niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_seg.py

@@ -0,0 +1,437 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_SEG_METADATA = Metadata(
+    id="f6e7c61caa09a93af688039024093f43ff4f67a3.boutiques",
+    name="3dSeg",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dSegParameters = typing.TypedDict('V3dSegParameters', {
+    "__STYX_TYPE__": typing.Literal["3dSeg"],
+    "anat": InputPathType,
+    "mask": typing.NotRequired[str | None],
+    "blur_meth": typing.NotRequired[str | None],
+    "bias_fwhm": typing.NotRequired[float | None],
+    "classes": typing.NotRequired[str | None],
+    "Bmrf": typing.NotRequired[float | None],
+    "bias_classes": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "overwrite": bool,
+    "debug": typing.NotRequired[float | None],
+    "mixfrac": typing.NotRequired[str | None],
+    "mixfloor": typing.NotRequired[float | None],
+    "gold": typing.NotRequired[InputPathType | None],
+    "gold_bias": typing.NotRequired[InputPathType | None],
+    "main_N": typing.NotRequired[float | None],
+    "cset": typing.NotRequired[InputPathType | None],
+    "labeltable": typing.NotRequired[InputPathType | None],
+    "vox_debug": typing.NotRequired[str | None],
+    "vox_debug_file": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dSeg": v_3d_seg_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 {
+        "3dSeg": v_3d_seg_outputs,
+    }.get(t)
+
+
+class V3dSegOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_seg(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    segmented_volume: OutputPathType | None
+    """Segmented brain volume output"""
+    bias_field: OutputPathType | None
+    """Bias field estimate output"""
+    classified_volume: OutputPathType | None
+    """Classified volume output"""
+
+
+def v_3d_seg_params(
+    anat: InputPathType,
+    mask: str | None = None,
+    blur_meth: str | None = None,
+    bias_fwhm: float | None = None,
+    classes: str | None = None,
+    bmrf: float | None = None,
+    bias_classes: str | None = None,
+    prefix: str | None = None,
+    overwrite: bool = False,
+    debug: float | None = None,
+    mixfrac: str | None = None,
+    mixfloor: float | None = None,
+    gold: InputPathType | None = None,
+    gold_bias: InputPathType | None = None,
+    main_n: float | None = None,
+    cset: InputPathType | None = None,
+    labeltable: InputPathType | None = None,
+    vox_debug: str | None = None,
+    vox_debug_file: str | None = None,
+) -> V3dSegParameters:
+    """
+    Build parameters.
+    
+    Args:
+        anat: Volume to segment.
+        mask: Mask of the volume to be segmented. Can be a dataset or 'AUTO' to\
+            use AFNI's automask function.
+        blur_meth: Blurring method for bias field estimation. Options: BFT,\
+            BIM, BNN, LSB. Default: BFT.
+        bias_fwhm: The amount of blurring used when estimating the field bias.\
+            Default: 25.0.
+        classes: String of class labels separated by semicolons. Default: 'CSF;\
+            GM; WM'.
+        bmrf: Weighting factor controlling spatial homogeneity of\
+            classifications. Default: 0.0.
+        bias_classes: Classes that contribute to the estimation of the bias\
+            field. Default: 'GM; WM'.
+        prefix: Prefix for all output volume.
+        overwrite: Automatically overwrite existing files with the same prefix.
+        debug: Set debug level (0, 1, or 2).
+        mixfrac: Volume-wide mixing fractions for initialization. Options: '0.1\
+            0.45 0.45', 'UNI', 'AVG152_BRAIN_MASK', 'IGNORE'. Default: UNI.
+        mixfloor: Set the minimum value for any class's mixing fraction.\
+            Default: 0.0001.
+        gold: Goldstandard segmentation volume for comparison.
+        gold_bias: Goldstandard bias volume for comparison.
+        main_n: Number of iterations to perform. Default: 5.
+        cset: Initial classification. Uses 3dkmean's engine if not provided.
+        labeltable: Label table containing integer keys and corresponding\
+            labels.
+        vox_debug: 1D index of voxel to debug or 3D voxel indices.
