niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_nl_align.py

@@ -0,0 +1,723 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_NL_ALIGN_METADATA = Metadata(
+    id="cd2a19b23e2fec00175500358afe679cc9ee7fc7.boutiques",
+    name="mri_nl_align",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriNlAlignParameters = typing.TypedDict('MriNlAlignParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_nl_align"],
+    "source": InputPathType,
+    "target": InputPathType,
+    "warp": str,
+    "debug_voxel": typing.NotRequired[list[float] | None],
+    "debug_node": typing.NotRequired[list[float] | None],
+    "no_neg": typing.NotRequired[float | None],
+    "renormalize": typing.NotRequired[float | None],
+    "aseg_flag": bool,
+    "diag_volume": typing.NotRequired[str | None],
+    "optimal_flag": bool,
+    "momentum_flag": bool,
+    "fixed_flag": bool,
+    "distance": typing.NotRequired[float | None],
+    "dtrans": typing.NotRequired[float | None],
+    "match_peak_flag": bool,
+    "erode": typing.NotRequired[float | None],
+    "match_mean": typing.NotRequired[float | None],
+    "intensity": typing.NotRequired[float | None],
+    "noregrid_flag": bool,
+    "regrid_flag": bool,
+    "view": typing.NotRequired[list[float] | None],
+    "levels": typing.NotRequired[float | None],
+    "area_smoothness": typing.NotRequired[float | None],
+    "area": typing.NotRequired[float | None],
+    "tolerance": typing.NotRequired[float | None],
+    "sigma": typing.NotRequired[float | None],
+    "min_sigma": typing.NotRequired[float | None],
+    "ribbon": typing.NotRequired[InputPathType | None],
+    "rthresh": typing.NotRequired[float | None],
+    "scale": typing.NotRequired[float | None],
+    "dt": typing.NotRequired[float | None],
+    "passes": typing.NotRequired[float | None],
+    "skip": typing.NotRequired[float | None],
+    "apply": typing.NotRequired[float | None],
+    "distance_log": typing.NotRequired[float | None],
+    "momentum": typing.NotRequired[float | None],
+    "iterations": typing.NotRequired[float | None],
+    "smoothness": typing.NotRequired[float | None],
+    "transform": typing.NotRequired[InputPathType | None],
+    "inverse_transform": typing.NotRequired[InputPathType | None],
+    "binary": typing.NotRequired[float | None],
+    "jacobian": typing.NotRequired[float | None],
+    "disable_zero_locations": typing.NotRequired[float | None],
+    "smooth_averages": typing.NotRequired[float | None],
+    "exp_k": typing.NotRequired[float | None],
+    "diagnostics": typing.NotRequired[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 {
+        "mri_nl_align": mri_nl_align_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 {
+        "mri_nl_align": mri_nl_align_outputs,
+    }.get(t)
+
+
+class MriNlAlignOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_nl_align(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    warp_output: OutputPathType
+    """Resulting warp output file after alignment"""
+
+
+def mri_nl_align_params(
+    source: InputPathType,
+    target: InputPathType,
+    warp: str,
+    debug_voxel: list[float] | None = None,
+    debug_node: list[float] | None = None,
+    no_neg: float | None = None,
+    renormalize: float | None = None,
+    aseg_flag: bool = False,
+    diag_volume: str | None = None,
+    optimal_flag: bool = False,
+    momentum_flag: bool = False,
+    fixed_flag: bool = False,
+    distance: float | None = None,
+    dtrans: float | None = None,
+    match_peak_flag: bool = False,
+    erode: float | None = None,
+    match_mean: float | None = None,
+    intensity: float | None = None,
+    noregrid_flag: bool = False,
+    regrid_flag: bool = False,
+    view: list[float] | None = None,
+    levels: float | None = None,
+    area_smoothness: float | None = None,
+    area: float | None = None,
+    tolerance: float | None = None,
+    sigma: float | None = None,
+    min_sigma: float | None = None,
+    ribbon: InputPathType | None = None,
+    rthresh: float | None = None,
+    scale: float | None = None,
+    dt: float | None = None,
+    passes: float | None = None,
+    skip: float | None = None,
+    apply: float | None = None,
+    distance_log: float | None = None,
+    momentum: float | None = None,
+    iterations: float | None = None,
+    smoothness: float | None = None,
+    transform: InputPathType | None = None,
+    inverse_transform: InputPathType | None = None,
+    binary: float | None = None,
+    jacobian: float | None = None,
+    disable_zero_locations: float | None = None,
+    smooth_averages: float | None = None,
+    exp_k: float | None = None,
+    diagnostics: float | None = None,
+) -> MriNlAlignParameters:
+    """
+    Build parameters.
