niwrap-freesurfer 0.5.0__py3-none-any.whl → 0.5.2__py3-none-any.whl

niwrap_freesurfer/freesurfer/bet_fsl.py

@@ -1,441 +0,0 @@
-# This file was auto generated by Styx.
-# Do not edit this file directly.
-
-import typing
-import pathlib
-from styxdefs import *
-
-BET_FSL_METADATA = Metadata(
-    id="05134dd9049bee70d91cad11059af4110900a569.boutiques",
-    name="bet.fsl",
-    package="freesurfer",
-    container_image_tag="freesurfer/freesurfer:7.4.1",
-)
-
-
-BetFslParameters = typing.TypedDict('BetFslParameters', {
-    "__STYX_TYPE__": typing.Literal["bet.fsl"],
-    "infile": InputPathType,
-    "maskfile": str,
-    "fractional_intensity": typing.NotRequired[float | None],
-    "vg_fractional_intensity": typing.NotRequired[float | None],
-    "center_of_gravity": typing.NotRequired[list[float] | None],
-    "overlay": bool,
-    "binary_mask": bool,
-    "approx_skull": bool,
-    "no_seg_output": bool,
-    "vtk_mesh": bool,
-    "head_radius": typing.NotRequired[float | None],
-    "thresholding": bool,
-    "robust_iters": bool,
-    "residual_optic_cleanup": bool,
-    "reduce_bias": bool,
-    "slice_padding": bool,
-    "whole_set_mask": bool,
-    "additional_surfaces": bool,
-    "additional_surfaces_t2": typing.NotRequired[InputPathType | None],
-    "verbose": bool,
-    "debug": bool,
-})
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "bet.fsl": bet_fsl_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 {
-        "bet.fsl": bet_fsl_outputs,
-    }.get(t)
-
-
-class BetFslOutputs(typing.NamedTuple):
-    """
-    Output object returned when calling `bet_fsl(...)`.
-    """
-    root: OutputPathType
-    """Output root folder. This is the root folder for all outputs."""
-    outfile: OutputPathType
-    """Main default mask output of BET"""
-    binary_mask: OutputPathType
-    """Binary mask file (from -m option)"""
-    overlay_file: OutputPathType
-    """Overlaid brain surface onto original image"""
-    approx_skull_img: OutputPathType
-    """Approximate skull image file"""
-    output_vtk_mesh: OutputPathType
-    """Mesh in VTK format"""
-    skull_mask: OutputPathType
-    """Output mask for skull image"""
-    out_inskull_mask: OutputPathType
-    """The in-skull mask file from betsurf"""
-    out_inskull_mesh: OutputPathType
-    """The in-skull mesh file from betsurf"""
-    out_inskull_off: OutputPathType
-    """The in-skull mesh .off file from betsurf"""
-    out_outskin_mask: OutputPathType
-    """The out-skin mask file from betsurf"""
-    out_outskin_mesh: OutputPathType
-    """The out-skin mesh file from betsurf"""
-    out_outskin_off: OutputPathType
-    """The out-skin mesh .off file from betsurf"""
-    out_outskull_mask: OutputPathType
-    """The out-skull mask file from betsurf"""
-    out_outskull_mesh: OutputPathType
-    """The out-skull mesh file from betsurf"""
-    out_outskull_off: OutputPathType
-    """The out-skull mesh .off file from betsurf"""
-
-
-def bet_fsl_params(
-    infile: InputPathType,
-    maskfile: str = "img_bet",
-    fractional_intensity: float | None = None,
-    vg_fractional_intensity: float | None = None,
-    center_of_gravity: list[float] | None = None,
-    overlay: bool = False,
-    binary_mask: bool = False,
-    approx_skull: bool = False,
-    no_seg_output: bool = False,
-    vtk_mesh: bool = False,
-    head_radius: float | None = None,
-    thresholding: bool = False,
-    robust_iters: bool = False,
-    residual_optic_cleanup: bool = False,
-    reduce_bias: bool = False,
-    slice_padding: bool = False,
-    whole_set_mask: bool = False,
-    additional_surfaces: bool = False,
-    additional_surfaces_t2: InputPathType | None = None,
-    verbose: bool = False,
-    debug: bool = False,
-) -> BetFslParameters:
-    """
-    Build parameters.
