niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_automask.py

@@ -0,0 +1,258 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_AUTOMASK_METADATA = Metadata(
+    id="82a07079691dfc6d4da9b82882274fb3db4cb678.boutiques",
+    name="3dAutomask",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dAutomaskParameters = typing.TypedDict('V3dAutomaskParameters', {
+    "__STYX_TYPE__": typing.Literal["3dAutomask"],
+    "prefix": typing.NotRequired[str | None],
+    "apply_prefix": typing.NotRequired[str | None],
+    "clfrac": typing.NotRequired[float | None],
+    "dilate": typing.NotRequired[int | None],
+    "erode": typing.NotRequired[int | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "in_file": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dAutomask": v_3d_automask_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 {
+        "3dAutomask": v_3d_automask_outputs,
+    }.get(t)
+
+
+class V3dAutomaskOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_automask(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    brain_file: OutputPathType | None
+    """Output file from 3dautomask."""
+    mask_file: OutputPathType | None
+    """Output image file name."""
+
+
+def v_3d_automask_params(
+    in_file: InputPathType,
+    prefix: str | None = None,
+    apply_prefix: str | None = None,
+    clfrac: float | None = None,
+    dilate: int | None = None,
+    erode: int | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+) -> V3dAutomaskParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_file: Input file to 3dautomask.
+        prefix: Write mask into dataset with prefix 'ppp'. [Default ==\
+            'automask'].
+        apply_prefix: Apply mask to input dataset and save masked dataset.
+        clfrac: Sets the clip level fraction (must be 0.1-0.9). a small value\
+            will tend to make the mask larger [default = 0.5].
+        dilate: Dilate the mask outwards.
+        erode: Erode the mask inwards.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dAutomask",
+        "in_file": in_file,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if apply_prefix is not None:
+        params["apply_prefix"] = apply_prefix
+    if clfrac is not None:
+        params["clfrac"] = clfrac
+    if dilate is not None:
+        params["dilate"] = dilate
+    if erode is not None:
+        params["erode"] = erode
+    if outputtype is not None:
+        params["outputtype"] = outputtype
+    return params
+
+
+def v_3d_automask_cargs(
+    params: V3dAutomaskParameters,
+    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("3dAutomask")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("apply_prefix") is not None:
+        cargs.extend([
+            "-apply_prefix",
+            params.get("apply_prefix")
+        ])
+    if params.get("clfrac") is not None:
+        cargs.extend([
+            "-clfrac",
+            str(params.get("clfrac"))
+        ])
+    if params.get("dilate") is not None:
+        cargs.extend([
+            "-dilate",
+            str(params.get("dilate"))
+        ])
+    if params.get("erode") is not None:
+        cargs.extend([
+            "-erode",
+            str(params.get("erode"))
+        ])
+    if params.get("outputtype") is not None:
+        cargs.append(params.get("outputtype"))
+    cargs.append(execution.input_file(params.get("in_file")))
+    return cargs
+
+
+def v_3d_automask_outputs(
+    params: V3dAutomaskParameters,
+    execution: Execution,
+) -> V3dAutomaskOutputs:
+    """
+    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 = V3dAutomaskOutputs(
+        root=execution.output_file("."),
+        brain_file=execution.output_file(params.get("apply_prefix")) if (params.get("apply_prefix") is not None) else None,
+        mask_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_automask_execute(
+    params: V3dAutomaskParameters,
+    execution: Execution,
+) -> V3dAutomaskOutputs:
+    """
+    Create a brain-only mask of the image using AFNI 3dAutomask command.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dAutomaskOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_automask_cargs(params, execution)
+    ret = v_3d_automask_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_automask(
+    in_file: InputPathType,
+    prefix: str | None = None,
+    apply_prefix: str | None = None,
+    clfrac: float | None = None,
+    dilate: int | None = None,
+    erode: int | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    runner: Runner | None = None,
+) -> V3dAutomaskOutputs:
+    """
+    Create a brain-only mask of the image using AFNI 3dAutomask command.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_file: Input file to 3dautomask.
+        prefix: Write mask into dataset with prefix 'ppp'. [Default ==\
+            'automask'].
+        apply_prefix: Apply mask to input dataset and save masked dataset.
+        clfrac: Sets the clip level fraction (must be 0.1-0.9). a small value\
+            will tend to make the mask larger [default = 0.5].
+        dilate: Dilate the mask outwards.
+        erode: Erode the mask inwards.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dAutomaskOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AUTOMASK_METADATA)
+    params = v_3d_automask_params(
+        prefix=prefix,
+        apply_prefix=apply_prefix,
+        clfrac=clfrac,
+        dilate=dilate,
+        erode=erode,
+        outputtype=outputtype,
+        in_file=in_file,
+    )
+    return v_3d_automask_execute(params, execution)
+
+
+__all__ = [
+    "V3dAutomaskOutputs",
+    "V3dAutomaskParameters",
+    "V_3D_AUTOMASK_METADATA",
+    "v_3d_automask",
+    "v_3d_automask_params",
+]

