niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_warp_drive.py

@@ -0,0 +1,596 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_WARP_DRIVE_METADATA = Metadata(
+    id="0c165837a84160290a1d8256b9238ca4ea37da6a.boutiques",
+    name="3dWarpDrive",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dWarpDriveParameters = typing.TypedDict('V3dWarpDriveParameters', {
+    "__STYX_TYPE__": typing.Literal["3dWarpDrive"],
+    "dataset": InputPathType,
+    "base_dataset": InputPathType,
+    "prefix": str,
+    "shift_only": bool,
+    "shift_rotate": bool,
+    "shift_rotate_scale": bool,
+    "affine_general": bool,
+    "bilinear_general": bool,
+    "linear": bool,
+    "cubic": bool,
+    "NN": bool,
+    "quintic": bool,
+    "input_dataset": typing.NotRequired[InputPathType | None],
+    "verbosity_flag": bool,
+    "summary_file": typing.NotRequired[str | None],
+    "max_iterations": typing.NotRequired[int | None],
+    "delta": typing.NotRequired[float | None],
+    "weight": typing.NotRequired[str | None],
+    "convergence_thresh": typing.NotRequired[float | None],
+    "twopass": bool,
+    "final_mode": typing.NotRequired[str | None],
+    "parfix": typing.NotRequired[list[str] | None],
+    "oned_file": typing.NotRequired[InputPathType | None],
+    "float_format": bool,
+    "coarserot_init": bool,
+    "oned_matrix_save": typing.NotRequired[InputPathType | None],
+    "sdu_order": bool,
+    "sud_order": bool,
+    "dsu_order": bool,
+    "dus_order": bool,
+    "usd_order": bool,
+    "uds_order": bool,
+    "supper_s_matrix": bool,
+    "slower_s_matrix": bool,
+    "ashift": bool,
+    "bshift": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dWarpDrive": v_3d_warp_drive_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 {
+        "3dWarpDrive": v_3d_warp_drive_outputs,
+    }.get(t)
+
+
+class V3dWarpDriveOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_warp_drive(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType
+    """Warped dataset output"""
+    output_summary: OutputPathType | None
+    """Summary of calculations"""
+    oned_output_file: OutputPathType | None
+    """File with warping parameters"""
+    matrix_output_file: OutputPathType | None
+    """File with transformation matrices"""
+
+
+def v_3d_warp_drive_params(
+    dataset: InputPathType,
+    base_dataset: InputPathType,
+    prefix: str,
+    shift_only: bool = False,
+    shift_rotate: bool = False,
+    shift_rotate_scale: bool = False,
+    affine_general: bool = False,
+    bilinear_general: bool = False,
+    linear: bool = False,
+    cubic: bool = False,
+    nn: bool = False,
+    quintic: bool = False,
+    input_dataset: InputPathType | None = None,
+    verbosity_flag: bool = False,
+    summary_file: str | None = None,
+    max_iterations: int | None = None,
+    delta: float | None = None,
+    weight: str | None = None,
+    convergence_thresh: float | None = None,
+    twopass: bool = False,
+    final_mode: str | None = None,
+    parfix: list[str] | None = None,
+    oned_file: InputPathType | None = None,
+    float_format: bool = False,
+    coarserot_init: bool = False,
+    oned_matrix_save: InputPathType | None = None,
+    sdu_order: bool = False,
+    sud_order: bool = False,
+    dsu_order: bool = False,
+    dus_order: bool = False,
+    usd_order: bool = False,
+    uds_order: bool = False,
+    supper_s_matrix: bool = False,
+    slower_s_matrix: bool = False,
+    ashift: bool = False,
+    bshift: bool = False,
+) -> V3dWarpDriveParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input dataset.
+        base_dataset: Load dataset as the base to which the input dataset will\
+            be matched. This is a mandatory option.
+        prefix: Sets the prefix of the output dataset. If 'NULL', no output\
+            dataset is written.
+        shift_only: 3 parameters (shifts).