-    
-    Args:
-        infile: Input image (e.g. img.nii.gz).
-        maskfile: Output brain mask (e.g. img_bet.nii.gz).
-        fractional_intensity: Fractional intensity threshold (0->1);\
-            default=0.5; smaller values give larger brain outline estimates.
-        vg_fractional_intensity: Vertical gradient in fractional intensity\
-            threshold (-1->1); default=0; positive values give larger brain outline\
-            at bottom, smaller at top.
-        center_of_gravity: The xyz coordinates of the center of gravity\
-            (voxels, not mm) of initial mesh surface. Must have exactly three\
-            numerical entries in the list (3-vector).
-        overlay: Generate brain surface outline overlaid onto original image.
-        binary_mask: Generate binary brain mask.
-        approx_skull: Generate approximate skull image.
-        no_seg_output: Don't generate segmented brain image output.
-        vtk_mesh: Generate brain surface as mesh in .vtk format.
-        head_radius: Head radius (mm not voxels); initial surface sphere is set\
-            to half of this.
-        thresholding: Apply thresholding to segmented brain image and mask.
-        robust_iters: Robust brain centre estimation (iterates BET several\
-            times).
-        residual_optic_cleanup: Eye & optic nerve cleanup (can be useful in\
-            SIENA).
-        reduce_bias: Bias field & neck cleanup (can be useful in SIENA).
-        slice_padding: Improve BET if FOV is very small in Z (by temporarily\
-            padding end slices).
-        whole_set_mask: Apply to 4D FMRI data (uses -f 0.3 and dilates brain\
-            mask slightly).
-        additional_surfaces: Run bet2 and then betsurf to get additional skull\
-            and scalp surfaces (includes registrations).
-        additional_surfaces_t2: As with -A, when also feeding in\
-            non-brain-extracted T2 (includes registrations).
-        verbose: Verbose (switch on diagnostic messages).
-        debug: Debug (don't delete temporary intermediate images).
-    Returns:
-        Parameter dictionary
-    """
-    params = {
-        "__STYXTYPE__": "bet.fsl",
-        "infile": infile,
-        "maskfile": maskfile,
-        "overlay": overlay,
-        "binary_mask": binary_mask,
-        "approx_skull": approx_skull,
-        "no_seg_output": no_seg_output,
-        "vtk_mesh": vtk_mesh,
-        "thresholding": thresholding,
-        "robust_iters": robust_iters,
-        "residual_optic_cleanup": residual_optic_cleanup,
-        "reduce_bias": reduce_bias,
-        "slice_padding": slice_padding,
-        "whole_set_mask": whole_set_mask,
-        "additional_surfaces": additional_surfaces,
-        "verbose": verbose,
-        "debug": debug,
-    }
-    if fractional_intensity is not None:
-        params["fractional_intensity"] = fractional_intensity
-    if vg_fractional_intensity is not None:
-        params["vg_fractional_intensity"] = vg_fractional_intensity
-    if center_of_gravity is not None:
-        params["center_of_gravity"] = center_of_gravity
-    if head_radius is not None:
-        params["head_radius"] = head_radius
-    if additional_surfaces_t2 is not None:
-        params["additional_surfaces_t2"] = additional_surfaces_t2
-    return params
-
-
-def bet_fsl_cargs(
-    params: BetFslParameters,
-    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("bet.fsl")
-    cargs.append(execution.input_file(params.get("infile")))
-    cargs.append(params.get("maskfile"))
-    if params.get("fractional_intensity") is not None:
-        cargs.extend([
-            "-f",