+    
+    Args:
+        source: Input source image file.
+        target: Input target image file.
+        warp: Output warp file.
+        debug_voxel: Debug voxel coordinates (Gx, Gy, Gz).
+        debug_node: Debug node coordinates (Gx, Gy, Gz).
+        no_neg: Control allowing temporary folds during numerical minimization.
+        renormalize: Control for renormalizing intensities.
+        aseg_flag: Treat inputs as segmentations.
+        diag_volume: Write d2 diagnostics for input volume.
+        optimal_flag: Use line search optimization.
+        momentum_flag: Use fixed time-step integration.
+        fixed_flag: Use fixed time-step integration.
+        distance: Expand border by specified mm every outer cycle.
+        dtrans: Set distance transform coefficient.
+        match_peak_flag: Match peak of intensity ratio histogram.
+        erode: Erode source and target image specified times before morphing.
+        match_mean: Control for matching peak of intensity ratio histogram.
+        intensity: Set l_log_likelihood to specified value.
+        noregrid_flag: Disable regridding.
+        regrid_flag: Enable regridding.
+        view: View voxel coordinates (Gx, Gy, Gz).
+        levels: Set levels to specified value.
+        area_smoothness: Set l_area_smoothness to specified value.
+        area: Set l_area to specified value.
+        tolerance: Set tolerance to specified value.
+        sigma: Set sigma to specified value.
+        min_sigma: Set minimum sigma value.
+        ribbon: Read ribbon from specified file and insert into aseg.
+        rthresh: Set compression ratio threshold to specified value.
+        scale: Scale input values by specified factor.
+        dt: Set dt to specified value.
+        passes: Integrate in specified number of passes.
+        skip: Skip specified number of voxels in source data.
+        apply: Control for applying transform after registration.
+        distance_log: Set l_distance to specified value.
+        momentum: Set momentum to specified value.
+        iterations: Set number of iterations to specified value.
+        smoothness: Set l_smoothness to specified value.
+        transform: Read the forward transform from specified file.
+        inverse_transform: Read the inverse transform from specified file.
+        binary: Set l_binary to specified value.
+        jacobian: Set l_jacobian to specified value.
+        disable_zero_locations: Control for disabling zero image locations.
+        smooth_averages: Smooth gradient with specified number of averages.
+        exp_k: Set exp_k to specified value.
+        diagnostics: Write diagnostics at each specified iteration.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_nl_align",
+        "source": source,
+        "target": target,
+        "warp": warp,
+        "aseg_flag": aseg_flag,
+        "optimal_flag": optimal_flag,
+        "momentum_flag": momentum_flag,
+        "fixed_flag": fixed_flag,
+        "match_peak_flag": match_peak_flag,
+        "noregrid_flag": noregrid_flag,
+        "regrid_flag": regrid_flag,
+    }
+    if debug_voxel is not None:
+        params["debug_voxel"] = debug_voxel
+    if debug_node is not None:
+        params["debug_node"] = debug_node
+    if no_neg is not None:
+        params["no_neg"] = no_neg
+    if renormalize is not None:
+        params["renormalize"] = renormalize
+    if diag_volume is not None:
+        params["diag_volume"] = diag_volume
+    if distance is not None:
+        params["distance"] = distance
+    if dtrans is not None:
+        params["dtrans"] = dtrans
+    if erode is not None:
+        params["erode"] = erode
+    if match_mean is not None:
+        params["match_mean"] = match_mean
+    if intensity is not None:
+        params["intensity"] = intensity
+    if view is not None:
+        params["view"] = view
+    if levels is not None:
+        params["levels"] = levels
+    if area_smoothness is not None:
+        params["area_smoothness"] = area_smoothness
+    if area is not None:
+        params["area"] = area
+    if tolerance is not None:
+        params["tolerance"] = tolerance
+    if sigma is not None:
+        params["sigma"] = sigma
+    if min_sigma is not None:
+        params["min_sigma"] = min_sigma
+    if ribbon is not None:
+        params["ribbon"] = ribbon
+    if rthresh is not None:
+        params["rthresh"] = rthresh
+    if scale is not None:
+        params["scale"] = scale
+    if dt is not None:
+        params["dt"] = dt
+    if passes is not None:
+        params["passes"] = passes
+    if skip is not None:
+        params["skip"] = skip
+    if apply is not None:
+        params["apply"] = apply
+    if distance_log is not None:
+        params["distance_log"] = distance_log
