niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/to3d.py

@@ -0,0 +1,643 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TO3D_METADATA = Metadata(
+    id="f1885e5a598e33eedbd9902b41caded7ca049613.boutiques",
+    name="to3d",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+To3dParameters = typing.TypedDict('To3dParameters', {
+    "__STYX_TYPE__": typing.Literal["to3d"],
+    "input_files": list[InputPathType],
+    "type": typing.NotRequired[typing.Literal["spgr", "fse", "epan", "anat", "ct", "spct", "pet", "mra", "bmap", "diff", "omri", "abuc", "fim", "fith", "fico", "fitt", "fift", "fizt", "fict", "fibt", "fibn", "figt", "fipt", "fbuc"] | None],
+    "statpar": typing.NotRequired[list[float] | None],
+    "prefix": typing.NotRequired[str | None],
+    "session": typing.NotRequired[str | None],
+    "geomparent": typing.NotRequired[InputPathType | None],
+    "anatparent": typing.NotRequired[InputPathType | None],
+    "nosave_flag": bool,
+    "nowritebrik_flag": bool,
+    "view": typing.NotRequired[typing.Literal["orig", "acpc", "tlrc"] | None],
+    "time_zt": typing.NotRequired[list[str] | None],
+    "time_tz": typing.NotRequired[list[str] | None],
+    "tr_units": typing.NotRequired[typing.Literal["ms", "msec", "s", "sec", "Hz", "Hertz"] | None],
+    "torg": typing.NotRequired[float | None],
+    "xFOV": typing.NotRequired[str | None],
+    "yFOV": typing.NotRequired[str | None],
+    "zFOV": typing.NotRequired[str | None],
+    "xSLAB": typing.NotRequired[str | None],
+    "ySLAB": typing.NotRequired[str | None],
+    "zSLAB": typing.NotRequired[str | None],
+    "zorigin": typing.NotRequired[float | None],
+    "data_type": typing.NotRequired[typing.Literal["short", "float", "byte", "complex"] | None],
+    "global_scaling_factor": typing.NotRequired[float | None],
+    "nofloatscan_flag": bool,
+    "in1_flag": bool,
+    "orient": typing.NotRequired[str | None],
+    "skip_outliers_flag": bool,
+    "text_outliers_flag": bool,
+    "save_outliers": typing.NotRequired[str | None],
+    "assume_dicom_mosaic_flag": bool,
+    "oblique_origin_flag": bool,
+    "reverse_list_flag": bool,
+    "use_last_elem_flag": bool,
+    "use_old_mosaic_code_flag": bool,
+    "ushort2float_flag": bool,
+    "verbose_flag": bool,
+    "gamma": typing.NotRequired[float | None],
+    "ncolors": typing.NotRequired[float | None],
+    "xtwarns_flag": bool,
+    "quit_on_err_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 {
+        "to3d": to3d_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 {
+        "to3d": to3d_outputs,
+    }.get(t)
+
+
+class To3dOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `to3d(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    headfile: OutputPathType | None
+    """Output AFNI HEAD file"""
+    brikfile: OutputPathType | None
+    """Output AFNI BRIK file"""
+    outfile_outliers: OutputPathType | None
+    """Outlier count file"""
+
+
+def to3d_params(
+    input_files: list[InputPathType],
+    type_: typing.Literal["spgr", "fse", "epan", "anat", "ct", "spct", "pet", "mra", "bmap", "diff", "omri", "abuc", "fim", "fith", "fico", "fitt", "fift", "fizt", "fict", "fibt", "fibn", "figt", "fipt", "fbuc"] | None = None,
+    statpar: list[float] | None = None,
+    prefix: str | None = None,
+    session: str | None = None,
+    geomparent: InputPathType | None = None,
+    anatparent: InputPathType | None = None,
+    nosave_flag: bool = False,
+    nowritebrik_flag: bool = False,
+    view: typing.Literal["orig", "acpc", "tlrc"] | None = None,
+    time_zt: list[str] | None = None,
+    time_tz: list[str] | None = None,
+    tr_units: typing.Literal["ms", "msec", "s", "sec", "Hz", "Hertz"] | None = None,
+    torg: float | None = None,
+    x_fov: str | None = None,
+    y_fov: str | None = None,
+    z_fov: str | None = None,
+    x_slab: str | None = None,
+    y_slab: str | None = None,
+    z_slab: str | None = None,
+    zorigin: float | None = None,
+    data_type: typing.Literal["short", "float", "byte", "complex"] | None = None,
+    global_scaling_factor: float | None = None,
+    nofloatscan_flag: bool = False,
+    in1_flag: bool = False,
+    orient: str | None = None,
+    skip_outliers_flag: bool = False,
+    text_outliers_flag: bool = False,
+    save_outliers: str | None = None,
+    assume_dicom_mosaic_flag: bool = False,
+    oblique_origin_flag: bool = False,
+    reverse_list_flag: bool = False,
+    use_last_elem_flag: bool = False,
+    use_old_mosaic_code_flag: bool = False,
+    ushort2float_flag: bool = False,
+    verbose_flag: bool = False,
+    gamma: float | None = None,
+    ncolors: float | None = None,
+    xtwarns_flag: bool = False,
+    quit_on_err_flag: bool = False,
+) -> To3dParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input 2D image files.
