niwrap-freesurfer 0.5.1__py3-none-any.whl → 0.5.3__py3-none-any.whl

niwrap_freesurfer/freesurfer/flirt_fsl.py

@@ -1,604 +0,0 @@
-# This file was auto generated by Styx.
-# Do not edit this file directly.
-
-import typing
-import pathlib
-from styxdefs import *
-
-FLIRT_FSL_METADATA = Metadata(
-    id="398eadb6f9dd1993cfd24de7b26c3a35c5d0f1cd.boutiques",
-    name="flirt.fsl",
-    package="freesurfer",
-    container_image_tag="freesurfer/freesurfer:7.4.1",
-)
-
-
-FlirtFslParameters = typing.TypedDict('FlirtFslParameters', {
-    "__STYX_TYPE__": typing.Literal["flirt.fsl"],
-    "input_volume": InputPathType,
-    "reference_volume": InputPathType,
-    "output_volume": typing.NotRequired[str | None],
-    "output_matrix": typing.NotRequired[str | None],
-    "initial_matrix": typing.NotRequired[InputPathType | None],
-    "data_type": typing.NotRequired[typing.Literal["char", "short", "int", "float", "double"] | None],
-    "cost_function": typing.NotRequired[typing.Literal["mutualinfo", "corratio", "normcorr", "normmi", "leastsq", "labeldiff"] | None],
-    "search_cost_function": typing.NotRequired[typing.Literal["mutualinfo", "corratio", "normcorr", "normmi", "leastsq", "labeldiff"] | None],
-    "use_sform_qform": bool,
-    "display_initial_matrix": bool,
-    "angle_representation": typing.NotRequired[typing.Literal["quaternion", "euler"] | None],
-    "interpolation_method": typing.NotRequired[typing.Literal["trilinear", "nearestneighbour", "sinc"] | None],
-    "sinc_width": typing.NotRequired[float | None],
-    "sinc_window": typing.NotRequired[typing.Literal["rectangular", "hanning", "blackman"] | None],
-    "histogram_bins": typing.NotRequired[float | None],
-    "degrees_of_freedom": typing.NotRequired[float | None],
-    "no_resample": bool,
-    "force_scaling": bool,
-    "min_voxel_dimension": typing.NotRequired[float | None],
-    "apply_transform": bool,
-    "apply_isotropic_transform": typing.NotRequired[float | None],
-    "padding_size": typing.NotRequired[float | None],
-    "search_range_x": typing.NotRequired[list[float] | None],
-    "search_range_y": typing.NotRequired[list[float] | None],
-    "search_range_z": typing.NotRequired[list[float] | None],
-    "no_search": bool,
-    "coarse_search_angle": typing.NotRequired[float | None],
-    "fine_search_angle": typing.NotRequired[float | None],
-    "schedule_file": typing.NotRequired[InputPathType | None],
-    "reference_weight": typing.NotRequired[InputPathType | None],
-    "input_weight": typing.NotRequired[InputPathType | None],
-    "no_clamp": bool,
-    "no_resample_blur": bool,
-    "rigid_body_mode": bool,
-    "verbose": bool,
-    "verbose_level": typing.NotRequired[float | None],
-    "pause_stages": bool,
-    "version_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 {
-        "flirt.fsl": flirt_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 {
-        "flirt.fsl": flirt_fsl_outputs,
-    }.get(t)
-
-
-class FlirtFslOutputs(typing.NamedTuple):
-    """
-    Output object returned when calling `flirt_fsl(...)`.
-    """
-    root: OutputPathType
-    """Output root folder. This is the root folder for all outputs."""