+    if momentum is not None:
+        params["momentum"] = momentum
+    if iterations is not None:
+        params["iterations"] = iterations
+    if smoothness is not None:
+        params["smoothness"] = smoothness
+    if transform is not None:
+        params["transform"] = transform
+    if inverse_transform is not None:
+        params["inverse_transform"] = inverse_transform
+    if binary is not None:
+        params["binary"] = binary
+    if jacobian is not None:
+        params["jacobian"] = jacobian
+    if disable_zero_locations is not None:
+        params["disable_zero_locations"] = disable_zero_locations
+    if smooth_averages is not None:
+        params["smooth_averages"] = smooth_averages
+    if exp_k is not None:
+        params["exp_k"] = exp_k
+    if diagnostics is not None:
+        params["diagnostics"] = diagnostics
+    return params
+
+
+def mri_nl_align_cargs(
+    params: MriNlAlignParameters,
+    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("mri_nl_align")
+    cargs.append(execution.input_file(params.get("source")))
+    cargs.append(execution.input_file(params.get("target")))
+    cargs.append(params.get("warp"))
+    if params.get("debug_voxel") is not None:
+        cargs.extend([
+            "-debug_voxel",
+            *map(str, params.get("debug_voxel"))
+        ])
+    if params.get("debug_node") is not None:
+        cargs.extend([
+            "-debug_node",
+            *map(str, params.get("debug_node"))
+        ])
+    if params.get("no_neg") is not None:
+        cargs.extend([
+            "-noneg",
+            str(params.get("no_neg"))
+        ])
+    if params.get("renormalize") is not None:
+        cargs.extend([
+            "-renormalize",
+            str(params.get("renormalize"))
+        ])
+    if params.get("aseg_flag"):
+        cargs.append("-aseg")
+    if params.get("diag_volume") is not None:
+        cargs.extend([
+            "-diag2",
+            params.get("diag_volume")
+        ])
+    if params.get("optimal_flag"):
+        cargs.append("-OPTIMAL")
+    if params.get("momentum_flag"):
+        cargs.append("-MOMENTUM")
+    if params.get("fixed_flag"):
+        cargs.append("-FIXED")
+    if params.get("distance") is not None:
+        cargs.extend([
+            "-distance",
+            str(params.get("distance"))
+        ])
+    if params.get("dtrans") is not None:
+        cargs.extend([
+            "-dtrans",
+            str(params.get("dtrans"))
+        ])
+    if params.get("match_peak_flag"):
+        cargs.append("-match_peak")
+    if params.get("erode") is not None:
+        cargs.extend([
+            "-erode",
+            str(params.get("erode"))
+        ])
+    if params.get("match_mean") is not None:
+        cargs.extend([
+            "-match_mean",
+            str(params.get("match_mean"))
+        ])
+    if params.get("intensity") is not None:
+        cargs.extend([
+            "-intensity",
+            str(params.get("intensity"))
+        ])
+    if params.get("noregrid_flag"):
+        cargs.append("-noregrid")
+    if params.get("regrid_flag"):
+        cargs.append("-regrid")
+    if params.get("view") is not None:
+        cargs.extend([
+            "-view",
+            *map(str, params.get("view"))
+        ])
+    if params.get("levels") is not None:
+        cargs.extend([
+            "-levels",
+            str(params.get("levels"))
+        ])
+    if params.get("area_smoothness") is not None:
+        cargs.extend([
+            "-areasmoothness",
+            str(params.get("area_smoothness"))
+        ])
+    if params.get("area") is not None:
+        cargs.extend([
+            "-area",
+            str(params.get("area"))
+        ])
+    if params.get("tolerance") is not None:
+        cargs.extend([
+            "-tol",
+            str(params.get("tolerance"))
+        ])
+    if params.get("sigma") is not None:
+        cargs.extend([
+            "-sigma",
+            str(params.get("sigma"))
+        ])
+    if params.get("min_sigma") is not None:
+        cargs.extend([
+            "-min_sigma",
+            str(params.get("min_sigma"))
+        ])
+    if params.get("ribbon") is not None:
+        cargs.extend([
+            "-ribbon",
+            execution.input_file(params.get("ribbon"))
+        ])
+    if params.get("rthresh") is not None:
+        cargs.extend([
+            "-rthresh",
+            str(params.get("rthresh"))
+        ])
+    if params.get("scale") is not None:
+        cargs.extend([
+            "-scale",
+            str(params.get("scale"))
+        ])
+    if params.get("dt") is not None:
+        cargs.extend([
+            "-dt",
+            str(params.get("dt"))
+        ])
+    if params.get("passes") is not None:
+        cargs.extend([
