niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__auto_tlrc.py

@@ -0,0 +1,642 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__AUTO_TLRC_METADATA = Metadata(
+    id="22feaa9f6bac760643cabb253973d50074192acb.boutiques",
+    name="@auto_tlrc",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VAutoTlrcParameters = typing.TypedDict('VAutoTlrcParameters', {
+    "__STYX_TYPE__": typing.Literal["@auto_tlrc"],
+    "base_template": InputPathType,
+    "input_anat": InputPathType,
+    "no_ss": bool,
+    "warp_orig_vol": bool,
+    "dxyz": typing.NotRequired[float | None],
+    "dx": typing.NotRequired[float | None],
+    "dy": typing.NotRequired[float | None],
+    "dz": typing.NotRequired[float | None],
+    "pad_base": typing.NotRequired[float | None],
+    "keep_tmp": bool,
+    "clean": bool,
+    "xform": typing.NotRequired[str | None],
+    "no_avoid_eyes": bool,
+    "ncr": bool,
+    "onepass": bool,
+    "twopass": bool,
+    "maxite": typing.NotRequired[float | None],
+    "not_OK_maxite": bool,
+    "inweight": bool,
+    "rigid_equiv": bool,
+    "init_xform": typing.NotRequired[str | None],
+    "no_pre": bool,
+    "out_space": typing.NotRequired[str | None],
+    "3dAllineate": bool,
+    "3dAlcost": typing.NotRequired[str | None],
+    "overwrite": bool,
+    "apar": InputPathType,
+    "input_dataset": InputPathType,
+    "pad_input": typing.NotRequired[float | None],
+    "onewarp": bool,
+    "twowarp": bool,
+    "rmode": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "suffix": typing.NotRequired[str | None],
+    "keep_view": bool,
+    "base_copy": typing.NotRequired[str | None],
+    "base_list": bool,
+    "use_gz": bool,
+    "verb": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@auto_tlrc": v__auto_tlrc_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 {
+        "@auto_tlrc": v__auto_tlrc_outputs,
+    }.get(t)
+
+
+class VAutoTlrcOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__auto_tlrc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType | None
+    """Transformed anatomical volume dataset in TLRC space."""
+    transform_file: OutputPathType | None
+    """Transform used to align the anatomical dataset to the template."""
+
+
+def v__auto_tlrc_params(
+    base_template: InputPathType,
+    input_anat: InputPathType,
+    apar: InputPathType,
+    input_dataset: InputPathType,
+    no_ss: bool = False,
+    warp_orig_vol: bool = False,
+    dxyz: float | None = None,
+    dx: float | None = None,
+    dy: float | None = None,
+    dz: float | None = None,
+    pad_base: float | None = None,
+    keep_tmp: bool = False,
+    clean: bool = False,
+    xform: str | None = None,
+    no_avoid_eyes: bool = False,
+    ncr: bool = False,
+    onepass: bool = False,
+    twopass: bool = False,
+    maxite: float | None = None,
+    not_ok_maxite: bool = False,
+    inweight: bool = False,
+    rigid_equiv: bool = False,
+    init_xform: str | None = None,
+    no_pre: bool = False,
+    out_space: str | None = None,
+    v_3d_allineate: bool = False,
+    v_3d_alcost: str | None = None,
+    overwrite: bool = False,
+    pad_input: float | None = None,
+    onewarp: bool = False,
+    twowarp: bool = False,
+    rmode: str | None = None,
+    prefix: str | None = None,
+    suffix: str | None = None,
+    keep_view: bool = False,
+    base_copy: str | None = None,
+    base_list: bool = False,
+    use_gz: bool = False,
+    verb: bool = False,
+) -> VAutoTlrcParameters:
+    """
+    Build parameters.
+    
+    Args:
+        base_template: Reference anatomical volume. Usually this volume is in\
+            some standard space like TLRC or MNI space.
+        input_anat: Original anatomical volume (+orig). The skull is removed by\
+            this script unless instructed otherwise (-no_ss).
+        apar: An anatomical dataset in TLRC space created using Usage 1 of\
+            @auto_tlrc.
+        input_dataset: Dataset (typically EPI time series or statistical\
+            dataset) to transform to TLRC space per the transform in TLRC_parent.