+        shift_rotate: 6 parameters (shifts + angles).
+        shift_rotate_scale: 9 parameters (shifts + angles + scale factors).
+        affine_general: 12 parameters (3 shifts + 3x3 matrix).
+        bilinear_general: 39 parameters (3 + 3x3 + 3x3x3). Not implemented and\
+            will never be.
+        linear: Linear interpolation method.
+        cubic: Cubic interpolation method.
+        nn: Nearest neighbor interpolation method [default].
+        quintic: Quintic interpolation method.
+        input_dataset: Specify the input dataset anywhere in the command line\
+            option list.
+        verbosity_flag: Print out lots of information along the way.
+        summary_file: Save summary of calculations into text file. If value is\
+            '-', summary goes to stdout.
+        max_iterations: Allow up to 'm' iterations for convergence.
+        delta: Distance, in voxel size, used to compute image derivatives using\
+            finite differences. [Default=1.0].
+        weight: Set the weighting applied to each voxel proportional to the\
+            brick specified here. [Default=computed by program from base].
+        convergence_thresh: Set the convergence parameter to be RMS 't' voxels\
+            movement between iterations. [Default=0.03].
+        twopass: Do the parameter estimation in two passes, coarse-but-fast\
+            first, then fine-but-slow second.
+        final_mode: Set the final warp to be interpolated using 'mode'.
+        parfix: Fix the n'th parameter of the warp model to the value 'v'. More\
+            than one -parfix option can be used.
+        oned_file: Write out the warping parameters to this file.
+        float_format: Write output dataset in float format, even if input\
+            dataset is short or byte.
+        coarserot_init: Initialize shift+rotation parameters by a brute force\
+            coarse search.
+        oned_matrix_save: Save base-to-input transformation matrices in\
+            specified file. If the file does not end in '.1D', the program will\
+            append '.aff12.1D'.
+        sdu_order: Set the order of the matrix multiplication for the affine\
+            transformations (S=triangular shear, D=diagonal scaling matrix,\
+            U=rotation matrix).
+        sud_order: Set the order of the matrix multiplication for the affine\
+            transformations (S=triangular shear, U=rotation matrix, D=diagonal\
+            scaling matrix).
+        dsu_order: Set the order of the matrix multiplication for the affine\
+            transformations (D=diagonal scaling matrix, S=triangular shear,\
+            U=rotation matrix).
+        dus_order: Set the order of the matrix multiplication for the affine\
+            transformations (D=diagonal scaling matrix, U=rotation matrix,\
+            S=triangular shear).
+        usd_order: Set the order of the matrix multiplication for the affine\
+            transformations (U=rotation matrix, S=triangular shear, D=diagonal\
+            scaling matrix).
+        uds_order: Set the order of the matrix multiplication for the affine\
+            transformations (U=rotation matrix, D=diagonal scaling matrix,\
+            S=triangular shear).
+        supper_s_matrix: Set the S matrix to be upper triangular.
+        slower_s_matrix: Set the S matrix to be lower triangular.
+        ashift: Apply the shift parameters after the matrix transformation.