niwrap_afni/afni/v_3d_ball_match.py

@@ -0,0 +1,229 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_BALL_MATCH_METADATA = Metadata(
+    id="fe3fd0a09e1cb0531678dcf999710e6d7163d194.boutiques",
+    name="3dBallMatch",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dBallMatchParameters = typing.TypedDict('V3dBallMatchParameters', {
+    "__STYX_TYPE__": typing.Literal["3dBallMatch"],
+    "input_dataset": InputPathType,
+    "radius": typing.NotRequired[float | None],
+    "dataset_option": typing.NotRequired[str | None],
+    "ball_radius": typing.NotRequired[float | None],
+    "spheroid_axes": typing.NotRequired[list[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 {
+        "3dBallMatch": v_3d_ball_match_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 {
+        "3dBallMatch": v_3d_ball_match_outputs,
+    }.get(t)
+
+
+class V3dBallMatchOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_ball_match(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_stdout: OutputPathType
+    """Output containing matching coordinates and related data"""
+
+
+def v_3d_ball_match_params(
+    input_dataset: InputPathType,
+    radius: float | None = None,
+    dataset_option: str | None = None,
+    ball_radius: float | None = None,
+    spheroid_axes: list[float] | None = None,
+) -> V3dBallMatchParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset (e.g., Fred.nii).
+        radius: Radius of the 3D ball to match (in mm).
+        dataset_option: Specifies the input dataset.
+        ball_radius: Set the radius of the 3D ball to match (mm).
+        spheroid_axes: Match with a spheroid of revolution, with principal axis\
+            radius 'a' and secondary axes radii 'b'.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dBallMatch",
+        "input_dataset": input_dataset,
+    }
+    if radius is not None:
+        params["radius"] = radius
+    if dataset_option is not None:
+        params["dataset_option"] = dataset_option
+    if ball_radius is not None:
+        params["ball_radius"] = ball_radius
+    if spheroid_axes is not None:
+        params["spheroid_axes"] = spheroid_axes
+    return params
+
+
+def v_3d_ball_match_cargs(
+    params: V3dBallMatchParameters,
+    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("3dBallMatch")
+    cargs.append(execution.input_file(params.get("input_dataset")))
+    if params.get("radius") is not None:
+        cargs.append(str(params.get("radius")))
+    if params.get("dataset_option") is not None:
+        cargs.extend([
+            "-input",
+            params.get("dataset_option")
+        ])
+    if params.get("ball_radius") is not None:
+        cargs.extend([
+            "-ball",
+            str(params.get("ball_radius"))
+        ])
+    if params.get("spheroid_axes") is not None:
+        cargs.extend([
+            "-spheroid",
+            *map(str, params.get("spheroid_axes"))
+        ])
+    return cargs
+
+
+def v_3d_ball_match_outputs(
+    params: V3dBallMatchParameters,
+    execution: Execution,
+) -> V3dBallMatchOutputs:
+    """
+    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 = V3dBallMatchOutputs(
+        root=execution.output_file("."),
+        output_stdout=execution.output_file("stdout"),
+    )
+    return ret
+
+
+def v_3d_ball_match_execute(
+    params: V3dBallMatchParameters,
+    execution: Execution,
+) -> V3dBallMatchOutputs:
+    """
+    A tool to find a good match between a ball (filled sphere) of the given radius
+    and a dataset to determine a crude approximate center of the brain quickly.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dBallMatchOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_ball_match_cargs(params, execution)
+    ret = v_3d_ball_match_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_ball_match(
+    input_dataset: InputPathType,
+    radius: float | None = None,
+    dataset_option: str | None = None,
+    ball_radius: float | None = None,
+    spheroid_axes: list[float] | None = None,
+    runner: Runner | None = None,
+) -> V3dBallMatchOutputs:
+    """
+    A tool to find a good match between a ball (filled sphere) of the given radius
+    and a dataset to determine a crude approximate center of the brain quickly.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset (e.g., Fred.nii).
+        radius: Radius of the 3D ball to match (in mm).
+        dataset_option: Specifies the input dataset.
+        ball_radius: Set the radius of the 3D ball to match (mm).
+        spheroid_axes: Match with a spheroid of revolution, with principal axis\
+            radius 'a' and secondary axes radii 'b'.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dBallMatchOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_BALL_MATCH_METADATA)
+    params = v_3d_ball_match_params(
+        input_dataset=input_dataset,
+        radius=radius,
+        dataset_option=dataset_option,
+        ball_radius=ball_radius,
+        spheroid_axes=spheroid_axes,
+    )
+    return v_3d_ball_match_execute(params, execution)
+
+
+__all__ = [
+    "V3dBallMatchOutputs",
+    "V3dBallMatchParameters",
+    "V_3D_BALL_MATCH_METADATA",
+    "v_3d_ball_match",
+    "v_3d_ball_match_params",
+]