+        type_: Declare images to contain data of a given type.
+        statpar: Supply auxiliary statistical parameters.
+        prefix: Prefix of the output 3D dataset.
+        session: Session directory for output 3D dataset.
+        geomparent: Read geometry data from dataset file.
+        anatparent: Take anatomy parent from dataset file.
+        nosave_flag: Suppress autosave of 3D dataset.
+        nowritebrik_flag: Suppress saving of the BRIK file.
+        view: Set the dataset's viewing coordinates.
+        time_zt: Specify time dependent dataset (z-axis first, then t-axis).
+        time_tz: Specify time dependent dataset (t-axis first, then z-axis).
+        tr_units: Specify TR units.
+        torg: Set time origin of dataset.
+        x_fov: Specify size and orientation of the x-axis extent.
+        y_fov: Specify size and orientation of the y-axis extent.
+        z_fov: Specify size and orientation of the z-axis extent.
+        x_slab: Specify x-axis slab.
+        y_slab: Specify y-axis slab.
+        z_slab: Specify z-axis slab.
+        zorigin: Set the center of the first slice offset in z-axis.
+        data_type: Set voxel data to be stored as given data type.
+        global_scaling_factor: Global scaling factor.
+        nofloatscan_flag: Do not scan for illegal floating point values.
+        in1_flag: Read and process images one slice at a time.
+        orient: Set the orientation of the 3D volumes.
+        skip_outliers_flag: Skip the outlier check for 3D+time datasets.
+        text_outliers_flag: Only print out the outlier check results in text\
+            form.
+        save_outliers: Save the outliers count into a 1D file.
+        assume_dicom_mosaic_flag: Assume any Siemens DICOM file is a potential\
+            MOSAIC image.
+        oblique_origin_flag: Assume origin and orientation from oblique\
+            transformation matrix.
+        reverse_list_flag: Reverse the input file list.
+        use_last_elem_flag: Search DICOM images for the last occurrence of each\
+            element.
+        use_old_mosaic_code_flag: Do not use the Dec 2010 updates to Siemens\
+            mosaic code.
+        ushort2float_flag: Convert input shorts to float and add 2^16 to any\
+            negatives.
+        verbose_flag: Show debugging information for reading DICOM files.
+        gamma: Gamma correction factor for the monitor.
+        ncolors: Number of gray levels for the image displays.
+        xtwarns_flag: Turn on display of Xt warning messages.
