niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3dedge3.py

@@ -0,0 +1,269 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DEDGE3_METADATA = Metadata(
+    id="313abf8e7b3a12af92fa8fc519ae8bca1a87eaf0.boutiques",
+    name="3dedge3",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dedge3Parameters = typing.TypedDict('V3dedge3Parameters', {
+    "__STYX_TYPE__": typing.Literal["3dedge3"],
+    "input_file": InputPathType,
+    "verbose": bool,
+    "prefix": typing.NotRequired[str | None],
+    "datum": typing.NotRequired[str | None],
+    "fscale": bool,
+    "gscale": bool,
+    "nscale": bool,
+    "scale_floats": typing.NotRequired[float | None],
+    "automask": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dedge3": v_3dedge3_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 {
+        "3dedge3": v_3dedge3_outputs,
+    }.get(t)
+
+
+class V3dedge3Outputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dedge3(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """Output dataset"""
+
+
+def v_3dedge3_params(
+    input_file: InputPathType,
+    verbose: bool = False,
+    prefix: str | None = None,
+    datum: str | None = None,
+    fscale: bool = False,
+    gscale: bool = False,
+    nscale: bool = False,
+    scale_floats: float | None = None,
+    automask: bool = False,
+) -> V3dedge3Parameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input dataset.
+        verbose: Print out some information along the way.
+        prefix: Sets the prefix of the output dataset.
+        datum: Sets the datum of the output dataset.
+        fscale: Force scaling of the output to the maximum integer range.
+        gscale: Same as '-fscale', but also forces each output sub-brick to get\
+            the same scaling factor.
+        nscale: Don't do any scaling on output to byte or short datasets.
+        scale_floats: Multiply input by VAL, but only if the input datum is\
+            float.
+        automask: For automatic internal calculation of a mask in the usual\
+            AFNI way.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dedge3",
+        "input_file": input_file,
+        "verbose": verbose,
+        "fscale": fscale,
+        "gscale": gscale,
+        "nscale": nscale,
+        "automask": automask,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if datum is not None:
+        params["datum"] = datum
+    if scale_floats is not None:
+        params["scale_floats"] = scale_floats
+    return params
+
+
+def v_3dedge3_cargs(
+    params: V3dedge3Parameters,
+    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("3dedge3")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    if params.get("verbose"):
+        cargs.append("-verbose")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("datum") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("datum")
+        ])
+    if params.get("fscale"):
+        cargs.append("-fscale")
+    if params.get("gscale"):
+        cargs.append("-gscale")
+    if params.get("nscale"):
+        cargs.append("-nscale")
+    if params.get("scale_floats") is not None:
+        cargs.extend([
+            "-scale_floats",
+            str(params.get("scale_floats"))
+        ])
+    if params.get("automask"):
+        cargs.append("-automask")
+    return cargs
+
+
+def v_3dedge3_outputs(
+    params: V3dedge3Parameters,
+    execution: Execution,
+) -> V3dedge3Outputs:
+    """
+    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 = V3dedge3Outputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3dedge3_execute(
+    params: V3dedge3Parameters,
+    execution: Execution,
+) -> V3dedge3Outputs:
+    """
+    Does 3D Edge detection using the library 3DEdge.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dedge3Outputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dedge3_cargs(params, execution)
+    ret = v_3dedge3_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dedge3(
+    input_file: InputPathType,
+    verbose: bool = False,
+    prefix: str | None = None,
+    datum: str | None = None,
+    fscale: bool = False,
+    gscale: bool = False,
+    nscale: bool = False,
+    scale_floats: float | None = None,
+    automask: bool = False,
+    runner: Runner | None = None,
+) -> V3dedge3Outputs:
+    """
+    Does 3D Edge detection using the library 3DEdge.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Input dataset.
+        verbose: Print out some information along the way.
+        prefix: Sets the prefix of the output dataset.
+        datum: Sets the datum of the output dataset.
+        fscale: Force scaling of the output to the maximum integer range.
+        gscale: Same as '-fscale', but also forces each output sub-brick to get\
+            the same scaling factor.
+        nscale: Don't do any scaling on output to byte or short datasets.
+        scale_floats: Multiply input by VAL, but only if the input datum is\
+            float.