-            str(params.get("fractional_intensity"))
-        ])
-    if params.get("vg_fractional_intensity") is not None:
-        cargs.extend([
-            "-g",
-            str(params.get("vg_fractional_intensity"))
-        ])
-    if params.get("center_of_gravity") is not None:
-        cargs.extend([
-            "-c",
-            *map(str, params.get("center_of_gravity"))
-        ])
-    if params.get("overlay"):
-        cargs.append("-o")
-    if params.get("binary_mask"):
-        cargs.append("-m")
-    if params.get("approx_skull"):
-        cargs.append("-s")
-    if params.get("no_seg_output"):
-        cargs.append("-n")
-    if params.get("vtk_mesh"):
-        cargs.append("-e")
-    if params.get("head_radius") is not None:
-        cargs.extend([
-            "-r",
-            str(params.get("head_radius"))
-        ])
-    if params.get("thresholding"):
-        cargs.append("-t")
-    if params.get("robust_iters"):
-        cargs.append("-R")
-    if params.get("residual_optic_cleanup"):
-        cargs.append("-S")
-    if params.get("reduce_bias"):
-        cargs.append("-B")
-    if params.get("slice_padding"):
-        cargs.append("-Z")
-    if params.get("whole_set_mask"):
-        cargs.append("-F")
-    if params.get("additional_surfaces"):
-        cargs.append("-A")
-    if params.get("additional_surfaces_t2") is not None:
-        cargs.extend([
-            "-A2",
-            execution.input_file(params.get("additional_surfaces_t2"))
-        ])
-    if params.get("verbose"):
-        cargs.append("-v")
-    if params.get("debug"):
-        cargs.append("-d")
-    return cargs
-
-
-def bet_fsl_outputs(
-    params: BetFslParameters,
-    execution: Execution,
-) -> BetFslOutputs:
-    """
-    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 = BetFslOutputs(
-        root=execution.output_file("."),
-        outfile=execution.output_file(params.get("maskfile") + ".nii.gz"),
-        binary_mask=execution.output_file(params.get("maskfile") + "_mask.nii.gz"),
-        overlay_file=execution.output_file(params.get("maskfile") + "_overlay.nii.gz"),
-        approx_skull_img=execution.output_file(params.get("maskfile") + "_skull.nii.gz"),
-        output_vtk_mesh=execution.output_file(params.get("maskfile") + "_mesh.vtk"),
-        skull_mask=execution.output_file(params.get("maskfile") + "_skull_mask.nii.gz"),
-        out_inskull_mask=execution.output_file(params.get("maskfile") + "_inskull_mask.nii.gz"),
-        out_inskull_mesh=execution.output_file(params.get("maskfile") + "_inskull_mesh.nii.gz"),
-        out_inskull_off=execution.output_file(params.get("maskfile") + "_inskull_mesh.off"),
-        out_outskin_mask=execution.output_file(params.get("maskfile") + "_outskin_mask.nii.gz"),
-        out_outskin_mesh=execution.output_file(params.get("maskfile") + "_outskin_mesh.nii.gz"),
-        out_outskin_off=execution.output_file(params.get("maskfile") + "_outskin_mesh.off"),
-        out_outskull_mask=execution.output_file(params.get("maskfile") + "_outskull_mask.nii.gz"),
-        out_outskull_mesh=execution.output_file(params.get("maskfile") + "_outskull_mesh.nii.gz"),
-        out_outskull_off=execution.output_file(params.get("maskfile") + "_outskull_mesh.off"),
-    )
-    return ret
-
-
-def bet_fsl_execute(
-    params: BetFslParameters,
-    execution: Execution,
-) -> BetFslOutputs:
-    """
-    Automated brain extraction tool for FSL.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        params: The parameters.
-        execution: The execution object.
-    Returns:
-        NamedTuple of outputs (described in `BetFslOutputs`).