+        bshift: Apply the shift parameters before the matrix transformation.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dWarpDrive",
+        "dataset": dataset,
+        "base_dataset": base_dataset,
+        "prefix": prefix,
+        "shift_only": shift_only,
+        "shift_rotate": shift_rotate,
+        "shift_rotate_scale": shift_rotate_scale,
+        "affine_general": affine_general,
+        "bilinear_general": bilinear_general,
+        "linear": linear,
+        "cubic": cubic,
+        "NN": nn,
+        "quintic": quintic,
+        "verbosity_flag": verbosity_flag,
+        "twopass": twopass,
+        "float_format": float_format,
+        "coarserot_init": coarserot_init,
+        "sdu_order": sdu_order,
+        "sud_order": sud_order,
+        "dsu_order": dsu_order,
+        "dus_order": dus_order,
+        "usd_order": usd_order,
+        "uds_order": uds_order,
+        "supper_s_matrix": supper_s_matrix,
+        "slower_s_matrix": slower_s_matrix,
+        "ashift": ashift,
+        "bshift": bshift,
+    }
+    if input_dataset is not None:
+        params["input_dataset"] = input_dataset
+    if summary_file is not None:
+        params["summary_file"] = summary_file
+    if max_iterations is not None:
+        params["max_iterations"] = max_iterations
+    if delta is not None:
+        params["delta"] = delta
+    if weight is not None:
+        params["weight"] = weight
+    if convergence_thresh is not None:
+        params["convergence_thresh"] = convergence_thresh
+    if final_mode is not None:
+        params["final_mode"] = final_mode
+    if parfix is not None:
+        params["parfix"] = parfix
+    if oned_file is not None:
+        params["oned_file"] = oned_file
+    if oned_matrix_save is not None:
+        params["oned_matrix_save"] = oned_matrix_save
+    return params
+
+
+def v_3d_warp_drive_cargs(
+    params: V3dWarpDriveParameters,
+    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("3dWarpDrive")
+    cargs.append(execution.input_file(params.get("dataset")))
+    cargs.extend([
+        "-base",
+        execution.input_file(params.get("base_dataset"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("shift_only"):
+        cargs.append("-shift_only")
+    if params.get("shift_rotate"):
+        cargs.append("-shift_rotate")
+    if params.get("shift_rotate_scale"):
+        cargs.append("-shift_rotate_scale")
+    if params.get("affine_general"):
+        cargs.append("-affine_general")
+    if params.get("bilinear_general"):
+        cargs.append("-bilinear_general")
+    if params.get("linear"):
+        cargs.append("-linear")
+    if params.get("cubic"):
+        cargs.append("-cubic")
+    if params.get("NN"):
+        cargs.append("-NN")
+    if params.get("quintic"):
+        cargs.append("-quintic")
+    if params.get("input_dataset") is not None:
+        cargs.extend([
+            "-input",
+            execution.input_file(params.get("input_dataset"))
+        ])
+    if params.get("verbosity_flag"):
+        cargs.append("-verb")
+    if params.get("summary_file") is not None:
+        cargs.extend([
+            "-summ",
+            params.get("summary_file")
+        ])
+    if params.get("max_iterations") is not None:
+        cargs.extend([
+            "-maxite",
+            str(params.get("max_iterations"))
+        ])
+    if params.get("delta") is not None:
+        cargs.extend([
+            "-delta",
+            str(params.get("delta"))
+        ])
+    if params.get("weight") is not None:
+        cargs.extend([
+            "-weight",
+            params.get("weight")
+        ])
+    if params.get("convergence_thresh") is not None:
+        cargs.extend([
+            "-thresh",
+            str(params.get("convergence_thresh"))
+        ])
+    if params.get("twopass"):
+        cargs.append("-twopass")
+    if params.get("final_mode") is not None:
+        cargs.extend([
+            "-final",
+            params.get("final_mode")
+        ])
+    if params.get("parfix") is not None:
+        cargs.extend([
+            "-parfix",
+            *params.get("parfix")
+        ])
+    if params.get("oned_file") is not None:
+        cargs.extend([
+            "-1Dfile",
+            execution.input_file(params.get("oned_file"))
+        ])
+    if params.get("float_format"):
+        cargs.append("-float")
+    if params.get("coarserot_init"):
+        cargs.append("-coarserot")
+    if params.get("oned_matrix_save") is not None:
+        cargs.extend([
+            "-1Dmatrix_save",