+        no_ss: Do not strip skull of input data set because the skull has\
+            already been removed or because the template still has the skull.
+        warp_orig_vol: Produce a TLRC version of the input volume, rather than\
+            a TLRC version of the skull-stripped input.
+        dxyz: Cubic voxel size of output DSET in TLRC space. Default is the\
+            resolution of the template.
+        dx: Size of voxel in the x direction (Right-Left). Default is 1mm.
+        dy: Size of voxel in the y direction (Anterior-Posterior). Default is\
+            1mm.
+        dz: Size of voxel in the z direction (Inferior-Superior). Default is\
+            1mm.
+        pad_base: Pad the base dataset by MM mm in each direction. Default is\
+            15 mm.
+        keep_tmp: Keep temporary files.
+        clean: Clean all temporary files, likely left from -keep_tmp option\
+            then exit.
+        xform: Transform to use for warping: Choose from affine_general or\
+            shift_rotate_scale. Default is affine_general.
+        no_avoid_eyes: An option that gets passed to 3dSkullStrip. Use it when\
+            parts of the frontal lobes get clipped.
+        ncr: Do not use -coarserot option for 3dWarpDrive, which is a default.
+        onepass: Turns off -twopass option for 3dWarpDrive. This will speed up\
+            the registration but might fail if the datasets are far apart.
+        twopass: Opposite of -onepass, default.
+        maxite: Maximum number of iterations for 3dWarpDrive. Default is 50 for\
+            first pass and then doubled to 100 in second pass.
+        not_ok_maxite: Continue running even if maximum iterations is reached.
+        inweight: Apply -weight INPUT (in 3dWarpDrive). By default, 3dWarpDrive\
+            uses the BASE dataset to weight the alignment cost.
+        rigid_equiv: Output the rigid-body version of the alignment. Resultant\
+            volume is NOT in TLRC space.
+        init_xform: Apply affine transform in XFORM0.1D before beginning\
+            registration and then include XFORM0.1D in the final transform.
+        no_pre: Delete temporary dataset created by -init_xform.
+        out_space: Set the output to a particular space.
+        v_3d_allineate: Use 3dAllineate with the lpa+ZZ cost function instead\
+            of 3dWarpDrive.
+        v_3d_alcost: Use another cost function like nmi for 3dAllineate.
+        overwrite: Overwrite existing output.
+        pad_input: Pad the input dataset by MM mm in each direction.
+        onewarp: Create follower data with one interpolation step, instead of\
+            two. This option reduces blurring of the output data.
+        twowarp: Create follower data with two interpolations step, instead of\
+            one. This option is for backward compatibility.
+        rmode: Resampling mode. Choose from: linear, cubic, NN or quintic.\
+            Default for 'Usage 1' is cubic.
+        prefix: Name of the output dataset.
+        suffix: Name the output dataset by appending this suffix to the prefix\
+            of the input data.
+        keep_view: Do not mark output dataset as +tlrc.
+        base_copy: Copy base (template) dataset into COPY_PREFIX.
+        base_list: List the full path of the base dataset.
+        use_gz: When using '-suffix ..', behave as if you had provided a prefix\
+            with '*.gz' at the end.