+        quit_on_err_flag: Do not launch interactive to3d mode if input has\
+            error.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "to3d",
+        "input_files": input_files,
+        "nosave_flag": nosave_flag,
+        "nowritebrik_flag": nowritebrik_flag,
+        "nofloatscan_flag": nofloatscan_flag,
+        "in1_flag": in1_flag,
+        "skip_outliers_flag": skip_outliers_flag,
+        "text_outliers_flag": text_outliers_flag,
+        "assume_dicom_mosaic_flag": assume_dicom_mosaic_flag,
+        "oblique_origin_flag": oblique_origin_flag,
+        "reverse_list_flag": reverse_list_flag,
+        "use_last_elem_flag": use_last_elem_flag,
+        "use_old_mosaic_code_flag": use_old_mosaic_code_flag,
+        "ushort2float_flag": ushort2float_flag,
+        "verbose_flag": verbose_flag,
+        "xtwarns_flag": xtwarns_flag,
+        "quit_on_err_flag": quit_on_err_flag,
+    }
+    if type_ is not None:
+        params["type"] = type_
+    if statpar is not None:
+        params["statpar"] = statpar
+    if prefix is not None:
+        params["prefix"] = prefix
+    if session is not None:
+        params["session"] = session
+    if geomparent is not None:
+        params["geomparent"] = geomparent
+    if anatparent is not None:
+        params["anatparent"] = anatparent
+    if view is not None:
+        params["view"] = view
+    if time_zt is not None:
+        params["time_zt"] = time_zt
+    if time_tz is not None:
+        params["time_tz"] = time_tz
+    if tr_units is not None:
+        params["tr_units"] = tr_units
+    if torg is not None:
+        params["torg"] = torg
+    if x_fov is not None:
+        params["xFOV"] = x_fov
+    if y_fov is not None:
+        params["yFOV"] = y_fov
+    if z_fov is not None:
+        params["zFOV"] = z_fov
+    if x_slab is not None:
+        params["xSLAB"] = x_slab
+    if y_slab is not None:
+        params["ySLAB"] = y_slab
+    if z_slab is not None:
+        params["zSLAB"] = z_slab
+    if zorigin is not None:
+        params["zorigin"] = zorigin
+    if data_type is not None:
+        params["data_type"] = data_type
+    if global_scaling_factor is not None:
+        params["global_scaling_factor"] = global_scaling_factor
+    if orient is not None:
+        params["orient"] = orient
+    if save_outliers is not None:
+        params["save_outliers"] = save_outliers
+    if gamma is not None:
+        params["gamma"] = gamma
+    if ncolors is not None:
+        params["ncolors"] = ncolors
+    return params
+
+
+def to3d_cargs(
+    params: To3dParameters,
+    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("to3d")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    if params.get("type") is not None:
+        cargs.extend([
+            "-type",
+            params.get("type")
+        ])
+    if params.get("statpar") is not None:
+        cargs.extend([
+            "-statpar",
+            *map(str, params.get("statpar"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("session") is not None:
+        cargs.extend([
+            "-session",
+            params.get("session")
+        ])
+    if params.get("geomparent") is not None:
+        cargs.extend([
+            "-geomparent",
+            execution.input_file(params.get("geomparent"))
+        ])
+    if params.get("anatparent") is not None:
+        cargs.extend([
+            "-anatparent",
+            execution.input_file(params.get("anatparent"))
+        ])
+    if params.get("nosave_flag"):
+        cargs.append("-nosave")
+    if params.get("nowritebrik_flag"):
+        cargs.append("-nowritebrik")
+    if params.get("view") is not None:
+        cargs.extend([
+            "-view",
+            params.get("view")
+        ])
+    if params.get("time_zt") is not None:
+        cargs.extend([
+            "-time:zt",
+            *params.get("time_zt")
+        ])
+    if params.get("time_tz") is not None:
+        cargs.extend([
+            "-time:tz",
+            *params.get("time_tz")
+        ])
+    if params.get("tr_units") is not None:
+        cargs.extend([
+            "-t",
+            params.get("tr_units")
+        ])
+    if params.get("torg") is not None:
+        cargs.extend([
+            "-Torg",
+            str(params.get("torg"))
+        ])
+    if params.get("xFOV") is not None:
+        cargs.extend([
+            "-xFOV",
+            params.get("xFOV")
+        ])
+    if params.get("yFOV") is not None:
+        cargs.extend([
+            "-yFOV",
+            params.get("yFOV")
+        ])
+    if params.get("zFOV") is not None:
+        cargs.extend([
+            "-zFOV",
+            params.get("zFOV")
+        ])
+    if params.get("xSLAB") is not None:
+        cargs.extend([
+            "-xSLAB",
+            params.get("xSLAB")
+        ])
+    if params.get("ySLAB") is not None:
+        cargs.extend([
+            "-ySLAB",
+            params.get("ySLAB")
+        ])
+    if params.get("zSLAB") is not None:
+        cargs.extend([
+            "-zSLAB",
+            params.get("zSLAB")