+        vox_debug_file: File in which debug information is output, use '-' for\
+            stdout, '+' for stderr.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dSeg",
+        "anat": anat,
+        "overwrite": overwrite,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if blur_meth is not None:
+        params["blur_meth"] = blur_meth
+    if bias_fwhm is not None:
+        params["bias_fwhm"] = bias_fwhm
+    if classes is not None:
+        params["classes"] = classes
+    if bmrf is not None:
+        params["Bmrf"] = bmrf
+    if bias_classes is not None:
+        params["bias_classes"] = bias_classes
+    if prefix is not None:
+        params["prefix"] = prefix
+    if debug is not None:
+        params["debug"] = debug
+    if mixfrac is not None:
+        params["mixfrac"] = mixfrac
+    if mixfloor is not None:
+        params["mixfloor"] = mixfloor
+    if gold is not None:
+        params["gold"] = gold
+    if gold_bias is not None:
+        params["gold_bias"] = gold_bias
+    if main_n is not None:
+        params["main_N"] = main_n
+    if cset is not None:
+        params["cset"] = cset
+    if labeltable is not None:
+        params["labeltable"] = labeltable
+    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
+    return params
+
+
+def v_3d_seg_cargs(
+    params: V3dSegParameters,
+    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("3dSeg")
+    cargs.extend([
+        "-anat",
+        execution.input_file(params.get("anat"))
+    ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            params.get("mask")
+        ])
+    if params.get("blur_meth") is not None:
+        cargs.extend([
+            "-blur_meth",
+            params.get("blur_meth")
+        ])
+    if params.get("bias_fwhm") is not None:
+        cargs.extend([
+            "-bias_fwhm",
+            str(params.get("bias_fwhm"))
+        ])
+    if params.get("classes") is not None:
+        cargs.extend([
+            "-classes",
+            params.get("classes")
+        ])
+    if params.get("Bmrf") is not None:
+        cargs.extend([
+            "-Bmrf",
+            str(params.get("Bmrf"))
+        ])
+    if params.get("bias_classes") is not None:
+        cargs.extend([
+            "-bias_classes",
+            params.get("bias_classes")
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("overwrite"):
+        cargs.append("-overwrite")
+    if params.get("debug") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug"))
+        ])
+    if params.get("mixfrac") is not None:
+        cargs.extend([
+            "-mixfrac",
+            params.get("mixfrac")
+        ])
+    if params.get("mixfloor") is not None:
+        cargs.extend([
+            "-mixfloor",
+            str(params.get("mixfloor"))
+        ])
+    if params.get("gold") is not None:
+        cargs.extend([
+            "-gold",
+            execution.input_file(params.get("gold"))
+        ])
+    if params.get("gold_bias") is not None:
+        cargs.extend([
+            "-gold_bias",
+            execution.input_file(params.get("gold_bias"))
+        ])
+    if params.get("main_N") is not None:
+        cargs.extend([
+            "-main_N",
+            str(params.get("main_N"))
+        ])
+    if params.get("cset") is not None:
+        cargs.extend([
+            "-cset",
+            execution.input_file(params.get("cset"))
+        ])
+    if params.get("labeltable") is not None:
+        cargs.extend([
+            "-labeltable",
+            execution.input_file(params.get("labeltable"))
+        ])
+    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")
+        ])
+    return cargs
+
+
+def v_3d_seg_outputs(
+    params: V3dSegParameters,
+    execution: Execution,
+) -> V3dSegOutputs:
+    """
+    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 = V3dSegOutputs(
+        root=execution.output_file("."),
+        segmented_volume=execution.output_file(params.get("prefix") + "_Segsy+orig.HEAD") if (params.get("prefix") is not None) else None,
+        bias_field=execution.output_file(params.get("prefix") + "_BiasField+orig.HEAD") if (params.get("prefix") is not None) else None,
+        classified_volume=execution.output_file(params.get("prefix") + "_Classes+orig.HEAD") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_seg_execute(
+    params: V3dSegParameters,
+    execution: Execution,
+) -> V3dSegOutputs:
+    """
+    Segments brain volumes into tissue classes with optional global and voxelwise
+    priors.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dSegOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_seg_cargs(params, execution)
+    ret = v_3d_seg_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_seg(
+    anat: InputPathType,
+    mask: str | None = None,
+    blur_meth: str | None = None,
+    bias_fwhm: float | None = None,
+    classes: str | None = None,
+    bmrf: float | None = None,
+    bias_classes: str | None = None,
+    prefix: str | None = None,
+    overwrite: bool = False,
+    debug: float | None = None,
+    mixfrac: str | None = None,
+    mixfloor: float | None = None,
+    gold: InputPathType | None = None,
+    gold_bias: InputPathType | None = None,
+    main_n: float | None = None,
+    cset: InputPathType | None = None,
+    labeltable: InputPathType | None = None,
+    vox_debug: str | None = None,
+    vox_debug_file: str | None = None,
+    runner: Runner | None = None,
+) -> V3dSegOutputs:
+    """
+    Segments brain volumes into tissue classes with optional global and voxelwise
+    priors.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        anat: Volume to segment.
+        mask: Mask of the volume to be segmented. Can be a dataset or 'AUTO' to\
+            use AFNI's automask function.
