niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3dmaxima.py

@@ -0,0 +1,373 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DMAXIMA_METADATA = Metadata(
+    id="f8ba8da054bfe915efd0d6532d6b8fe26bfcc7a9.boutiques",
+    name="3dmaxima",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dmaximaParameters = typing.TypedDict('V3dmaximaParameters', {
+    "__STYX_TYPE__": typing.Literal["3dmaxima"],
+    "input_dataset": InputPathType,
+    "output_prefix": typing.NotRequired[str | None],
+    "threshold": typing.NotRequired[float | None],
+    "min_dist": typing.NotRequired[float | None],
+    "out_rad": typing.NotRequired[float | None],
+    "input_flag": bool,
+    "spheres_1_flag": bool,
+    "spheres_1toN_flag": bool,
+    "spheres_Nto1_flag": bool,
+    "neg_ext_flag": bool,
+    "true_max_flag": bool,
+    "dset_coords_flag": bool,
+    "no_text_flag": bool,
+    "coords_only_flag": bool,
+    "n_style_sort_flag": bool,
+    "n_style_weight_ave_flag": bool,
+    "debug_level": typing.NotRequired[float | None],
+    "help_flag": bool,
+    "hist_flag": bool,
+    "ver_flag": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dmaxima": v_3dmaxima_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 {
+        "3dmaxima": v_3dmaxima_outputs,
+    }.get(t)
+
+
+class V3dmaximaOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dmaxima(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_mask: OutputPathType | None
+    """Output mask dataset with extrema locations"""
+
+
+def v_3dmaxima_params(
+    input_dataset: InputPathType,
+    output_prefix: str | None = None,
+    threshold: float | None = None,
+    min_dist: float | None = None,
+    out_rad: float | None = None,
+    input_flag: bool = False,
+    spheres_1_flag: bool = False,
+    spheres_1to_n_flag: bool = False,
+    spheres_nto1_flag: bool = False,
+    neg_ext_flag: bool = False,
+    true_max_flag: bool = False,
+    dset_coords_flag: bool = False,
+    no_text_flag: bool = False,
+    coords_only_flag: bool = False,
+    n_style_sort_flag: bool = False,
+    n_style_weight_ave_flag: bool = False,
+    debug_level: float | None = None,
+    help_flag: bool = False,
+    hist_flag: bool = False,
+    ver_flag: bool = False,
+) -> V3dmaximaParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Specify input dataset (e.g. func+orig'[7]').
+        output_prefix: Prefix for an output mask dataset (e.g. -prefix\
+            maskNto1).
+        threshold: Provides a cutoff value for extrema (e.g. -thresh 17.4).
+        min_dist: Minimum acceptable distance between extrema in voxels (e.g.\
+            -min_dist 4).
+        out_rad: Set the output radius around extrema voxels in voxel units\
+            (e.g. -out_rad 9).
+        input_flag: Specify input dataset (e.g. -input func+orig'[7]').
+        spheres_1_flag: Set all output values to 1.
+        spheres_1to_n_flag: Output values will range from 1 to N.
+        spheres_nto1_flag: Output values will range from N to 1.
+        neg_ext_flag: Search for negative extrema (minima).
+        true_max_flag: Extrema may not have equal neighbors.
+        dset_coords_flag: Display output in the dataset orientation.
+        no_text_flag: Do not display the extrema points as text.
+        coords_only_flag: Only output coordinates (no text or values).
+        n_style_sort_flag: Use 'Sort-n-Remove' style (default).
+        n_style_weight_ave_flag: Use 'Weighted-Average' style.
+        debug_level: Output extra information to the terminal (e.g. -debug 2).
+        help_flag: Display help information.
+        hist_flag: Display module history.
