niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3drotate.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DROTATE_METADATA = Metadata(
+    id="dae9478b93184d9121e61e24d56f3c564e520ade.boutiques",
+    name="3drotate",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3drotateParameters = typing.TypedDict('V3drotateParameters', {
+    "__STYX_TYPE__": typing.Literal["3drotate"],
+    "dataset": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "verbose": bool,
+    "ashift": typing.NotRequired[list[float] | None],
+    "bshift": typing.NotRequired[list[float] | None],
+    "rotate": typing.NotRequired[list[str] | None],
+    "rotparent": typing.NotRequired[InputPathType | None],
+    "gridparent": typing.NotRequired[InputPathType | None],
+    "matvec_dicom": typing.NotRequired[InputPathType | None],
+    "matvec_order": typing.NotRequired[InputPathType | None],
+    "matvec_dset": typing.NotRequired[InputPathType | None],
+    "dfile": typing.NotRequired[InputPathType | None],
+    "1Dfile": typing.NotRequired[InputPathType | None],
+    "points": bool,
+    "origin": typing.NotRequired[list[float] | None],
+    "Fourier": bool,
+    "NN": bool,
+    "linear": bool,
+    "cubic": bool,
+    "quintic": bool,
+    "heptic": bool,
+    "Fourier_nopad": bool,
+    "clipit": bool,
+    "noclip": bool,
+    "zpad": 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 {
+        "3drotate": v_3drotate_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 {
+        "3drotate": v_3drotate_outputs,
+    }.get(t)
+
+
+class V3drotateOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3drotate(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_head: OutputPathType | None
+    """Output dataset header file"""
+    out_brick: OutputPathType | None
+    """Output dataset brick file"""
+
+
+def v_3drotate_params(
+    dataset: InputPathType,
+    prefix: str | None = None,
+    verbose: bool = False,
+    ashift: list[float] | None = None,
+    bshift: list[float] | None = None,
+    rotate: list[str] | None = None,
+    rotparent: InputPathType | None = None,
+    gridparent: InputPathType | None = None,
+    matvec_dicom: InputPathType | None = None,
+    matvec_order: InputPathType | None = None,
+    matvec_dset: InputPathType | None = None,
+    dfile: InputPathType | None = None,
+    v_1_dfile: InputPathType | None = None,
+    points: bool = False,
+    origin: list[float] | None = None,
+    fourier: bool = False,
+    nn: bool = False,
+    linear: bool = False,
+    cubic: bool = False,
+    quintic: bool = False,
+    heptic: bool = False,
+    fourier_nopad: bool = False,
+    clipit: bool = False,
+    noclip: bool = False,
+    zpad: float | None = None,
+) -> V3drotateParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input AFNI dataset, may contain a sub-brick selector list.
+        prefix: Sets the output dataset prefix name.
+        verbose: Prints out progress reports (to stderr).
+        ashift: Shifts the dataset by specified distances (dx, dy, dz) in mm in\
+            x, y, z directions respectively, AFTER rotation.
+        bshift: Shifts the dataset by specified distances (dx, dy, dz) in mm in\
+            x, y, z directions respectively, BEFORE rotation.
+        rotate: Specifies the 3D rotation angles (th1, th2, th3) about certain\
+            axes.
+        rotparent: Rotation and translation should be taken from the first\
+            3dvolreg transformation found in the header of dataset 'rset'.
+        gridparent: Output dataset should be shifted to match the grid of\
+            dataset 'gset'. Can only be used with -rotparent.
+        matvec_dicom: Rotation and translation should be read from DICOM file\
+            'mfile'.
+        matvec_order: Rotation and translation should be read from file 'mfile'\
+            with dataset coordinate order.
+        matvec_dset: Rotation and translation should be read from the .HEAD\
+            file of dataset 'mset' created by 3dTagalign.
+        dfile: Reads movement parameters for each sub-brick from an ASCII file\
+            'dname'.
+        v_1_dfile: Reads movement parameters for each sub-brick from a 1D ASCII\
+            file 'dname'.
+        points: Specifies that (x,y,z) points are to be rotated instead of a\
+            dataset.
+        origin: Specifies the rotation origin point (xo, yo, zo).
+        fourier: Use Fourier interpolation method during transformation.
+        nn: Use nearest neighbor interpolation method during transformation.
+        linear: Use linear interpolation (1st order polynomial) during\
+            transformation.
+        cubic: Use cubic interpolation (3rd order polynomial) during\
+            transformation.
+        quintic: Use quintic interpolation (5th order Lagrange polynomial)\
+            during transformation.