-    registered_volume: OutputPathType | None
-    """Resulting registered volume"""
-    transformation_matrix: OutputPathType | None
-    """Resulting transformation matrix in ASCII format"""
-
-
-def flirt_fsl_params(
-    input_volume: InputPathType,
-    reference_volume: InputPathType,
-    output_volume: str | None = None,
-    output_matrix: str | None = None,
-    initial_matrix: InputPathType | None = None,
-    data_type: typing.Literal["char", "short", "int", "float", "double"] | None = None,
-    cost_function: typing.Literal["mutualinfo", "corratio", "normcorr", "normmi", "leastsq", "labeldiff"] | None = "corratio",
-    search_cost_function: typing.Literal["mutualinfo", "corratio", "normcorr", "normmi", "leastsq", "labeldiff"] | None = "corratio",
-    use_sform_qform: bool = False,
-    display_initial_matrix: bool = False,
-    angle_representation: typing.Literal["quaternion", "euler"] | None = "euler",
-    interpolation_method: typing.Literal["trilinear", "nearestneighbour", "sinc"] | None = "trilinear",
-    sinc_width: float | None = 7,
-    sinc_window: typing.Literal["rectangular", "hanning", "blackman"] | None = None,
-    histogram_bins: float | None = 256,
-    degrees_of_freedom: float | None = 12,
-    no_resample: bool = False,
-    force_scaling: bool = False,
-    min_voxel_dimension: float | None = None,
-    apply_transform: bool = False,
-    apply_isotropic_transform: float | None = None,
-    padding_size: float | None = None,
-    search_range_x: list[float] | None = [-90, 90],
-    search_range_y: list[float] | None = [-90, 90],
-    search_range_z: list[float] | None = [-90, 90],
-    no_search: bool = False,
-    coarse_search_angle: float | None = 60,
-    fine_search_angle: float | None = 18,
-    schedule_file: InputPathType | None = None,
-    reference_weight: InputPathType | None = None,
-    input_weight: InputPathType | None = None,
-    no_clamp: bool = False,
-    no_resample_blur: bool = False,
-    rigid_body_mode: bool = False,
-    verbose: bool = False,
-    verbose_level: float | None = 0,
-    pause_stages: bool = False,
-    version_flag: bool = False,
-) -> FlirtFslParameters:
-    """
-    Build parameters.
-    
-    Args:
-        input_volume: Input volume.
-        reference_volume: Reference volume.
-        output_volume: Output volume.
-        output_matrix: Output matrix filename (4x4 ASCII format).
-        initial_matrix: Input 4x4 affine matrix filename.
-        data_type: Force output data type.
-        cost_function: Cost function for registration.
-        search_cost_function: Cost function for search.
-        use_sform_qform: Initialize using appropriate sform or qform.
-        display_initial_matrix: Display initial matrix.
-        angle_representation: Set angle representation.
-        interpolation_method: Interpolation method.
-        sinc_width: Sinc interpolation width.
-        sinc_window: Sinc interpolation window.
-        histogram_bins: Number of histogram bins.
-        degrees_of_freedom: Degrees of freedom.
-        no_resample: Do not change input sampling.
-        force_scaling: Force rescaling even for low-res images.
-        min_voxel_dimension: Minimum voxel dimension for sampling (in mm).
-        apply_transform: Apply transform (no optimisation), requires -init.
-        apply_isotropic_transform: Apply transform with isotropic resampling.
-        padding_size: Padding size for interpolation outside image.
-        search_range_x: Search range for rotation around x-axis.
-        search_range_y: Search range for rotation around y-axis.
-        search_range_z: Search range for rotation around z-axis.
-        no_search: Set all angular search ranges to 0.
-        coarse_search_angle: Coarse search angle in degrees.
-        fine_search_angle: Fine search angle in degrees.
-        schedule_file: Custom schedule filename.
-        reference_weight: Weights for reference volume.
-        input_weight: Weights for input volume.
-        no_clamp: Do not use intensity clamping.
-        no_resample_blur: Do not use blurring on downsampling.
-        rigid_body_mode: Use 2D rigid body mode (ignores dof).
-        verbose: Equivalent to -verbose 1.
-        verbose_level: Level of verbosity.
-        pause_stages: Pause at each stage.
-        version_flag: Print version number.