+        ver_flag: Display version number.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dmaxima",
+        "input_dataset": input_dataset,
+        "input_flag": input_flag,
+        "spheres_1_flag": spheres_1_flag,
+        "spheres_1toN_flag": spheres_1to_n_flag,
+        "spheres_Nto1_flag": spheres_nto1_flag,
+        "neg_ext_flag": neg_ext_flag,
+        "true_max_flag": true_max_flag,
+        "dset_coords_flag": dset_coords_flag,
+        "no_text_flag": no_text_flag,
+        "coords_only_flag": coords_only_flag,
+        "n_style_sort_flag": n_style_sort_flag,
+        "n_style_weight_ave_flag": n_style_weight_ave_flag,
+        "help_flag": help_flag,
+        "hist_flag": hist_flag,
+        "ver_flag": ver_flag,
+    }
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    if threshold is not None:
+        params["threshold"] = threshold
+    if min_dist is not None:
+        params["min_dist"] = min_dist
+    if out_rad is not None:
+        params["out_rad"] = out_rad
+    if debug_level is not None:
+        params["debug_level"] = debug_level
+    return params
+
+
+def v_3dmaxima_cargs(
+    params: V3dmaximaParameters,
+    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("3dmaxima")
+    cargs.append(execution.input_file(params.get("input_dataset")))
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    if params.get("threshold") is not None:
+        cargs.extend([
+            "-thresh",
+            str(params.get("threshold"))
+        ])
+    if params.get("min_dist") is not None:
+        cargs.extend([
+            "-min_dist",
+            str(params.get("min_dist"))
+        ])
+    if params.get("out_rad") is not None:
+        cargs.extend([
+            "-out_rad",
+            str(params.get("out_rad"))
+        ])
+    if params.get("input_flag"):
+        cargs.append("-input")
+    if params.get("spheres_1_flag"):
+        cargs.append("-spheres_1")
+    if params.get("spheres_1toN_flag"):
+        cargs.append("-spheres_1toN")
+    if params.get("spheres_Nto1_flag"):
+        cargs.append("-spheres_Nto1")
+    if params.get("neg_ext_flag"):
+        cargs.append("-neg_ext")
+    if params.get("true_max_flag"):
+        cargs.append("-true_max")
+    if params.get("dset_coords_flag"):
+        cargs.append("-dset_coords")
+    if params.get("no_text_flag"):
+        cargs.append("-no_text")
+    if params.get("coords_only_flag"):
+        cargs.append("-coords_only")
+    if params.get("n_style_sort_flag"):
+        cargs.append("-n_style_sort")
+    if params.get("n_style_weight_ave_flag"):
+        cargs.append("-n_style_weight_ave")
+    if params.get("debug_level") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug_level"))
+        ])
+    if params.get("help_flag"):
+        cargs.append("-help")
+    if params.get("hist_flag"):
+        cargs.append("-hist")
+    if params.get("ver_flag"):
+        cargs.append("-ver")
+    return cargs
+
+
+def v_3dmaxima_outputs(
+    params: V3dmaximaParameters,
+    execution: Execution,
+) -> V3dmaximaOutputs:
+    """
+    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 = V3dmaximaOutputs(
+        root=execution.output_file("."),
+        output_mask=execution.output_file(params.get("output_prefix") + "_mask+orig.[HEAD | BRIK]") if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3dmaxima_execute(
+    params: V3dmaximaParameters,
+    execution: Execution,
+) -> V3dmaximaOutputs:
+    """
+    Locate extrema in a functional dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dmaximaOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dmaxima_cargs(params, execution)
+    ret = v_3dmaxima_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dmaxima(
+    input_dataset: InputPathType,
+    output_prefix: str | None = None,
+    threshold: float | None = None,
+    min_dist: float | None = None,
+    out_rad: float | None = None,
+    input_flag: bool = False,
+    spheres_1_flag: bool = False,
+    spheres_1to_n_flag: bool = False,
+    spheres_nto1_flag: bool = False,
+    neg_ext_flag: bool = False,
+    true_max_flag: bool = False,
+    dset_coords_flag: bool = False,
+    no_text_flag: bool = False,
+    coords_only_flag: bool = False,
+    n_style_sort_flag: bool = False,
+    n_style_weight_ave_flag: bool = False,
+    debug_level: float | None = None,
+    help_flag: bool = False,
+    hist_flag: bool = False,
+    ver_flag: bool = False,
+    runner: Runner | None = None,
+) -> V3dmaximaOutputs:
+    """
+    Locate extrema in a functional dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Specify input dataset (e.g. func+orig'[7]').
+        output_prefix: Prefix for an output mask dataset (e.g. -prefix\
+            maskNto1).
+        threshold: Provides a cutoff value for extrema (e.g. -thresh 17.4).
+        min_dist: Minimum acceptable distance between extrema in voxels (e.g.\
+            -min_dist 4).
+        out_rad: Set the output radius around extrema voxels in voxel units\
+            (e.g. -out_rad 9).
+        input_flag: Specify input dataset (e.g. -input func+orig'[7]').
+        spheres_1_flag: Set all output values to 1.
+        spheres_1to_n_flag: Output values will range from 1 to N.