+        heptic: Use heptic interpolation (7th order Lagrange polynomial) during\
+            transformation.
+        fourier_nopad: Use the Fourier method WITHOUT padding.
+        clipit: Clip results to input brick range [default option].
+        noclip: Do not clip results to input brick range.
+        zpad: Zero pad around the edges by 'n' voxels during rotations.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3drotate",
+        "dataset": dataset,
+        "verbose": verbose,
+        "points": points,
+        "Fourier": fourier,
+        "NN": nn,
+        "linear": linear,
+        "cubic": cubic,
+        "quintic": quintic,
+        "heptic": heptic,
+        "Fourier_nopad": fourier_nopad,
+        "clipit": clipit,
+        "noclip": noclip,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if ashift is not None:
+        params["ashift"] = ashift
+    if bshift is not None:
+        params["bshift"] = bshift
+    if rotate is not None:
+        params["rotate"] = rotate
+    if rotparent is not None:
+        params["rotparent"] = rotparent
+    if gridparent is not None:
+        params["gridparent"] = gridparent
+    if matvec_dicom is not None:
+        params["matvec_dicom"] = matvec_dicom
+    if matvec_order is not None:
+        params["matvec_order"] = matvec_order
+    if matvec_dset is not None:
+        params["matvec_dset"] = matvec_dset
+    if dfile is not None:
+        params["dfile"] = dfile
+    if v_1_dfile is not None:
+        params["1Dfile"] = v_1_dfile
+    if origin is not None:
+        params["origin"] = origin
+    if zpad is not None:
+        params["zpad"] = zpad
+    return params
+
+
+def v_3drotate_cargs(
+    params: V3drotateParameters,
+    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("3drotate")
+    cargs.append(execution.input_file(params.get("dataset")))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("verbose"):
+        cargs.append("-verbose")
+    if params.get("ashift") is not None:
+        cargs.extend([
+            "-ashift",
+            *map(str, params.get("ashift"))
+        ])
+    if params.get("bshift") is not None:
+        cargs.extend([
+            "-bshift",
+            *map(str, params.get("bshift"))
+        ])
+    if params.get("rotate") is not None:
+        cargs.extend([
+            "-rotate",
+            *params.get("rotate")
+        ])
+    if params.get("rotparent") is not None:
+        cargs.extend([
+            "-rotparent",
+            execution.input_file(params.get("rotparent"))
+        ])
+    if params.get("gridparent") is not None:
+        cargs.extend([
+            "-gridparent",
+            execution.input_file(params.get("gridparent"))
+        ])
+    if params.get("matvec_dicom") is not None:
+        cargs.extend([
+            "-matvec_dicom",
+            execution.input_file(params.get("matvec_dicom"))
+        ])
+    if params.get("matvec_order") is not None:
+        cargs.extend([
+            "-matvec_order",
+            execution.input_file(params.get("matvec_order"))
+        ])
+    if params.get("matvec_dset") is not None:
+        cargs.extend([
+            "-matvec_dset",
+            execution.input_file(params.get("matvec_dset"))
+        ])
+    if params.get("dfile") is not None:
+        cargs.extend([
+            "-dfile",
+            execution.input_file(params.get("dfile"))
+        ])
+    if params.get("1Dfile") is not None:
+        cargs.extend([
+            "-1Dfile",
+            execution.input_file(params.get("1Dfile"))
+        ])
+    if params.get("points"):
+        cargs.append("-points")
+    if params.get("origin") is not None:
+        cargs.extend([
+            "-origin",
+            *map(str, params.get("origin"))
+        ])
+    if params.get("Fourier"):
+        cargs.append("-Fourier")
+    if params.get("NN"):
+        cargs.append("-NN")
+    if params.get("linear"):
+        cargs.append("-linear")
+    if params.get("cubic"):
+        cargs.append("-cubic")
+    if params.get("quintic"):
+        cargs.append("-quintic")
+    if params.get("heptic"):
+        cargs.append("-heptic")
+    if params.get("Fourier_nopad"):
+        cargs.append("-Fourier_nopad")
+    if params.get("clipit"):
+        cargs.append("-clipit")
+    if params.get("noclip"):
+        cargs.append("-noclip")
+    if params.get("zpad") is not None:
+        cargs.extend([
+            "-zpad",
+            str(params.get("zpad"))
+        ])
+    return cargs
+
+
+def v_3drotate_outputs(
+    params: V3drotateParameters,
+    execution: Execution,
+) -> V3drotateOutputs:
+    """
+    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 = V3drotateOutputs(
+        root=execution.output_file("."),
+        out_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        out_brick=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3drotate_execute(
+    params: V3drotateParameters,
+    execution: Execution,
+) -> V3drotateOutputs:
+    """
+    Rotates and/or translates all bricks from an AFNI dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3drotateOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3drotate_cargs(params, execution)
+    ret = v_3drotate_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3drotate(
+    dataset: InputPathType,
+    prefix: str | None = None,
+    verbose: bool = False,
+    ashift: list[float] | None = None,
+    bshift: list[float] | None = None,
+    rotate: list[str] | None = None,
+    rotparent: InputPathType | None = None,
+    gridparent: InputPathType | None = None,
+    matvec_dicom: InputPathType | None = None,
+    matvec_order: InputPathType | None = None,
+    matvec_dset: InputPathType | None = None,
+    dfile: InputPathType | None = None,
+    v_1_dfile: InputPathType | None = None,
+    points: bool = False,
+    origin: list[float] | None = None,
+    fourier: bool = False,
+    nn: bool = False,
+    linear: bool = False,
+    cubic: bool = False,
+    quintic: bool = False,
+    heptic: bool = False,
+    fourier_nopad: bool = False,
+    clipit: bool = False,
+    noclip: bool = False,
+    zpad: float | None = None,
+    runner: Runner | None = None,
+) -> V3drotateOutputs:
+    """
+    Rotates and/or translates all bricks from an AFNI dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input AFNI dataset, may contain a sub-brick selector list.