+        automask: For automatic internal calculation of a mask in the usual\
+            AFNI way.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dedge3Outputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DEDGE3_METADATA)
+    params = v_3dedge3_params(
+        input_file=input_file,
+        verbose=verbose,
+        prefix=prefix,
+        datum=datum,
+        fscale=fscale,
+        gscale=gscale,
+        nscale=nscale,
+        scale_floats=scale_floats,
+        automask=automask,
+    )
+    return v_3dedge3_execute(params, execution)
+
+
+__all__ = [
+    "V3dedge3Outputs",
+    "V3dedge3Parameters",
+    "V_3DEDGE3_METADATA",
+    "v_3dedge3",
+    "v_3dedge3_params",
+]

niwrap_afni/afni/v_3dedgedog.py

@@ -0,0 +1,344 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DEDGEDOG_METADATA = Metadata(
+    id="9e99566b54cfbbe32a2b727088bdd1879b2a5924.boutiques",
+    name="3dedgedog",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dedgedogParameters = typing.TypedDict('V3dedgedogParameters', {
+    "__STYX_TYPE__": typing.Literal["3dedgedog"],
+    "input": InputPathType,
+    "prefix": str,
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": typing.NotRequired[str | None],
+    "sigma_rad": typing.NotRequired[float | None],
+    "sigma_nvox": typing.NotRequired[float | None],
+    "ratio_sigma": typing.NotRequired[float | None],
+    "output_intermed": bool,
+    "edge_bnd_nn": typing.NotRequired[float | None],
+    "edge_bnd_side": typing.NotRequired[str | None],
+    "edge_bnd_scale": bool,
+    "only2d": 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 {
+        "3dedgedog": v_3dedgedog_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 {
+        "3dedgedog": v_3dedgedog_outputs,
+    }.get(t)
+
+
+class V3dedgedogOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dedgedog(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_edge: OutputPathType
+    """Output edge dataset"""
+    out_dog: OutputPathType
+    """Output difference of Gaussian dataset"""
+    out_edt2: OutputPathType
+    """Output Euclidean Distance Transform squared dataset"""
+    out_blur_inner: OutputPathType
+    """Output inner Gaussian blurred dataset"""
+    out_blur_outer: OutputPathType
+    """Output outer Gaussian blurred dataset"""
+
+
+def v_3dedgedog_params(
+    input_: InputPathType,
+    prefix: str,
+    mask: InputPathType | None = None,
+    automask: str | None = None,
+    sigma_rad: float | None = None,
+    sigma_nvox: float | None = None,
+    ratio_sigma: float | None = None,
+    output_intermed: bool = False,
+    edge_bnd_nn: float | None = None,
+    edge_bnd_side: str | None = None,
+    edge_bnd_scale: bool = False,
+    only2d: str | None = None,
+) -> V3dedgedogParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: Input dataset.
+        prefix: Output prefix name.
+        mask: Mask dataset applied after Euclidean Distance Transform\
+            calculation.
+        automask: Calculate mask automatically. Optionally, you can provide an\
+            integer X to dilate the initial automask X times (e.g., -automask+X).
+        sigma_rad: Radius for 'inner' Gaussian, in mm; must be greater than 0\
+            (default: 1.40).
+        sigma_nvox: Define radius for 'inner' Gaussian by providing a\
+            multiplicative factor for voxel edge length greater than 0 (default:\
+            use sigma_rad).
+        ratio_sigma: Ratio of inner and outer Gaussian sigma values (default:\
+            1.40).
+        output_intermed: Output intermediate datasets: DOG, EDT2, BLURS\
+            (default: not output).
+        edge_bnd_nn: Nearest neighbor (NN) value for connectedness of\
+            boundaries; must be 1 (face only), 2 (face+edge), or 3 (face+edge+node)\
+            (default: 1).
+        edge_bnd_side: Specify boundary layer to use: NEG, POS, BOTH, BOTH_SIGN\
+            (default: NEG).
+        edge_bnd_scale: Scale edge values to have relative magnitude between 0\
+            and 100 (default: edge locations have value=1).
+        only2d: Calculate edges in 2D per plane specified by SLI: 'axi', 'cor',\
+            'sag'.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dedgedog",
+        "input": input_,
+        "prefix": prefix,
+        "output_intermed": output_intermed,
+        "edge_bnd_scale": edge_bnd_scale,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if automask is not None:
+        params["automask"] = automask
+    if sigma_rad is not None:
+        params["sigma_rad"] = sigma_rad
+    if sigma_nvox is not None:
+        params["sigma_nvox"] = sigma_nvox
+    if ratio_sigma is not None:
+        params["ratio_sigma"] = ratio_sigma
+    if edge_bnd_nn is not None:
+        params["edge_bnd_nn"] = edge_bnd_nn
+    if edge_bnd_side is not None:
+        params["edge_bnd_side"] = edge_bnd_side
+    if only2d is not None:
+        params["only2d"] = only2d
+    return params
+
+
+def v_3dedgedog_cargs(
+    params: V3dedgedogParameters,
+    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("3dedgedog")
+    cargs.append(execution.input_file(params.get("input")))
+    cargs.append(params.get("prefix"))