+            execution.input_file(params.get("oned_matrix_save"))
+        ])
+    if params.get("sdu_order"):
+        cargs.append("-SDU")
+    if params.get("sud_order"):
+        cargs.append("-SUD")
+    if params.get("dsu_order"):
+        cargs.append("-DSU")
+    if params.get("dus_order"):
+        cargs.append("-DUS")
+    if params.get("usd_order"):
+        cargs.append("-USD")
+    if params.get("uds_order"):
+        cargs.append("-UDS")
+    if params.get("supper_s_matrix"):
+        cargs.append("-Supper")
+    if params.get("slower_s_matrix"):
+        cargs.append("-Slower")
+    if params.get("ashift"):
+        cargs.append("-ashift")
+    if params.get("bshift"):
+        cargs.append("-bshift")
+    return cargs
+
+
+def v_3d_warp_drive_outputs(
+    params: V3dWarpDriveParameters,
+    execution: Execution,
+) -> V3dWarpDriveOutputs:
+    """
+    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 = V3dWarpDriveOutputs(
+        root=execution.output_file("."),
+        output_dataset=execution.output_file(params.get("prefix") + "+orig"),
+        output_summary=execution.output_file(params.get("summary_file")) if (params.get("summary_file") is not None) else None,
+        oned_output_file=execution.output_file(pathlib.Path(params.get("oned_file")).name) if (params.get("oned_file") is not None) else None,
+        matrix_output_file=execution.output_file(pathlib.Path(params.get("oned_matrix_save")).name) if (params.get("oned_matrix_save") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_warp_drive_execute(
+    params: V3dWarpDriveParameters,
+    execution: Execution,
+) -> V3dWarpDriveOutputs:
+    """
+    Warp a dataset to match another one (the base) using an affine transformation.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dWarpDriveOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_warp_drive_cargs(params, execution)
+    ret = v_3d_warp_drive_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_warp_drive(
+    dataset: InputPathType,
+    base_dataset: InputPathType,
+    prefix: str,
+    shift_only: bool = False,
+    shift_rotate: bool = False,
+    shift_rotate_scale: bool = False,
+    affine_general: bool = False,
+    bilinear_general: bool = False,
+    linear: bool = False,
+    cubic: bool = False,
+    nn: bool = False,
+    quintic: bool = False,
+    input_dataset: InputPathType | None = None,
+    verbosity_flag: bool = False,
+    summary_file: str | None = None,
+    max_iterations: int | None = None,
+    delta: float | None = None,
+    weight: str | None = None,
+    convergence_thresh: float | None = None,
+    twopass: bool = False,
+    final_mode: str | None = None,
+    parfix: list[str] | None = None,
+    oned_file: InputPathType | None = None,
+    float_format: bool = False,
+    coarserot_init: bool = False,
+    oned_matrix_save: InputPathType | None = None,
+    sdu_order: bool = False,
+    sud_order: bool = False,
+    dsu_order: bool = False,
+    dus_order: bool = False,
+    usd_order: bool = False,
+    uds_order: bool = False,
+    supper_s_matrix: bool = False,
+    slower_s_matrix: bool = False,
+    ashift: bool = False,
+    bshift: bool = False,
+    runner: Runner | None = None,
+) -> V3dWarpDriveOutputs:
+    """
+    Warp a dataset to match another one (the base) using an affine transformation.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input dataset.
+        base_dataset: Load dataset as the base to which the input dataset will\
+            be matched. This is a mandatory option.
+        prefix: Sets the prefix of the output dataset. If 'NULL', no output\
+            dataset is written.
+        shift_only: 3 parameters (shifts).
+        shift_rotate: 6 parameters (shifts + angles).
+        shift_rotate_scale: 9 parameters (shifts + angles + scale factors).
+        affine_general: 12 parameters (3 shifts + 3x3 matrix).
+        bilinear_general: 39 parameters (3 + 3x3 + 3x3x3). Not implemented and\
+            will never be.
+        linear: Linear interpolation method.
+        cubic: Cubic interpolation method.
+        nn: Nearest neighbor interpolation method [default].
+        quintic: Quintic interpolation method.
+        input_dataset: Specify the input dataset anywhere in the command line\
+            option list.
+        verbosity_flag: Print out lots of information along the way.
+        summary_file: Save summary of calculations into text file. If value is\
+            '-', summary goes to stdout.
+        max_iterations: Allow up to 'm' iterations for convergence.