+        blur_meth: Blurring method for bias field estimation. Options: BFT,\
+            BIM, BNN, LSB. Default: BFT.
+        bias_fwhm: The amount of blurring used when estimating the field bias.\
+            Default: 25.0.
+        classes: String of class labels separated by semicolons. Default: 'CSF;\
+            GM; WM'.
+        bmrf: Weighting factor controlling spatial homogeneity of\
+            classifications. Default: 0.0.
+        bias_classes: Classes that contribute to the estimation of the bias\
+            field. Default: 'GM; WM'.
+        prefix: Prefix for all output volume.
+        overwrite: Automatically overwrite existing files with the same prefix.
+        debug: Set debug level (0, 1, or 2).
+        mixfrac: Volume-wide mixing fractions for initialization. Options: '0.1\
+            0.45 0.45', 'UNI', 'AVG152_BRAIN_MASK', 'IGNORE'. Default: UNI.
+        mixfloor: Set the minimum value for any class's mixing fraction.\
+            Default: 0.0001.
+        gold: Goldstandard segmentation volume for comparison.
+        gold_bias: Goldstandard bias volume for comparison.
+        main_n: Number of iterations to perform. Default: 5.
+        cset: Initial classification. Uses 3dkmean's engine if not provided.
+        labeltable: Label table containing integer keys and corresponding\
+            labels.
+        vox_debug: 1D index of voxel to debug or 3D voxel indices.
+        vox_debug_file: File in which debug information is output, use '-' for\
+            stdout, '+' for stderr.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dSegOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SEG_METADATA)
+    params = v_3d_seg_params(
+        anat=anat,
+        mask=mask,
+        blur_meth=blur_meth,
+        bias_fwhm=bias_fwhm,
+        classes=classes,
+        bmrf=bmrf,
+        bias_classes=bias_classes,
+        prefix=prefix,
+        overwrite=overwrite,
+        debug=debug,
+        mixfrac=mixfrac,
+        mixfloor=mixfloor,
+        gold=gold,
+        gold_bias=gold_bias,
+        main_n=main_n,
+        cset=cset,
+        labeltable=labeltable,
+        vox_debug=vox_debug,
+        vox_debug_file=vox_debug_file,
+    )
+    return v_3d_seg_execute(params, execution)
+
+
+__all__ = [
+    "V3dSegOutputs",
+    "V3dSegParameters",
+    "V_3D_SEG_METADATA",
+    "v_3d_seg",
+    "v_3d_seg_params",
+]

niwrap_afni/afni/v_3d_setup_group_in_corr.py

@@ -0,0 +1,273 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_SETUP_GROUP_IN_CORR_METADATA = Metadata(
+    id="de29e68b50548580e79210d656042b141dbd77c7.boutiques",
+    name="3dSetupGroupInCorr",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dSetupGroupInCorrParameters = typing.TypedDict('V3dSetupGroupInCorrParameters', {
+    "__STYX_TYPE__": typing.Literal["3dSetupGroupInCorr"],
+    "datasets": list[InputPathType],
+    "mask_dataset": typing.NotRequired[InputPathType | None],
+    "prefix": str,
+    "short_flag": bool,
+    "byte_flag": bool,
+    "labels_file": typing.NotRequired[InputPathType | None],
+    "delete_flag": bool,
+    "prep_method": typing.NotRequired[str | None],
+    "lr_pairs": typing.NotRequired[list[str] | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dSetupGroupInCorr": v_3d_setup_group_in_corr_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 {
+        "3dSetupGroupInCorr": v_3d_setup_group_in_corr_outputs,
+    }.get(t)
+
+
+class V3dSetupGroupInCorrOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_setup_group_in_corr(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    niml_file: OutputPathType
+    """Text file containing the header information describing the data file."""
+    data_file: OutputPathType
+    """Data file containing all the time series from all the datasets."""
+
+
+def v_3d_setup_group_in_corr_params(
+    datasets: list[InputPathType],
+    prefix: str,
+    mask_dataset: InputPathType | None = None,
+    short_flag: bool = False,
+    byte_flag: bool = False,
+    labels_file: InputPathType | None = None,
+    delete_flag: bool = False,
+    prep_method: str | None = None,
+    lr_pairs: list[str] | None = None,
+) -> V3dSetupGroupInCorrParameters:
+    """
+    Build parameters.
+    
+    Args:
+        datasets: AFNI 3D+time datasets to be processed.
+        prefix: Prefix for output dataset names.
+        mask_dataset: Mask dataset for voxel selection.
+        short_flag: Store data as 16-bit shorts.
+        byte_flag: Store data as 8-bit bytes.
+        labels_file: File containing a list of labels for each dataset.
+        delete_flag: Delete input datasets from disk after processing.