+        verb: Increase verbosity of the script.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@auto_tlrc",
+        "base_template": base_template,
+        "input_anat": input_anat,
+        "no_ss": no_ss,
+        "warp_orig_vol": warp_orig_vol,
+        "keep_tmp": keep_tmp,
+        "clean": clean,
+        "no_avoid_eyes": no_avoid_eyes,
+        "ncr": ncr,
+        "onepass": onepass,
+        "twopass": twopass,
+        "not_OK_maxite": not_ok_maxite,
+        "inweight": inweight,
+        "rigid_equiv": rigid_equiv,
+        "no_pre": no_pre,
+        "3dAllineate": v_3d_allineate,
+        "overwrite": overwrite,
+        "apar": apar,
+        "input_dataset": input_dataset,
+        "onewarp": onewarp,
+        "twowarp": twowarp,
+        "keep_view": keep_view,
+        "base_list": base_list,
+        "use_gz": use_gz,
+        "verb": verb,
+    }
+    if dxyz is not None:
+        params["dxyz"] = dxyz
+    if dx is not None:
+        params["dx"] = dx
+    if dy is not None:
+        params["dy"] = dy
+    if dz is not None:
+        params["dz"] = dz
+    if pad_base is not None:
+        params["pad_base"] = pad_base
+    if xform is not None:
+        params["xform"] = xform
+    if maxite is not None:
+        params["maxite"] = maxite
+    if init_xform is not None:
+        params["init_xform"] = init_xform
+    if out_space is not None:
+        params["out_space"] = out_space
+    if v_3d_alcost is not None:
+        params["3dAlcost"] = v_3d_alcost
+    if pad_input is not None:
+        params["pad_input"] = pad_input
+    if rmode is not None:
+        params["rmode"] = rmode
+    if prefix is not None:
+        params["prefix"] = prefix
+    if suffix is not None:
+        params["suffix"] = suffix
+    if base_copy is not None:
+        params["base_copy"] = base_copy
+    return params
+
+
+def v__auto_tlrc_cargs(
+    params: VAutoTlrcParameters,
+    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("@auto_tlrc")
+    cargs.extend([
+        "-base",
+        execution.input_file(params.get("base_template"))
+    ])
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_anat"))
+    ])
+    if params.get("no_ss"):
+        cargs.append("-no_ss")
+    if params.get("warp_orig_vol"):
+        cargs.append("-warp_orig_vol")
+    if params.get("dxyz") is not None:
+        cargs.extend([
+            "-dxyz",
+            str(params.get("dxyz"))
+        ])
+    if params.get("dx") is not None:
+        cargs.extend([
+            "-dx",
+            str(params.get("dx"))
+        ])
+    if params.get("dy") is not None:
+        cargs.extend([
+            "-dy",
+            str(params.get("dy"))
+        ])
+    if params.get("dz") is not None:
+        cargs.extend([
+            "-dz",
+            str(params.get("dz"))
+        ])
+    if params.get("pad_base") is not None:
+        cargs.extend([
+            "-pad_base",
+            str(params.get("pad_base"))
+        ])
+    if params.get("keep_tmp"):
+        cargs.append("-keep_tmp")
+    if params.get("clean"):
+        cargs.append("-clean")
+    if params.get("xform") is not None:
+        cargs.extend([
+            "-xform",
+            params.get("xform")
+        ])
+    if params.get("no_avoid_eyes"):
+        cargs.append("-no_avoid_eyes")
+    if params.get("ncr"):
+        cargs.append("-ncr")
+    if params.get("onepass"):
+        cargs.append("-onepass")
+    if params.get("twopass"):
+        cargs.append("-twopass")
+    if params.get("maxite") is not None:
+        cargs.extend([
+            "-maxite",
+            str(params.get("maxite"))
+        ])
+    if params.get("not_OK_maxite"):
+        cargs.append("-not_OK_maxite")
+    if params.get("inweight"):
+        cargs.append("-inweight")
+    if params.get("rigid_equiv"):
+        cargs.append("-rigid_equiv")
+    if params.get("init_xform") is not None:
+        cargs.extend([
+            "-init_xform",
+            params.get("init_xform")
+        ])
+    if params.get("no_pre"):
+        cargs.append("-no_pre")
+    if params.get("out_space") is not None:
+        cargs.extend([
+            "-out_space",
+            params.get("out_space")
+        ])
+    if params.get("3dAllineate"):
+        cargs.append("-3dAllineate")
+    if params.get("3dAlcost") is not None:
+        cargs.extend([
+            "-3dAlcost",
+            params.get("3dAlcost")
+        ])
+    if params.get("overwrite"):
+        cargs.append("-overwrite")
+    cargs.extend([
+        "-apar",
+        execution.input_file(params.get("apar"))
+    ])
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_dataset"))
+    ])
+    if params.get("pad_input") is not None:
+        cargs.extend([
+            "-pad_input",