+        delta: Distance, in voxel size, used to compute image derivatives using\
+            finite differences. [Default=1.0].
+        weight: Set the weighting applied to each voxel proportional to the\
+            brick specified here. [Default=computed by program from base].
+        convergence_thresh: Set the convergence parameter to be RMS 't' voxels\
+            movement between iterations. [Default=0.03].
+        twopass: Do the parameter estimation in two passes, coarse-but-fast\
+            first, then fine-but-slow second.
+        final_mode: Set the final warp to be interpolated using 'mode'.
+        parfix: Fix the n'th parameter of the warp model to the value 'v'. More\
+            than one -parfix option can be used.
+        oned_file: Write out the warping parameters to this file.
+        float_format: Write output dataset in float format, even if input\
+            dataset is short or byte.
+        coarserot_init: Initialize shift+rotation parameters by a brute force\
+            coarse search.
+        oned_matrix_save: Save base-to-input transformation matrices in\
+            specified file. If the file does not end in '.1D', the program will\
+            append '.aff12.1D'.
+        sdu_order: Set the order of the matrix multiplication for the affine\
+            transformations (S=triangular shear, D=diagonal scaling matrix,\
+            U=rotation matrix).
+        sud_order: Set the order of the matrix multiplication for the affine\
+            transformations (S=triangular shear, U=rotation matrix, D=diagonal\
+            scaling matrix).
+        dsu_order: Set the order of the matrix multiplication for the affine\
+            transformations (D=diagonal scaling matrix, S=triangular shear,\
+            U=rotation matrix).
+        dus_order: Set the order of the matrix multiplication for the affine\
+            transformations (D=diagonal scaling matrix, U=rotation matrix,\
+            S=triangular shear).
+        usd_order: Set the order of the matrix multiplication for the affine\
+            transformations (U=rotation matrix, S=triangular shear, D=diagonal\
+            scaling matrix).
+        uds_order: Set the order of the matrix multiplication for the affine\
+            transformations (U=rotation matrix, D=diagonal scaling matrix,\
+            S=triangular shear).
+        supper_s_matrix: Set the S matrix to be upper triangular.
+        slower_s_matrix: Set the S matrix to be lower triangular.
+        ashift: Apply the shift parameters after the matrix transformation.
+        bshift: Apply the shift parameters before the matrix transformation.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dWarpDriveOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_WARP_DRIVE_METADATA)
+    params = v_3d_warp_drive_params(
+        dataset=dataset,
+        base_dataset=base_dataset,
+        prefix=prefix,
+        shift_only=shift_only,
+        shift_rotate=shift_rotate,
+        shift_rotate_scale=shift_rotate_scale,
+        affine_general=affine_general,
+        bilinear_general=bilinear_general,
+        linear=linear,
+        cubic=cubic,
+        nn=nn,
+        quintic=quintic,
+        input_dataset=input_dataset,
+        verbosity_flag=verbosity_flag,
+        summary_file=summary_file,
+        max_iterations=max_iterations,
+        delta=delta,
+        weight=weight,
+        convergence_thresh=convergence_thresh,
+        twopass=twopass,
+        final_mode=final_mode,
+        parfix=parfix,
+        oned_file=oned_file,
+        float_format=float_format,
+        coarserot_init=coarserot_init,
+        oned_matrix_save=oned_matrix_save,
+        sdu_order=sdu_order,
+        sud_order=sud_order,
+        dsu_order=dsu_order,
+        dus_order=dus_order,
+        usd_order=usd_order,
+        uds_order=uds_order,
+        supper_s_matrix=supper_s_matrix,
+        slower_s_matrix=slower_s_matrix,
+        ashift=ashift,
+        bshift=bshift,
+    )
+    return v_3d_warp_drive_execute(params, execution)
+
+
+__all__ = [
+    "V3dWarpDriveOutputs",
+    "V3dWarpDriveParameters",
+    "V_3D_WARP_DRIVE_METADATA",
+    "v_3d_warp_drive",
+    "v_3d_warp_drive_params",
+]