+        prep_method: Preprocess each data time series with the specified\
+            method.
+        lr_pairs: Set the domains for left and right hemisphere surfaces and\
+            indicate that the datasets are arranged in (Left, Right) pairs.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dSetupGroupInCorr",
+        "datasets": datasets,
+        "prefix": prefix,
+        "short_flag": short_flag,
+        "byte_flag": byte_flag,
+        "delete_flag": delete_flag,
+    }
+    if mask_dataset is not None:
+        params["mask_dataset"] = mask_dataset
+    if labels_file is not None:
+        params["labels_file"] = labels_file
+    if prep_method is not None:
+        params["prep_method"] = prep_method
+    if lr_pairs is not None:
+        params["lr_pairs"] = lr_pairs
+    return params
+
+
+def v_3d_setup_group_in_corr_cargs(
+    params: V3dSetupGroupInCorrParameters,
+    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("3dSetupGroupInCorr")
+    cargs.extend([execution.input_file(f) for f in params.get("datasets")])
+    if params.get("mask_dataset") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_dataset"))
+        ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("short_flag"):
+        cargs.append("-short")
+    if params.get("byte_flag"):
+        cargs.append("-byte")
+    if params.get("labels_file") is not None:
+        cargs.extend([
+            "-labels",
+            execution.input_file(params.get("labels_file"))
+        ])
+    if params.get("delete_flag"):
+        cargs.append("-DELETE")
+    if params.get("prep_method") is not None:
+        cargs.extend([
+            "-prep",
+            params.get("prep_method")
+        ])
+    if params.get("lr_pairs") is not None:
+        cargs.extend([
+            "-LRpairs",
+            *params.get("lr_pairs")
+        ])
+    return cargs
+
+
+def v_3d_setup_group_in_corr_outputs(
+    params: V3dSetupGroupInCorrParameters,
+    execution: Execution,
+) -> V3dSetupGroupInCorrOutputs:
+    """
+    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 = V3dSetupGroupInCorrOutputs(
+        root=execution.output_file("."),
+        niml_file=execution.output_file(params.get("prefix") + ".grpincorr.niml"),
+        data_file=execution.output_file(params.get("prefix") + ".grpincorr.data"),
+    )
+    return ret
+
+
+def v_3d_setup_group_in_corr_execute(
+    params: V3dSetupGroupInCorrParameters,
+    execution: Execution,
+) -> V3dSetupGroupInCorrOutputs:
+    """
+    Pre-process a collection of AFNI 3D+time datasets for use with Group InstaCorr.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dSetupGroupInCorrOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_setup_group_in_corr_cargs(params, execution)
+    ret = v_3d_setup_group_in_corr_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_setup_group_in_corr(
+    datasets: list[InputPathType],
+    prefix: str,
+    mask_dataset: InputPathType | None = None,
+    short_flag: bool = False,
+    byte_flag: bool = False,
+    labels_file: InputPathType | None = None,
+    delete_flag: bool = False,
+    prep_method: str | None = None,
+    lr_pairs: list[str] | None = None,
+    runner: Runner | None = None,
+) -> V3dSetupGroupInCorrOutputs:
+    """
+    Pre-process a collection of AFNI 3D+time datasets for use with Group InstaCorr.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        datasets: AFNI 3D+time datasets to be processed.
+        prefix: Prefix for output dataset names.
+        mask_dataset: Mask dataset for voxel selection.
+        short_flag: Store data as 16-bit shorts.
+        byte_flag: Store data as 8-bit bytes.
+        labels_file: File containing a list of labels for each dataset.
+        delete_flag: Delete input datasets from disk after processing.
+        prep_method: Preprocess each data time series with the specified\
+            method.
+        lr_pairs: Set the domains for left and right hemisphere surfaces and\
+            indicate that the datasets are arranged in (Left, Right) pairs.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dSetupGroupInCorrOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SETUP_GROUP_IN_CORR_METADATA)
+    params = v_3d_setup_group_in_corr_params(
+        datasets=datasets,
+        mask_dataset=mask_dataset,
+        prefix=prefix,
+        short_flag=short_flag,
+        byte_flag=byte_flag,
+        labels_file=labels_file,
+        delete_flag=delete_flag,
+        prep_method=prep_method,
+        lr_pairs=lr_pairs,
+    )
+    return v_3d_setup_group_in_corr_execute(params, execution)
+
+
+__all__ = [
+    "V3dSetupGroupInCorrOutputs",
+    "V3dSetupGroupInCorrParameters",
+    "V_3D_SETUP_GROUP_IN_CORR_METADATA",
+    "v_3d_setup_group_in_corr",
+    "v_3d_setup_group_in_corr_params",
+]