-    Returns:
-        Parameter dictionary
-    """
-    params = {
-        "__STYXTYPE__": "flirt.fsl",
-        "input_volume": input_volume,
-        "reference_volume": reference_volume,
-        "use_sform_qform": use_sform_qform,
-        "display_initial_matrix": display_initial_matrix,
-        "no_resample": no_resample,
-        "force_scaling": force_scaling,
-        "apply_transform": apply_transform,
-        "no_search": no_search,
-        "no_clamp": no_clamp,
-        "no_resample_blur": no_resample_blur,
-        "rigid_body_mode": rigid_body_mode,
-        "verbose": verbose,
-        "pause_stages": pause_stages,
-        "version_flag": version_flag,
-    }
-    if output_volume is not None:
-        params["output_volume"] = output_volume
-    if output_matrix is not None:
-        params["output_matrix"] = output_matrix
-    if initial_matrix is not None:
-        params["initial_matrix"] = initial_matrix
-    if data_type is not None:
-        params["data_type"] = data_type
-    if cost_function is not None:
-        params["cost_function"] = cost_function
-    if search_cost_function is not None:
-        params["search_cost_function"] = search_cost_function
-    if angle_representation is not None:
-        params["angle_representation"] = angle_representation
-    if interpolation_method is not None:
-        params["interpolation_method"] = interpolation_method
-    if sinc_width is not None:
-        params["sinc_width"] = sinc_width
-    if sinc_window is not None:
-        params["sinc_window"] = sinc_window
-    if histogram_bins is not None:
-        params["histogram_bins"] = histogram_bins
-    if degrees_of_freedom is not None:
-        params["degrees_of_freedom"] = degrees_of_freedom
-    if min_voxel_dimension is not None:
-        params["min_voxel_dimension"] = min_voxel_dimension
-    if apply_isotropic_transform is not None:
-        params["apply_isotropic_transform"] = apply_isotropic_transform
-    if padding_size is not None:
-        params["padding_size"] = padding_size
-    if search_range_x is not None:
-        params["search_range_x"] = search_range_x
-    if search_range_y is not None:
-        params["search_range_y"] = search_range_y
-    if search_range_z is not None:
-        params["search_range_z"] = search_range_z
-    if coarse_search_angle is not None:
-        params["coarse_search_angle"] = coarse_search_angle
-    if fine_search_angle is not None:
-        params["fine_search_angle"] = fine_search_angle
-    if schedule_file is not None:
-        params["schedule_file"] = schedule_file
-    if reference_weight is not None:
-        params["reference_weight"] = reference_weight
-    if input_weight is not None:
-        params["input_weight"] = input_weight
-    if verbose_level is not None:
-        params["verbose_level"] = verbose_level
-    return params
-
-
-def flirt_fsl_cargs(
-    params: FlirtFslParameters,
-    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("flirt")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(execution.input_file(params.get("reference_volume")))
-    if params.get("output_volume") is not None:
-        cargs.append(params.get("output_volume"))
-    if params.get("output_matrix") is not None:
-        cargs.extend([
-            "-omat",
-            params.get("output_matrix")
-        ])
-    if params.get("initial_matrix") is not None:
-        cargs.extend([
-            "-init",
-            execution.input_file(params.get("initial_matrix"))
-        ])
-    if params.get("data_type") is not None:
-        cargs.extend([
-            "-datatype",
-            params.get("data_type")
-        ])
-    if params.get("cost_function") is not None:
-        cargs.extend([
-            "-cost",
-            params.get("cost_function")
-        ])
-    if params.get("search_cost_function") is not None:
-        cargs.extend([
-            "-searchcost",
-            params.get("search_cost_function")
-        ])
-    if params.get("use_sform_qform"):
-        cargs.append("-usesqform")
-    if params.get("display_initial_matrix"):
-        cargs.append("-displayinit")
-    if params.get("angle_representation") is not None:
-        cargs.extend([
-            "-anglerep",
-            params.get("angle_representation")
-        ])
-    if params.get("interpolation_method") is not None:
-        cargs.extend([
-            "-interp",
-            params.get("interpolation_method")
-        ])
-    if params.get("sinc_width") is not None:
-        cargs.extend([
-            "-sincwidth",
-            str(params.get("sinc_width"))
-        ])
-    if params.get("sinc_window") is not None:
-        cargs.extend([
-            "-sincwindow",
-            params.get("sinc_window")
-        ])
-    if params.get("histogram_bins") is not None:
-        cargs.extend([
-            "-bins",
-            str(params.get("histogram_bins"))
-        ])
-    if params.get("degrees_of_freedom") is not None:
-        cargs.extend([
-            "-dof",
-            str(params.get("degrees_of_freedom"))
-        ])
-    if params.get("no_resample"):
-        cargs.append("-noresample")
-    if params.get("force_scaling"):
-        cargs.append("-forcescaling")
-    if params.get("min_voxel_dimension") is not None:
-        cargs.extend([
-            "-minsampling",
-            str(params.get("min_voxel_dimension"))
-        ])
-    if params.get("apply_transform"):
-        cargs.append("-applyxfm")