+        ])
+    if params.get("zorigin") is not None:
+        cargs.extend([
+            "-zorigin",
+            str(params.get("zorigin"))
+        ])
+    if params.get("data_type") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("data_type")
+        ])
+    if params.get("global_scaling_factor") is not None:
+        cargs.extend([
+            "-gsfac",
+            str(params.get("global_scaling_factor"))
+        ])
+    if params.get("nofloatscan_flag"):
+        cargs.append("-nofloatscan")
+    if params.get("in1_flag"):
+        cargs.append("-in:1")
+    if params.get("orient") is not None:
+        cargs.extend([
+            "-orient",
+            params.get("orient")
+        ])
+    if params.get("skip_outliers_flag"):
+        cargs.append("-skip_outliers")
+    if params.get("text_outliers_flag"):
+        cargs.append("-text_outliers")
+    if params.get("save_outliers") is not None:
+        cargs.extend([
+            "-save_outliers",
+            params.get("save_outliers")
+        ])
+    if params.get("assume_dicom_mosaic_flag"):
+        cargs.append("-assume_dicom_mosaic")
+    if params.get("oblique_origin_flag"):
+        cargs.append("-oblique_origin")
+    if params.get("reverse_list_flag"):
+        cargs.append("-reverse_list")
+    if params.get("use_last_elem_flag"):
+        cargs.append("-use_last_elem")
+    if params.get("use_old_mosaic_code_flag"):
+        cargs.append("-use_old_mosaic_code")
+    if params.get("ushort2float_flag"):
+        cargs.append("-ushort2float")
+    if params.get("verbose_flag"):
+        cargs.append("-verb")
+    if params.get("gamma") is not None:
+        cargs.extend([
+            "-gamma",
+            str(params.get("gamma"))
+        ])
+    if params.get("ncolors") is not None:
+        cargs.extend([
+            "-ncolors",
+            str(params.get("ncolors"))
+        ])
+    if params.get("xtwarns_flag"):
+        cargs.append("-xtwarns")
+    if params.get("quit_on_err_flag"):
+        cargs.append("-quit_on_err")
+    return cargs
+
+
+def to3d_outputs(
+    params: To3dParameters,
+    execution: Execution,
+) -> To3dOutputs:
+    """
+    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 = To3dOutputs(
+        root=execution.output_file("."),
+        headfile=execution.output_file(params.get("prefix") + ".HEAD") if (params.get("prefix") is not None) else None,
+        brikfile=execution.output_file(params.get("prefix") + ".BRIK") if (params.get("prefix") is not None) else None,
+        outfile_outliers=execution.output_file(params.get("save_outliers")) if (params.get("save_outliers") is not None) else None,
+    )
+    return ret
+
+
+def to3d_execute(
+    params: To3dParameters,
+    execution: Execution,
+) -> To3dOutputs:
+    """
+    Creates 3D datasets for use with AFNI from 2D image files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `To3dOutputs`).
+    """
+    params = execution.params(params)
+    cargs = to3d_cargs(params, execution)
+    ret = to3d_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def to3d(
+    input_files: list[InputPathType],
+    type_: typing.Literal["spgr", "fse", "epan", "anat", "ct", "spct", "pet", "mra", "bmap", "diff", "omri", "abuc", "fim", "fith", "fico", "fitt", "fift", "fizt", "fict", "fibt", "fibn", "figt", "fipt", "fbuc"] | None = None,
+    statpar: list[float] | None = None,
+    prefix: str | None = None,
+    session: str | None = None,
+    geomparent: InputPathType | None = None,
+    anatparent: InputPathType | None = None,
+    nosave_flag: bool = False,
+    nowritebrik_flag: bool = False,
+    view: typing.Literal["orig", "acpc", "tlrc"] | None = None,
+    time_zt: list[str] | None = None,
+    time_tz: list[str] | None = None,
+    tr_units: typing.Literal["ms", "msec", "s", "sec", "Hz", "Hertz"] | None = None,
+    torg: float | None = None,
+    x_fov: str | None = None,
+    y_fov: str | None = None,
+    z_fov: str | None = None,
+    x_slab: str | None = None,
+    y_slab: str | None = None,
+    z_slab: str | None = None,
+    zorigin: float | None = None,
+    data_type: typing.Literal["short", "float", "byte", "complex"] | None = None,
+    global_scaling_factor: float | None = None,
+    nofloatscan_flag: bool = False,
+    in1_flag: bool = False,
+    orient: str | None = None,
+    skip_outliers_flag: bool = False,
+    text_outliers_flag: bool = False,
+    save_outliers: str | None = None,
+    assume_dicom_mosaic_flag: bool = False,
+    oblique_origin_flag: bool = False,
+    reverse_list_flag: bool = False,
+    use_last_elem_flag: bool = False,
+    use_old_mosaic_code_flag: bool = False,
+    ushort2float_flag: bool = False,
+    verbose_flag: bool = False,
+    gamma: float | None = None,
+    ncolors: float | None = None,
+    xtwarns_flag: bool = False,
+    quit_on_err_flag: bool = False,
+    runner: Runner | None = None,
+) -> To3dOutputs:
+    """
+    Creates 3D datasets for use with AFNI from 2D image files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input 2D image files.