+            str(params.get("pad_input"))
+        ])
+    if params.get("onewarp"):
+        cargs.append("-onewarp")
+    if params.get("twowarp"):
+        cargs.append("-twowarp")
+    if params.get("rmode") is not None:
+        cargs.extend([
+            "-rmode",
+            params.get("rmode")
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("suffix") is not None:
+        cargs.extend([
+            "-suffix",
+            params.get("suffix")
+        ])
+    if params.get("keep_view"):
+        cargs.append("-keep_view")
+    if params.get("base_copy") is not None:
+        cargs.extend([
+            "-base_copy",
+            params.get("base_copy")
+        ])
+    if params.get("base_list"):
+        cargs.append("-base_list")
+    if params.get("use_gz"):
+        cargs.append("-use_gz")
+    if params.get("verb"):
+        cargs.append("-verb")
+    return cargs
+
+
+def v__auto_tlrc_outputs(
+    params: VAutoTlrcParameters,
+    execution: Execution,
+) -> VAutoTlrcOutputs:
+    """
+    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 = VAutoTlrcOutputs(
+        root=execution.output_file("."),
+        output_dataset=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+        transform_file=execution.output_file(params.get("prefix") + ".Xat.1D") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v__auto_tlrc_execute(
+    params: VAutoTlrcParameters,
+    execution: Execution,
+) -> VAutoTlrcOutputs:
+    """
+    A script to transform an anatomical dataset to align with some standard space
+    template and to apply the same TLRC transform obtained with @auto_tlrc in Usage
+    1 mode to other datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VAutoTlrcOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__auto_tlrc_cargs(params, execution)
+    ret = v__auto_tlrc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__auto_tlrc(
+    base_template: InputPathType,
+    input_anat: InputPathType,
+    apar: InputPathType,
+    input_dataset: InputPathType,
+    no_ss: bool = False,
+    warp_orig_vol: bool = False,
+    dxyz: float | None = None,
+    dx: float | None = None,
+    dy: float | None = None,
+    dz: float | None = None,
+    pad_base: float | None = None,
+    keep_tmp: bool = False,
+    clean: bool = False,
+    xform: str | None = None,
+    no_avoid_eyes: bool = False,
+    ncr: bool = False,
+    onepass: bool = False,
+    twopass: bool = False,
+    maxite: float | None = None,
+    not_ok_maxite: bool = False,
+    inweight: bool = False,
+    rigid_equiv: bool = False,
+    init_xform: str | None = None,
+    no_pre: bool = False,
+    out_space: str | None = None,
+    v_3d_allineate: bool = False,
+    v_3d_alcost: str | None = None,
+    overwrite: bool = False,
+    pad_input: float | None = None,
+    onewarp: bool = False,
+    twowarp: bool = False,
+    rmode: str | None = None,
+    prefix: str | None = None,
+    suffix: str | None = None,
+    keep_view: bool = False,
+    base_copy: str | None = None,
+    base_list: bool = False,
+    use_gz: bool = False,
+    verb: bool = False,
+    runner: Runner | None = None,
+) -> VAutoTlrcOutputs:
+    """
+    A script to transform an anatomical dataset to align with some standard space
+    template and to apply the same TLRC transform obtained with @auto_tlrc in Usage
+    1 mode to other datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        base_template: Reference anatomical volume. Usually this volume is in\
+            some standard space like TLRC or MNI space.
+        input_anat: Original anatomical volume (+orig). The skull is removed by\
+            this script unless instructed otherwise (-no_ss).
+        apar: An anatomical dataset in TLRC space created using Usage 1 of\
+            @auto_tlrc.
+        input_dataset: Dataset (typically EPI time series or statistical\
+            dataset) to transform to TLRC space per the transform in TLRC_parent.
+        no_ss: Do not strip skull of input data set because the skull has\
+            already been removed or because the template still has the skull.
+        warp_orig_vol: Produce a TLRC version of the input volume, rather than\
+            a TLRC version of the skull-stripped input.
+        dxyz: Cubic voxel size of output DSET in TLRC space. Default is the\
+            resolution of the template.
+        dx: Size of voxel in the x direction (Right-Left). Default is 1mm.
+        dy: Size of voxel in the y direction (Anterior-Posterior). Default is\
+            1mm.
+        dz: Size of voxel in the z direction (Inferior-Superior). Default is\
+            1mm.
+        pad_base: Pad the base dataset by MM mm in each direction. Default is\
+            15 mm.