+            "-passes",
+            str(params.get("passes"))
+        ])
+    if params.get("skip") is not None:
+        cargs.extend([
+            "-skip",
+            str(params.get("skip"))
+        ])
+    if params.get("apply") is not None:
+        cargs.extend([
+            "-apply",
+            str(params.get("apply"))
+        ])
+    if params.get("distance_log") is not None:
+        cargs.extend([
+            "-D",
+            str(params.get("distance_log"))
+        ])
+    if params.get("momentum") is not None:
+        cargs.extend([
+            "-M",
+            str(params.get("momentum"))
+        ])
+    if params.get("iterations") is not None:
+        cargs.extend([
+            "-N",
+            str(params.get("iterations"))
+        ])
+    if params.get("smoothness") is not None:
+        cargs.extend([
+            "-s",
+            str(params.get("smoothness"))
+        ])
+    if params.get("transform") is not None:
+        cargs.extend([
+            "-T",
+            execution.input_file(params.get("transform"))
+        ])
+    if params.get("inverse_transform") is not None:
+        cargs.extend([
+            "-I",
+            execution.input_file(params.get("inverse_transform"))
+        ])
+    if params.get("binary") is not None:
+        cargs.extend([
+            "-B",
+            str(params.get("binary"))
+        ])
+    if params.get("jacobian") is not None:
+        cargs.extend([
+            "-J",
+            str(params.get("jacobian"))
+        ])
+    if params.get("disable_zero_locations") is not None:
+        cargs.extend([
+            "-Z",
+            str(params.get("disable_zero_locations"))
+        ])
+    if params.get("smooth_averages") is not None:
+        cargs.extend([
+            "-a",
+            str(params.get("smooth_averages"))
+        ])
+    if params.get("exp_k") is not None:
+        cargs.extend([
+            "-K",
+            str(params.get("exp_k"))
+        ])
+    if params.get("diagnostics") is not None:
+        cargs.extend([
+            "-W",
+            str(params.get("diagnostics"))
+        ])
+    return cargs
+
+
+def mri_nl_align_outputs(
+    params: MriNlAlignParameters,
+    execution: Execution,
+) -> MriNlAlignOutputs:
+    """
+    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 = MriNlAlignOutputs(
+        root=execution.output_file("."),
+        warp_output=execution.output_file(params.get("warp")),
+    )
+    return ret
+
+
+def mri_nl_align_execute(
+    params: MriNlAlignParameters,
+    execution: Execution,
+) -> MriNlAlignOutputs:
+    """
+    mri_nl_align aligns two images using nonlinear registration.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriNlAlignOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_nl_align_cargs(params, execution)
+    ret = mri_nl_align_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_nl_align(
+    source: InputPathType,
+    target: InputPathType,
+    warp: str,
+    debug_voxel: list[float] | None = None,
+    debug_node: list[float] | None = None,
+    no_neg: float | None = None,
+    renormalize: float | None = None,
+    aseg_flag: bool = False,
+    diag_volume: str | None = None,
+    optimal_flag: bool = False,
+    momentum_flag: bool = False,
+    fixed_flag: bool = False,
+    distance: float | None = None,
+    dtrans: float | None = None,
+    match_peak_flag: bool = False,
+    erode: float | None = None,
+    match_mean: float | None = None,
+    intensity: float | None = None,
+    noregrid_flag: bool = False,
+    regrid_flag: bool = False,
+    view: list[float] | None = None,
+    levels: float | None = None,
+    area_smoothness: float | None = None,
+    area: float | None = None,
+    tolerance: float | None = None,
+    sigma: float | None = None,
+    min_sigma: float | None = None,
+    ribbon: InputPathType | None = None,
+    rthresh: float | None = None,
+    scale: float | None = None,
+    dt: float | None = None,
+    passes: float | None = None,
+    skip: float | None = None,
+    apply: float | None = None,
+    distance_log: float | None = None,
+    momentum: float | None = None,
+    iterations: float | None = None,
+    smoothness: float | None = None,
+    transform: InputPathType | None = None,
+    inverse_transform: InputPathType | None = None,
+    binary: float | None = None,
+    jacobian: float | None = None,
+    disable_zero_locations: float | None = None,
+    smooth_averages: float | None = None,
+    exp_k: float | None = None,
+    diagnostics: float | None = None,
+    runner: Runner | None = None,
+) -> MriNlAlignOutputs:
+    """
+    mri_nl_align aligns two images using nonlinear registration.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        source: Input source image file.