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("automask") is not None:
+        cargs.extend([
+            "-automask",
+            params.get("automask")
+        ])
+    if params.get("sigma_rad") is not None:
+        cargs.extend([
+            "-sigma_rad",
+            str(params.get("sigma_rad"))
+        ])
+    if params.get("sigma_nvox") is not None:
+        cargs.extend([
+            "-sigma_nvox",
+            str(params.get("sigma_nvox"))
+        ])
+    if params.get("ratio_sigma") is not None:
+        cargs.extend([
+            "-ratio_sigma",
+            str(params.get("ratio_sigma"))
+        ])
+    if params.get("output_intermed"):
+        cargs.append("-output_intermed")
+    if params.get("edge_bnd_nn") is not None:
+        cargs.extend([
+            "-edge_bnd_NN",
+            str(params.get("edge_bnd_nn"))
+        ])
+    if params.get("edge_bnd_side") is not None:
+        cargs.extend([
+            "-edge_bnd_side",
+            params.get("edge_bnd_side")
+        ])
+    if params.get("edge_bnd_scale"):
+        cargs.append("-edge_bnd_scale")
+    if params.get("only2d") is not None:
+        cargs.extend([
+            "-only2D",
+            params.get("only2d")
+        ])
+    return cargs
+
+
+def v_3dedgedog_outputs(
+    params: V3dedgedogParameters,
+    execution: Execution,
+) -> V3dedgedogOutputs:
+    """
+    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 = V3dedgedogOutputs(
+        root=execution.output_file("."),
+        out_edge=execution.output_file(params.get("prefix") + "_edge.nii.gz"),
+        out_dog=execution.output_file(params.get("prefix") + "_dog.nii.gz"),
+        out_edt2=execution.output_file(params.get("prefix") + "_edt2.nii.gz"),
+        out_blur_inner=execution.output_file(params.get("prefix") + "_blur_inner.nii.gz"),
+        out_blur_outer=execution.output_file(params.get("prefix") + "_blur_outer.nii.gz"),
+    )
+    return ret
+
+
+def v_3dedgedog_execute(
+    params: V3dedgedogParameters,
+    execution: Execution,
+) -> V3dedgedogOutputs:
+    """
+    Calculate edges in an image using the Difference of Gaussians (DOG) method with
+    extensions/tweaks of the Marr-Hildreth algorithm.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dedgedogOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dedgedog_cargs(params, execution)
+    ret = v_3dedgedog_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dedgedog(
+    input_: InputPathType,
+    prefix: str,
+    mask: InputPathType | None = None,
+    automask: str | None = None,
+    sigma_rad: float | None = None,
+    sigma_nvox: float | None = None,
+    ratio_sigma: float | None = None,
+    output_intermed: bool = False,
+    edge_bnd_nn: float | None = None,
+    edge_bnd_side: str | None = None,
+    edge_bnd_scale: bool = False,
+    only2d: str | None = None,
+    runner: Runner | None = None,
+) -> V3dedgedogOutputs:
+    """
+    Calculate edges in an image using the Difference of Gaussians (DOG) method with
+    extensions/tweaks of the Marr-Hildreth algorithm.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_: Input dataset.
+        prefix: Output prefix name.
+        mask: Mask dataset applied after Euclidean Distance Transform\
+            calculation.
+        automask: Calculate mask automatically. Optionally, you can provide an\
+            integer X to dilate the initial automask X times (e.g., -automask+X).
+        sigma_rad: Radius for 'inner' Gaussian, in mm; must be greater than 0\
+            (default: 1.40).
+        sigma_nvox: Define radius for 'inner' Gaussian by providing a\
+            multiplicative factor for voxel edge length greater than 0 (default:\
+            use sigma_rad).
+        ratio_sigma: Ratio of inner and outer Gaussian sigma values (default:\
+            1.40).
+        output_intermed: Output intermediate datasets: DOG, EDT2, BLURS\
+            (default: not output).
+        edge_bnd_nn: Nearest neighbor (NN) value for connectedness of\
+            boundaries; must be 1 (face only), 2 (face+edge), or 3 (face+edge+node)\
+            (default: 1).
+        edge_bnd_side: Specify boundary layer to use: NEG, POS, BOTH, BOTH_SIGN\
+            (default: NEG).
+        edge_bnd_scale: Scale edge values to have relative magnitude between 0\
+            and 100 (default: edge locations have value=1).
+        only2d: Calculate edges in 2D per plane specified by SLI: 'axi', 'cor',\
+            'sag'.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dedgedogOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DEDGEDOG_METADATA)
+    params = v_3dedgedog_params(
+        input_=input_,
+        prefix=prefix,
+        mask=mask,
+        automask=automask,
+        sigma_rad=sigma_rad,
+        sigma_nvox=sigma_nvox,
+        ratio_sigma=ratio_sigma,
+        output_intermed=output_intermed,
+        edge_bnd_nn=edge_bnd_nn,
+        edge_bnd_side=edge_bnd_side,
+        edge_bnd_scale=edge_bnd_scale,
+        only2d=only2d,
+    )
+    return v_3dedgedog_execute(params, execution)
+
+
+__all__ = [
+    "V3dedgedogOutputs",
+    "V3dedgedogParameters",
+    "V_3DEDGEDOG_METADATA",
+    "v_3dedgedog",
+    "v_3dedgedog_params",
+]