-    if params.get("apply_isotropic_transform") is not None:
-        cargs.extend([
-            "-applyisoxfm",
-            str(params.get("apply_isotropic_transform"))
-        ])
-    if params.get("padding_size") is not None:
-        cargs.extend([
-            "-paddingsize",
-            str(params.get("padding_size"))
-        ])
-    if params.get("search_range_x") is not None:
-        cargs.extend([
-            "-searchrx",
-            *map(str, params.get("search_range_x"))
-        ])
-    if params.get("search_range_y") is not None:
-        cargs.extend([
-            "-searchry",
-            *map(str, params.get("search_range_y"))
-        ])
-    if params.get("search_range_z") is not None:
-        cargs.extend([
-            "-searchrz",
-            *map(str, params.get("search_range_z"))
-        ])
-    if params.get("no_search"):
-        cargs.append("-nosearch")
-    if params.get("coarse_search_angle") is not None:
-        cargs.extend([
-            "-coarsesearch",
-            str(params.get("coarse_search_angle"))
-        ])
-    if params.get("fine_search_angle") is not None:
-        cargs.extend([
-            "-finesearch",
-            str(params.get("fine_search_angle"))
-        ])
-    if params.get("schedule_file") is not None:
-        cargs.extend([
-            "-schedule",
-            execution.input_file(params.get("schedule_file"))
-        ])
-    if params.get("reference_weight") is not None:
-        cargs.extend([
-            "-refweight",
-            execution.input_file(params.get("reference_weight"))
-        ])
-    if params.get("input_weight") is not None:
-        cargs.extend([
-            "-inweight",
-            execution.input_file(params.get("input_weight"))
-        ])
-    if params.get("no_clamp"):
-        cargs.append("-noclamp")
-    if params.get("no_resample_blur"):
-        cargs.append("-noresampblur")
-    if params.get("rigid_body_mode"):
-        cargs.append("-2D")
-    if params.get("verbose"):
-        cargs.append("-v")
-    if params.get("verbose_level") is not None:
-        cargs.extend([
-            "-verbose",
-            str(params.get("verbose_level"))
-        ])
-    if params.get("pause_stages"):
-        cargs.append("-i")
-    if params.get("version_flag"):
-        cargs.append("-version")
-    return cargs
-
-
-def flirt_fsl_outputs(
-    params: FlirtFslParameters,
-    execution: Execution,
-) -> FlirtFslOutputs:
-    """
-    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 = FlirtFslOutputs(
-        root=execution.output_file("."),
-        registered_volume=execution.output_file(params.get("output_volume") + ".nii") if (params.get("output_volume") is not None) else None,
-        transformation_matrix=execution.output_file(params.get("output_matrix")) if (params.get("output_matrix") is not None) else None,
-    )
-    return ret
-
-
-def flirt_fsl_execute(
-    params: FlirtFslParameters,
-    execution: Execution,
-) -> FlirtFslOutputs:
-    """
-    FMRIB's Linear Image Registration Tool.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        params: The parameters.
-        execution: The execution object.
-    Returns:
-        NamedTuple of outputs (described in `FlirtFslOutputs`).
-    """
-    params = execution.params(params)
-    cargs = flirt_fsl_cargs(params, execution)
-    ret = flirt_fsl_outputs(params, execution)
-    execution.run(cargs)
-    return ret
-
-
-def flirt_fsl(
-    input_volume: InputPathType,
-    reference_volume: InputPathType,
-    output_volume: str | None = None,
-    output_matrix: str | None = None,
-    initial_matrix: InputPathType | None = None,
-    data_type: typing.Literal["char", "short", "int", "float", "double"] | None = None,
-    cost_function: typing.Literal["mutualinfo", "corratio", "normcorr", "normmi", "leastsq", "labeldiff"] | None = "corratio",
-    search_cost_function: typing.Literal["mutualinfo", "corratio", "normcorr", "normmi", "leastsq", "labeldiff"] | None = "corratio",
-    use_sform_qform: bool = False,
-    display_initial_matrix: bool = False,
-    angle_representation: typing.Literal["quaternion", "euler"] | None = "euler",
-    interpolation_method: typing.Literal["trilinear", "nearestneighbour", "sinc"] | None = "trilinear",
-    sinc_width: float | None = 7,
-    sinc_window: typing.Literal["rectangular", "hanning", "blackman"] | None = None,
-    histogram_bins: float | None = 256,
-    degrees_of_freedom: float | None = 12,
-    no_resample: bool = False,
-    force_scaling: bool = False,
-    min_voxel_dimension: float | None = None,
-    apply_transform: bool = False,
-    apply_isotropic_transform: float | None = None,
-    padding_size: float | None = None,
-    search_range_x: list[float] | None = [-90, 90],
-    search_range_y: list[float] | None = [-90, 90],
-    search_range_z: list[float] | None = [-90, 90],
-    no_search: bool = False,
-    coarse_search_angle: float | None = 60,
-    fine_search_angle: float | None = 18,
-    schedule_file: InputPathType | None = None,
-    reference_weight: InputPathType | None = None,
-    input_weight: InputPathType | None = None,
-    no_clamp: bool = False,
-    no_resample_blur: bool = False,
-    rigid_body_mode: bool = False,
-    verbose: bool = False,
-    verbose_level: float | None = 0,
-    pause_stages: bool = False,
-    version_flag: bool = False,
-    runner: Runner | None = None,
-) -> FlirtFslOutputs:
-    """
-    FMRIB's Linear Image Registration Tool.