-    """
-    params = execution.params(params)
-    cargs = bet_fsl_cargs(params, execution)
-    ret = bet_fsl_outputs(params, execution)
-    execution.run(cargs)
-    return ret
-
-
-def bet_fsl(
-    infile: InputPathType,
-    maskfile: str = "img_bet",
-    fractional_intensity: float | None = None,
-    vg_fractional_intensity: float | None = None,
-    center_of_gravity: list[float] | None = None,
-    overlay: bool = False,
-    binary_mask: bool = False,
-    approx_skull: bool = False,
-    no_seg_output: bool = False,
-    vtk_mesh: bool = False,
-    head_radius: float | None = None,
-    thresholding: bool = False,
-    robust_iters: bool = False,
-    residual_optic_cleanup: bool = False,
-    reduce_bias: bool = False,
-    slice_padding: bool = False,
-    whole_set_mask: bool = False,
-    additional_surfaces: bool = False,
-    additional_surfaces_t2: InputPathType | None = None,
-    verbose: bool = False,
-    debug: bool = False,
-    runner: Runner | None = None,
-) -> BetFslOutputs:
-    """
-    Automated brain extraction tool for FSL.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        infile: Input image (e.g. img.nii.gz).
-        maskfile: Output brain mask (e.g. img_bet.nii.gz).
-        fractional_intensity: Fractional intensity threshold (0->1);\
-            default=0.5; smaller values give larger brain outline estimates.
-        vg_fractional_intensity: Vertical gradient in fractional intensity\
-            threshold (-1->1); default=0; positive values give larger brain outline\
-            at bottom, smaller at top.
-        center_of_gravity: The xyz coordinates of the center of gravity\
-            (voxels, not mm) of initial mesh surface. Must have exactly three\
-            numerical entries in the list (3-vector).
-        overlay: Generate brain surface outline overlaid onto original image.
-        binary_mask: Generate binary brain mask.
-        approx_skull: Generate approximate skull image.
-        no_seg_output: Don't generate segmented brain image output.
-        vtk_mesh: Generate brain surface as mesh in .vtk format.
-        head_radius: Head radius (mm not voxels); initial surface sphere is set\
-            to half of this.
-        thresholding: Apply thresholding to segmented brain image and mask.
-        robust_iters: Robust brain centre estimation (iterates BET several\
-            times).
-        residual_optic_cleanup: Eye & optic nerve cleanup (can be useful in\
-            SIENA).
-        reduce_bias: Bias field & neck cleanup (can be useful in SIENA).
-        slice_padding: Improve BET if FOV is very small in Z (by temporarily\
-            padding end slices).
-        whole_set_mask: Apply to 4D FMRI data (uses -f 0.3 and dilates brain\
-            mask slightly).
-        additional_surfaces: Run bet2 and then betsurf to get additional skull\
-            and scalp surfaces (includes registrations).
-        additional_surfaces_t2: As with -A, when also feeding in\
-            non-brain-extracted T2 (includes registrations).
-        verbose: Verbose (switch on diagnostic messages).
-        debug: Debug (don't delete temporary intermediate images).
-        runner: Command runner.
-    Returns:
-        NamedTuple of outputs (described in `BetFslOutputs`).
-    """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(BET_FSL_METADATA)
-    params = bet_fsl_params(
-        infile=infile,
-        maskfile=maskfile,
-        fractional_intensity=fractional_intensity,
-        vg_fractional_intensity=vg_fractional_intensity,
-        center_of_gravity=center_of_gravity,
-        overlay=overlay,
-        binary_mask=binary_mask,
-        approx_skull=approx_skull,
-        no_seg_output=no_seg_output,
-        vtk_mesh=vtk_mesh,
-        head_radius=head_radius,
-        thresholding=thresholding,
-        robust_iters=robust_iters,
-        residual_optic_cleanup=residual_optic_cleanup,
-        reduce_bias=reduce_bias,
-        slice_padding=slice_padding,
-        whole_set_mask=whole_set_mask,
-        additional_surfaces=additional_surfaces,
-        additional_surfaces_t2=additional_surfaces_t2,
-        verbose=verbose,
-        debug=debug,
-    )
-    return bet_fsl_execute(params, execution)
-
-
-__all__ = [
-    "BET_FSL_METADATA",
-    "BetFslOutputs",
-    "BetFslParameters",
-    "bet_fsl",
-    "bet_fsl_params",
-]