+        spheres_nto1_flag: Output values will range from N to 1.
+        neg_ext_flag: Search for negative extrema (minima).
+        true_max_flag: Extrema may not have equal neighbors.
+        dset_coords_flag: Display output in the dataset orientation.
+        no_text_flag: Do not display the extrema points as text.
+        coords_only_flag: Only output coordinates (no text or values).
+        n_style_sort_flag: Use 'Sort-n-Remove' style (default).
+        n_style_weight_ave_flag: Use 'Weighted-Average' style.
+        debug_level: Output extra information to the terminal (e.g. -debug 2).
+        help_flag: Display help information.
+        hist_flag: Display module history.
+        ver_flag: Display version number.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dmaximaOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DMAXIMA_METADATA)
+    params = v_3dmaxima_params(
+        input_dataset=input_dataset,
+        output_prefix=output_prefix,
+        threshold=threshold,
+        min_dist=min_dist,
+        out_rad=out_rad,
+        input_flag=input_flag,
+        spheres_1_flag=spheres_1_flag,
+        spheres_1to_n_flag=spheres_1to_n_flag,
+        spheres_nto1_flag=spheres_nto1_flag,
+        neg_ext_flag=neg_ext_flag,
+        true_max_flag=true_max_flag,
+        dset_coords_flag=dset_coords_flag,
+        no_text_flag=no_text_flag,
+        coords_only_flag=coords_only_flag,
+        n_style_sort_flag=n_style_sort_flag,
+        n_style_weight_ave_flag=n_style_weight_ave_flag,
+        debug_level=debug_level,
+        help_flag=help_flag,
+        hist_flag=hist_flag,
+        ver_flag=ver_flag,
+    )
+    return v_3dmaxima_execute(params, execution)
+
+
+__all__ = [
+    "V3dmaximaOutputs",
+    "V3dmaximaParameters",
+    "V_3DMAXIMA_METADATA",
+    "v_3dmaxima",
+    "v_3dmaxima_params",
+]

niwrap_afni/afni/v_3dmerge.py

@@ -0,0 +1,305 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DMERGE_METADATA = Metadata(
+    id="7f1c2ca1745d4893ae0eaf6d19b9cf828f0a6f25.boutiques",
+    name="3dmerge",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dmergeParameters = typing.TypedDict('V3dmergeParameters', {
+    "__STYX_TYPE__": typing.Literal["3dmerge"],
+    "input_files": list[InputPathType],
+    "output_file": str,
+    "blur_fwhm": typing.NotRequired[float | None],
+    "threshold": typing.NotRequired[float | None],
+    "clust": typing.NotRequired[list[float] | None],
+    "dindex": typing.NotRequired[float | None],
+    "tindex": typing.NotRequired[float | None],
+    "absolute": bool,
+    "dxyz": bool,
+    "gmean": bool,
+    "gmax": bool,
+    "quiet": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dmerge": v_3dmerge_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 {
+        "3dmerge": v_3dmerge_outputs,
+    }.get(t)
+
+
+class V3dmergeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dmerge(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType
+    """Output dataset file"""
+
+
+def v_3dmerge_params(
+    input_files: list[InputPathType],
+    output_file: str,
+    blur_fwhm: float | None = None,
+    threshold: float | None = None,
+    clust: list[float] | None = None,
+    dindex: float | None = None,
+    tindex: float | None = None,
+    absolute: bool = False,
+    dxyz: bool = False,
+    gmean: bool = False,
+    gmax: bool = False,
+    quiet: bool = False,
+) -> V3dmergeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input dataset files.
+        output_file: Output dataset prefix.
+        blur_fwhm: Gaussian blur with FWHM in mm.
+        threshold: Threshold data to censor the intensities; only valid for\
+            'fith', 'fico', or 'fitt' datasets.
+        clust: Form clusters with connection distance and clip off data not in\
+            clusters of a minimum volume.
+        dindex: Specify sub-brick #j as the data source.
+        tindex: Specify sub-brick #k as the threshold source.
+        absolute: Take absolute values of intensities.
+        dxyz: Force cluster editing to behave as if all voxel dimensions were\
+            set to 1 mm.
+        gmean: Combine datasets by averaging intensities (default).
+        gmax: Combine datasets by taking max intensity.