+        type_: Declare images to contain data of a given type.
+        statpar: Supply auxiliary statistical parameters.
+        prefix: Prefix of the output 3D dataset.
+        session: Session directory for output 3D dataset.
+        geomparent: Read geometry data from dataset file.
+        anatparent: Take anatomy parent from dataset file.
+        nosave_flag: Suppress autosave of 3D dataset.
+        nowritebrik_flag: Suppress saving of the BRIK file.
+        view: Set the dataset's viewing coordinates.
+        time_zt: Specify time dependent dataset (z-axis first, then t-axis).
+        time_tz: Specify time dependent dataset (t-axis first, then z-axis).
+        tr_units: Specify TR units.
+        torg: Set time origin of dataset.
+        x_fov: Specify size and orientation of the x-axis extent.
+        y_fov: Specify size and orientation of the y-axis extent.
+        z_fov: Specify size and orientation of the z-axis extent.
+        x_slab: Specify x-axis slab.
+        y_slab: Specify y-axis slab.
+        z_slab: Specify z-axis slab.
+        zorigin: Set the center of the first slice offset in z-axis.
+        data_type: Set voxel data to be stored as given data type.
+        global_scaling_factor: Global scaling factor.
+        nofloatscan_flag: Do not scan for illegal floating point values.
+        in1_flag: Read and process images one slice at a time.
+        orient: Set the orientation of the 3D volumes.
+        skip_outliers_flag: Skip the outlier check for 3D+time datasets.
+        text_outliers_flag: Only print out the outlier check results in text\
+            form.
+        save_outliers: Save the outliers count into a 1D file.
+        assume_dicom_mosaic_flag: Assume any Siemens DICOM file is a potential\
+            MOSAIC image.
+        oblique_origin_flag: Assume origin and orientation from oblique\
+            transformation matrix.
+        reverse_list_flag: Reverse the input file list.
+        use_last_elem_flag: Search DICOM images for the last occurrence of each\
+            element.
+        use_old_mosaic_code_flag: Do not use the Dec 2010 updates to Siemens\
+            mosaic code.
+        ushort2float_flag: Convert input shorts to float and add 2^16 to any\
+            negatives.
+        verbose_flag: Show debugging information for reading DICOM files.
+        gamma: Gamma correction factor for the monitor.
+        ncolors: Number of gray levels for the image displays.
+        xtwarns_flag: Turn on display of Xt warning messages.
+        quit_on_err_flag: Do not launch interactive to3d mode if input has\
+            error.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `To3dOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TO3D_METADATA)
+    params = to3d_params(
+        input_files=input_files,
+        type_=type_,
+        statpar=statpar,
+        prefix=prefix,
+        session=session,
+        geomparent=geomparent,
+        anatparent=anatparent,
+        nosave_flag=nosave_flag,
+        nowritebrik_flag=nowritebrik_flag,
+        view=view,
+        time_zt=time_zt,
+        time_tz=time_tz,
+        tr_units=tr_units,
+        torg=torg,
+        x_fov=x_fov,
+        y_fov=y_fov,
+        z_fov=z_fov,
+        x_slab=x_slab,
+        y_slab=y_slab,
+        z_slab=z_slab,
+        zorigin=zorigin,
+        data_type=data_type,
+        global_scaling_factor=global_scaling_factor,
+        nofloatscan_flag=nofloatscan_flag,
+        in1_flag=in1_flag,
+        orient=orient,
+        skip_outliers_flag=skip_outliers_flag,
+        text_outliers_flag=text_outliers_flag,
+        save_outliers=save_outliers,
+        assume_dicom_mosaic_flag=assume_dicom_mosaic_flag,
+        oblique_origin_flag=oblique_origin_flag,
+        reverse_list_flag=reverse_list_flag,
+        use_last_elem_flag=use_last_elem_flag,
+        use_old_mosaic_code_flag=use_old_mosaic_code_flag,
+        ushort2float_flag=ushort2float_flag,
+        verbose_flag=verbose_flag,
+        gamma=gamma,
+        ncolors=ncolors,
+        xtwarns_flag=xtwarns_flag,
+        quit_on_err_flag=quit_on_err_flag,
+    )
+    return to3d_execute(params, execution)
+
+
+__all__ = [
+    "TO3D_METADATA",
+    "To3dOutputs",
+    "To3dParameters",
+    "to3d",
+    "to3d_params",
+]