+        target: Input target image file.
+        warp: Output warp file.
+        debug_voxel: Debug voxel coordinates (Gx, Gy, Gz).
+        debug_node: Debug node coordinates (Gx, Gy, Gz).
+        no_neg: Control allowing temporary folds during numerical minimization.
+        renormalize: Control for renormalizing intensities.
+        aseg_flag: Treat inputs as segmentations.
+        diag_volume: Write d2 diagnostics for input volume.
+        optimal_flag: Use line search optimization.
+        momentum_flag: Use fixed time-step integration.
+        fixed_flag: Use fixed time-step integration.
+        distance: Expand border by specified mm every outer cycle.
+        dtrans: Set distance transform coefficient.
+        match_peak_flag: Match peak of intensity ratio histogram.
+        erode: Erode source and target image specified times before morphing.
+        match_mean: Control for matching peak of intensity ratio histogram.
+        intensity: Set l_log_likelihood to specified value.
+        noregrid_flag: Disable regridding.
+        regrid_flag: Enable regridding.
+        view: View voxel coordinates (Gx, Gy, Gz).
+        levels: Set levels to specified value.
+        area_smoothness: Set l_area_smoothness to specified value.
+        area: Set l_area to specified value.
+        tolerance: Set tolerance to specified value.
+        sigma: Set sigma to specified value.
+        min_sigma: Set minimum sigma value.
+        ribbon: Read ribbon from specified file and insert into aseg.
+        rthresh: Set compression ratio threshold to specified value.
+        scale: Scale input values by specified factor.
+        dt: Set dt to specified value.
+        passes: Integrate in specified number of passes.
+        skip: Skip specified number of voxels in source data.
+        apply: Control for applying transform after registration.
+        distance_log: Set l_distance to specified value.
+        momentum: Set momentum to specified value.
+        iterations: Set number of iterations to specified value.
+        smoothness: Set l_smoothness to specified value.
+        transform: Read the forward transform from specified file.
+        inverse_transform: Read the inverse transform from specified file.
+        binary: Set l_binary to specified value.
+        jacobian: Set l_jacobian to specified value.
+        disable_zero_locations: Control for disabling zero image locations.
+        smooth_averages: Smooth gradient with specified number of averages.
+        exp_k: Set exp_k to specified value.
+        diagnostics: Write diagnostics at each specified iteration.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriNlAlignOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_NL_ALIGN_METADATA)
+    params = mri_nl_align_params(
+        source=source,
+        target=target,
+        warp=warp,
+        debug_voxel=debug_voxel,
+        debug_node=debug_node,
+        no_neg=no_neg,
+        renormalize=renormalize,
+        aseg_flag=aseg_flag,
+        diag_volume=diag_volume,
+        optimal_flag=optimal_flag,
+        momentum_flag=momentum_flag,
+        fixed_flag=fixed_flag,
+        distance=distance,
+        dtrans=dtrans,
+        match_peak_flag=match_peak_flag,
+        erode=erode,
+        match_mean=match_mean,
+        intensity=intensity,
+        noregrid_flag=noregrid_flag,
+        regrid_flag=regrid_flag,
+        view=view,
+        levels=levels,
+        area_smoothness=area_smoothness,
+        area=area,
+        tolerance=tolerance,
+        sigma=sigma,
+        min_sigma=min_sigma,
+        ribbon=ribbon,
+        rthresh=rthresh,
+        scale=scale,
+        dt=dt,
+        passes=passes,
+        skip=skip,
+        apply=apply,
+        distance_log=distance_log,
+        momentum=momentum,
+        iterations=iterations,
+        smoothness=smoothness,
+        transform=transform,
+        inverse_transform=inverse_transform,
+        binary=binary,
+        jacobian=jacobian,
+        disable_zero_locations=disable_zero_locations,
+        smooth_averages=smooth_averages,
+        exp_k=exp_k,
+        diagnostics=diagnostics,
+    )
+    return mri_nl_align_execute(params, execution)
+
+
+__all__ = [
+    "MRI_NL_ALIGN_METADATA",
+    "MriNlAlignOutputs",
+    "MriNlAlignParameters",
+    "mri_nl_align",
+    "mri_nl_align_params",
+]