niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/flirt_fsl.py

@@ -0,0 +1,604 @@
+# 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",
+]