+        keep_tmp: Keep temporary files.
+        clean: Clean all temporary files, likely left from -keep_tmp option\
+            then exit.
+        xform: Transform to use for warping: Choose from affine_general or\
+            shift_rotate_scale. Default is affine_general.
+        no_avoid_eyes: An option that gets passed to 3dSkullStrip. Use it when\
+            parts of the frontal lobes get clipped.
+        ncr: Do not use -coarserot option for 3dWarpDrive, which is a default.
+        onepass: Turns off -twopass option for 3dWarpDrive. This will speed up\
+            the registration but might fail if the datasets are far apart.
+        twopass: Opposite of -onepass, default.
+        maxite: Maximum number of iterations for 3dWarpDrive. Default is 50 for\
+            first pass and then doubled to 100 in second pass.
+        not_ok_maxite: Continue running even if maximum iterations is reached.
+        inweight: Apply -weight INPUT (in 3dWarpDrive). By default, 3dWarpDrive\
+            uses the BASE dataset to weight the alignment cost.
+        rigid_equiv: Output the rigid-body version of the alignment. Resultant\
+            volume is NOT in TLRC space.
+        init_xform: Apply affine transform in XFORM0.1D before beginning\
+            registration and then include XFORM0.1D in the final transform.
+        no_pre: Delete temporary dataset created by -init_xform.
+        out_space: Set the output to a particular space.
+        v_3d_allineate: Use 3dAllineate with the lpa+ZZ cost function instead\
+            of 3dWarpDrive.
+        v_3d_alcost: Use another cost function like nmi for 3dAllineate.
+        overwrite: Overwrite existing output.
+        pad_input: Pad the input dataset by MM mm in each direction.
+        onewarp: Create follower data with one interpolation step, instead of\
+            two. This option reduces blurring of the output data.
+        twowarp: Create follower data with two interpolations step, instead of\
+            one. This option is for backward compatibility.
+        rmode: Resampling mode. Choose from: linear, cubic, NN or quintic.\
+            Default for 'Usage 1' is cubic.
+        prefix: Name of the output dataset.
+        suffix: Name the output dataset by appending this suffix to the prefix\
+            of the input data.
+        keep_view: Do not mark output dataset as +tlrc.
+        base_copy: Copy base (template) dataset into COPY_PREFIX.
+        base_list: List the full path of the base dataset.
+        use_gz: When using '-suffix ..', behave as if you had provided a prefix\
+            with '*.gz' at the end.
+        verb: Increase verbosity of the script.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VAutoTlrcOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AUTO_TLRC_METADATA)
+    params = v__auto_tlrc_params(
+        base_template=base_template,
+        input_anat=input_anat,
+        no_ss=no_ss,
+        warp_orig_vol=warp_orig_vol,
+        dxyz=dxyz,
+        dx=dx,
+        dy=dy,
+        dz=dz,
+        pad_base=pad_base,
+        keep_tmp=keep_tmp,
+        clean=clean,
+        xform=xform,
+        no_avoid_eyes=no_avoid_eyes,
+        ncr=ncr,
+        onepass=onepass,
+        twopass=twopass,
+        maxite=maxite,
+        not_ok_maxite=not_ok_maxite,
+        inweight=inweight,
+        rigid_equiv=rigid_equiv,
+        init_xform=init_xform,
+        no_pre=no_pre,
+        out_space=out_space,
+        v_3d_allineate=v_3d_allineate,
+        v_3d_alcost=v_3d_alcost,
+        overwrite=overwrite,
+        apar=apar,
+        input_dataset=input_dataset,
+        pad_input=pad_input,
+        onewarp=onewarp,
+        twowarp=twowarp,
+        rmode=rmode,
+        prefix=prefix,
+        suffix=suffix,
+        keep_view=keep_view,
+        base_copy=base_copy,
+        base_list=base_list,
+        use_gz=use_gz,
+        verb=verb,
+    )
+    return v__auto_tlrc_execute(params, execution)
+
+
+__all__ = [
+    "VAutoTlrcOutputs",
+    "VAutoTlrcParameters",
+    "V__AUTO_TLRC_METADATA",
+    "v__auto_tlrc",
+    "v__auto_tlrc_params",
+]