-    
-    Author: FreeSurfer Developers
-    
-    URL: https://github.com/freesurfer/freesurfer
-    
-    Args:
-        input_volume: Input volume.
-        reference_volume: Reference volume.
-        output_volume: Output volume.
-        output_matrix: Output matrix filename (4x4 ASCII format).
-        initial_matrix: Input 4x4 affine matrix filename.
-        data_type: Force output data type.
-        cost_function: Cost function for registration.
-        search_cost_function: Cost function for search.
-        use_sform_qform: Initialize using appropriate sform or qform.
-        display_initial_matrix: Display initial matrix.
-        angle_representation: Set angle representation.
-        interpolation_method: Interpolation method.
-        sinc_width: Sinc interpolation width.
-        sinc_window: Sinc interpolation window.
-        histogram_bins: Number of histogram bins.
-        degrees_of_freedom: Degrees of freedom.
-        no_resample: Do not change input sampling.
-        force_scaling: Force rescaling even for low-res images.
-        min_voxel_dimension: Minimum voxel dimension for sampling (in mm).
-        apply_transform: Apply transform (no optimisation), requires -init.
-        apply_isotropic_transform: Apply transform with isotropic resampling.
-        padding_size: Padding size for interpolation outside image.
-        search_range_x: Search range for rotation around x-axis.
-        search_range_y: Search range for rotation around y-axis.
-        search_range_z: Search range for rotation around z-axis.
-        no_search: Set all angular search ranges to 0.
-        coarse_search_angle: Coarse search angle in degrees.
-        fine_search_angle: Fine search angle in degrees.
-        schedule_file: Custom schedule filename.
-        reference_weight: Weights for reference volume.
-        input_weight: Weights for input volume.
-        no_clamp: Do not use intensity clamping.
-        no_resample_blur: Do not use blurring on downsampling.
-        rigid_body_mode: Use 2D rigid body mode (ignores dof).
-        verbose: Equivalent to -verbose 1.
-        verbose_level: Level of verbosity.
-        pause_stages: Pause at each stage.
-        version_flag: Print version number.
-        runner: Command runner.
-    Returns:
-        NamedTuple of outputs (described in `FlirtFslOutputs`).
-    """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FLIRT_FSL_METADATA)
-    params = flirt_fsl_params(
-        input_volume=input_volume,
-        reference_volume=reference_volume,
-        output_volume=output_volume,
-        output_matrix=output_matrix,
-        initial_matrix=initial_matrix,
-        data_type=data_type,
-        cost_function=cost_function,
-        search_cost_function=search_cost_function,
-        use_sform_qform=use_sform_qform,
-        display_initial_matrix=display_initial_matrix,
-        angle_representation=angle_representation,
-        interpolation_method=interpolation_method,
-        sinc_width=sinc_width,
-        sinc_window=sinc_window,
-        histogram_bins=histogram_bins,
-        degrees_of_freedom=degrees_of_freedom,
-        no_resample=no_resample,
-        force_scaling=force_scaling,
-        min_voxel_dimension=min_voxel_dimension,
-        apply_transform=apply_transform,
-        apply_isotropic_transform=apply_isotropic_transform,
-        padding_size=padding_size,
-        search_range_x=search_range_x,
-        search_range_y=search_range_y,
-        search_range_z=search_range_z,
-        no_search=no_search,
-        coarse_search_angle=coarse_search_angle,
-        fine_search_angle=fine_search_angle,
-        schedule_file=schedule_file,
-        reference_weight=reference_weight,
-        input_weight=input_weight,
-        no_clamp=no_clamp,
-        no_resample_blur=no_resample_blur,
-        rigid_body_mode=rigid_body_mode,
-        verbose=verbose,
-        verbose_level=verbose_level,
-        pause_stages=pause_stages,
-        version_flag=version_flag,
-    )
-    return flirt_fsl_execute(params, execution)
-
-
-__all__ = [
-    "FLIRT_FSL_METADATA",
-    "FlirtFslOutputs",
-    "FlirtFslParameters",
-    "flirt_fsl",
-    "flirt_fsl_params",
-]