+        prefix: Sets the output dataset prefix name.
+        verbose: Prints out progress reports (to stderr).
+        ashift: Shifts the dataset by specified distances (dx, dy, dz) in mm in\
+            x, y, z directions respectively, AFTER rotation.
+        bshift: Shifts the dataset by specified distances (dx, dy, dz) in mm in\
+            x, y, z directions respectively, BEFORE rotation.
+        rotate: Specifies the 3D rotation angles (th1, th2, th3) about certain\
+            axes.
+        rotparent: Rotation and translation should be taken from the first\
+            3dvolreg transformation found in the header of dataset 'rset'.
+        gridparent: Output dataset should be shifted to match the grid of\
+            dataset 'gset'. Can only be used with -rotparent.
+        matvec_dicom: Rotation and translation should be read from DICOM file\
+            'mfile'.
+        matvec_order: Rotation and translation should be read from file 'mfile'\
+            with dataset coordinate order.
+        matvec_dset: Rotation and translation should be read from the .HEAD\
+            file of dataset 'mset' created by 3dTagalign.
+        dfile: Reads movement parameters for each sub-brick from an ASCII file\
+            'dname'.
+        v_1_dfile: Reads movement parameters for each sub-brick from a 1D ASCII\
+            file 'dname'.
+        points: Specifies that (x,y,z) points are to be rotated instead of a\
+            dataset.
+        origin: Specifies the rotation origin point (xo, yo, zo).
+        fourier: Use Fourier interpolation method during transformation.
+        nn: Use nearest neighbor interpolation method during transformation.
+        linear: Use linear interpolation (1st order polynomial) during\
+            transformation.
+        cubic: Use cubic interpolation (3rd order polynomial) during\
+            transformation.
+        quintic: Use quintic interpolation (5th order Lagrange polynomial)\
+            during transformation.
+        heptic: Use heptic interpolation (7th order Lagrange polynomial) during\
+            transformation.
+        fourier_nopad: Use the Fourier method WITHOUT padding.
+        clipit: Clip results to input brick range [default option].
+        noclip: Do not clip results to input brick range.
+        zpad: Zero pad around the edges by 'n' voxels during rotations.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3drotateOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DROTATE_METADATA)
+    params = v_3drotate_params(
+        dataset=dataset,
+        prefix=prefix,
+        verbose=verbose,
+        ashift=ashift,
+        bshift=bshift,
+        rotate=rotate,
+        rotparent=rotparent,
+        gridparent=gridparent,
+        matvec_dicom=matvec_dicom,
+        matvec_order=matvec_order,
+        matvec_dset=matvec_dset,
+        dfile=dfile,
+        v_1_dfile=v_1_dfile,
+        points=points,
+        origin=origin,
+        fourier=fourier,
+        nn=nn,
+        linear=linear,
+        cubic=cubic,
+        quintic=quintic,
+        heptic=heptic,
+        fourier_nopad=fourier_nopad,
+        clipit=clipit,
+        noclip=noclip,
+        zpad=zpad,
+    )
+    return v_3drotate_execute(params, execution)
+
+
+__all__ = [
+    "V3drotateOutputs",
+    "V3drotateParameters",
+    "V_3DROTATE_METADATA",
+    "v_3drotate",
+    "v_3drotate_params",
+]