3dGenPriorsParameters",
+    "V_3D_GEN_PRIORS_METADATA",
+    "v_3d_gen_priors",
+    "v_3d_gen_priors_params",
+]