+        quiet: Reduce the number of messages shown.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dmerge",
+        "input_files": input_files,
+        "output_file": output_file,
+        "absolute": absolute,
+        "dxyz": dxyz,
+        "gmean": gmean,
+        "gmax": gmax,
+        "quiet": quiet,
+    }
+    if blur_fwhm is not None:
+        params["blur_fwhm"] = blur_fwhm
+    if threshold is not None:
+        params["threshold"] = threshold
+    if clust is not None:
+        params["clust"] = clust
+    if dindex is not None:
+        params["dindex"] = dindex
+    if tindex is not None:
+        params["tindex"] = tindex
+    return params
+
+
+def v_3dmerge_cargs(
+    params: V3dmergeParameters,
+    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("3dmerge")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    cargs.extend([
+        "-prefix",
+        params.get("output_file")
+    ])
+    if params.get("blur_fwhm") is not None:
+        cargs.extend([
+            "-1blur_fwhm",
+            str(params.get("blur_fwhm"))
+        ])
+    if params.get("threshold") is not None:
+        cargs.extend([
+            "-1thresh",
+            str(params.get("threshold"))
+        ])
+    if params.get("clust") is not None:
+        cargs.extend([
+            "-1clust",
+            *map(str, params.get("clust"))
+        ])
+    if params.get("dindex") is not None:
+        cargs.extend([
+            "-1dindex",
+            str(params.get("dindex"))
+        ])
+    if params.get("tindex") is not None:
+        cargs.extend([
+            "-1tindex",
+            str(params.get("tindex"))
+        ])
+    if params.get("absolute"):
+        cargs.append("-1abs")
+    if params.get("dxyz"):
+        cargs.append("-dxyz=1")
+    if params.get("gmean"):
+        cargs.append("-gmean")
+    if params.get("gmax"):
+        cargs.append("-gmax")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    return cargs
+
+
+def v_3dmerge_outputs(
+    params: V3dmergeParameters,
+    execution: Execution,
+) -> V3dmergeOutputs:
+    """
+    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 = V3dmergeOutputs(
+        root=execution.output_file("."),
+        output_dataset=execution.output_file(params.get("output_file")),
+    )
+    return ret
+
+
+def v_3dmerge_execute(
+    params: V3dmergeParameters,
+    execution: Execution,
+) -> V3dmergeOutputs:
+    """
+    3dmerge edits and merges 3D datasets by applying various operations like
+    thresholding, blurring, clustering, and more.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dmergeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dmerge_cargs(params, execution)
+    ret = v_3dmerge_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dmerge(
+    input_files: list[InputPathType],
+    output_file: str,
+    blur_fwhm: float | None = None,
+    threshold: float | None = None,
+    clust: list[float] | None = None,
+    dindex: float | None = None,
+    tindex: float | None = None,
+    absolute: bool = False,
+    dxyz: bool = False,
+    gmean: bool = False,
+    gmax: bool = False,
+    quiet: bool = False,
+    runner: Runner | None = None,
+) -> V3dmergeOutputs:
+    """
+    3dmerge edits and merges 3D datasets by applying various operations like
+    thresholding, blurring, clustering, and more.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input dataset files.
+        output_file: Output dataset prefix.
+        blur_fwhm: Gaussian blur with FWHM in mm.
+        threshold: Threshold data to censor the intensities; only valid for\
+            'fith', 'fico', or 'fitt' datasets.
+        clust: Form clusters with connection distance and clip off data not in\
+            clusters of a minimum volume.
+        dindex: Specify sub-brick #j as the data source.
+        tindex: Specify sub-brick #k as the threshold source.
+        absolute: Take absolute values of intensities.
+        dxyz: Force cluster editing to behave as if all voxel dimensions were\
+            set to 1 mm.
+        gmean: Combine datasets by averaging intensities (default).
+        gmax: Combine datasets by taking max intensity.
+        quiet: Reduce the number of messages shown.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dmergeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DMERGE_METADATA)
+    params = v_3dmerge_params(
+        input_files=input_files,
+        output_file=output_file,
+        blur_fwhm=blur_fwhm,
+        threshold=threshold,
+        clust=clust,
+        dindex=dindex,
+        tindex=tindex,
+        absolute=absolute,
+        dxyz=dxyz,
+        gmean=gmean,
+        gmax=gmax,
+        quiet=quiet,
+    )
+    return v_3dmerge_execute(params, execution)
+
+
+__all__ = [
+    "V3dmergeOutputs",
+    "V3dmergeParameters",
+    "V_3DMERGE_METADATA",
+    "v_3dmerge",
+    "v_3dmerge_params",
+]