niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_2d_im_reg.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_2D_IM_REG_METADATA = Metadata(
+    id="d655dfc4a50826c5464b081b8ed2c58c03db91d0.boutiques",
+    name="2dImReg",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V2dImRegParameters = typing.TypedDict('V2dImRegParameters', {
+    "__STYX_TYPE__": typing.Literal["2dImReg"],
+    "input_file": InputPathType,
+    "base_file": typing.NotRequired[InputPathType | None],
+    "base": typing.NotRequired[float | None],
+    "nofine": bool,
+    "fine_blur": typing.NotRequired[float | None],
+    "fine_dxy": typing.NotRequired[float | None],
+    "fine_dphi": typing.NotRequired[float | None],
+    "prefix": str,
+    "dprefix": typing.NotRequired[str | None],
+    "dmm": bool,
+    "rprefix": typing.NotRequired[str | None],
+    "debug": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "2dImReg": v_2d_im_reg_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 {
+        "2dImReg": v_2d_im_reg_outputs,
+    }.get(t)
+
+
+class V2dImRegOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_2d_im_reg(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType
+    """Output 3d+time dataset"""
+    dx_file: OutputPathType | None
+    """File containing dx registration parameters in pixels/mm"""
+    dy_file: OutputPathType | None
+    """File containing dy registration parameters in pixels/mm"""
+    psi_file: OutputPathType | None
+    """File containing psi registration parameters in degrees"""
+    oldrms_file: OutputPathType | None
+    """File containing the volume RMS error for the original dataset"""
+    newrms_file: OutputPathType | None
+    """File containing the volume RMS error for the registered dataset"""
+
+
+def v_2d_im_reg_params(
+    input_file: InputPathType,
+    prefix: str,
+    base_file: InputPathType | None = None,
+    base: float | None = None,
+    nofine: bool = False,
+    fine_blur: float | None = None,
+    fine_dxy: float | None = None,
+    fine_dphi: float | None = None,
+    dprefix: str | None = None,
+    dmm: bool = False,
+    rprefix: str | None = None,
+    debug: bool = False,
+) -> V2dImRegParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Filename of input 3d+time dataset to process.
+        prefix: Prefix name for output 3d+time dataset.
+        base_file: Filename of 3d+time dataset for base image (default =\
+            current input dataset).
+        base: Time index for base image (0 <= num) (default: num = 3).
+        nofine: Deactivate fine fit phase of image registration (default: fine\
+            fit is active).
+        fine_blur: FWHM of blurring prior to registration (in pixels) (default:\
+            blur = 1.0).
+        fine_dxy: Convergence tolerance for translations (in pixels) (default:\
+            dxy = 0.07).
+        fine_dphi: Convergence tolerance for rotations (in degrees) (default:\
+            dphi = 0.21).
+        dprefix: Write files containing the registration parameters for each\
+            slice in chronological order.
+        dmm: Change dx and dy output format from pixels to mm.
+        rprefix: Write files containing the volume RMS error for the original\
+            and the registered datasets.
+        debug: Lots of additional output to screen.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "2dImReg",
+        "input_file": input_file,
+        "nofine": nofine,
+        "prefix": prefix,
+        "dmm": dmm,
+        "debug": debug,
+    }
+    if base_file is not None:
+        params["base_file"] = base_file
+    if base is not None:
+        params["base"] = base
+    if fine_blur is not None:
+        params["fine_blur"] = fine_blur
+    if fine_dxy is not None:
+        params["fine_dxy"] = fine_dxy
+    if fine_dphi is not None:
+        params["fine_dphi"] = fine_dphi
+    if dprefix is not None:
+        params["dprefix"] = dprefix
+    if rprefix is not None:
+        params["rprefix"] = rprefix
+    return params
+
+
+def v_2d_im_reg_cargs(
+    params: V2dImRegParameters,
+    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("2dImReg")
+    cargs.append(execution.input_file(params.get("input_file")))
+    if params.get("base_file") is not None:
+        cargs.append(execution.input_file(params.get("base_file")))
+    if params.get("base") is not None:
+        cargs.append(str(params.get("base")))
+    if params.get("nofine"):
+        cargs.append("-nofine")
+    if params.get("fine_blur") is not None:
+        cargs.append(str(params.get("fine_blur")))
+    if params.get("fine_dxy") is not None:
+        cargs.append(str(params.get("fine_dxy")))
+    if params.get("fine_dphi") is not None:
+        cargs.append(str(params.get("fine_dphi")))
+    cargs.append(params.get("prefix"))
+    if params.get("dprefix") is not None:
+        cargs.append(params.get("dprefix"))
+    if params.get("dmm"):
+        cargs.append("-dmm")
+    if params.get("rprefix") is not None:
+        cargs.append(params.get("rprefix"))
+    if params.get("debug"):
+        cargs.append("-debug")
+    return cargs
+
+
+def v_2d_im_reg_outputs(
+    params: V2dImRegParameters,
+    execution: Execution,
+) -> V2dImRegOutputs:
+    """
+    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 = V2dImRegOutputs(
+        root=execution.output_file("."),
+        output_dataset=execution.output_file(params.get("prefix") + ".nii"),
+        dx_file=execution.output_file(params.get("dprefix") + ".dx") if (params.get("dprefix") is not None) else None,
+        dy_file=execution.output_file(params.get("dprefix") + ".dy") if (params.get("dprefix") is not None) else None,
+        psi_file=execution.output_file(params.get("dprefix") + ".psi") if (params.get("dprefix") is not None) else None,
+        oldrms_file=execution.output_file(params.get("rprefix") + ".oldrms") if (params.get("rprefix") is not None) else None,
+        newrms_file=execution.output_file(params.get("rprefix") + ".newrms") if (params.get("rprefix") is not None) else None,
+    )
+    return ret
+
+
+def v_2d_im_reg_execute(
+    params: V2dImRegParameters,
+    execution: Execution,
+) -> V2dImRegOutputs:
+    """
+    2D image registration tool for 3D+time datasets, aligning images on a
+    slice-by-slice basis to a specified base image.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V2dImRegOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_2d_im_reg_cargs(params, execution)
+    ret = v_2d_im_reg_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_2d_im_reg(
+    input_file: InputPathType,
+    prefix: str,
+    base_file: InputPathType | None = None,
+    base: float | None = None,
+    nofine: bool = False,
+    fine_blur: float | None = None,
+    fine_dxy: float | None = None,
+    fine_dphi: float | None = None,
+    dprefix: str | None = None,
+    dmm: bool = False,
+    rprefix: str | None = None,
+    debug: bool = False,
+    runner: Runner | None = None,
+) -> V2dImRegOutputs:
+    """
+    2D image registration tool for 3D+time datasets, aligning images on a
+    slice-by-slice basis to a specified base image.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Filename of input 3d+time dataset to process.
+        prefix: Prefix name for output 3d+time dataset.
+        base_file: Filename of 3d+time dataset for base image (default =\
+            current input dataset).
+        base: Time index for base image (0 <= num) (default: num = 3).
+        nofine: Deactivate fine fit phase of image registration (default: fine\
+            fit is active).
+        fine_blur: FWHM of blurring prior to registration (in pixels) (default:\
+            blur = 1.0).
+        fine_dxy: Convergence tolerance for translations (in pixels) (default:\
+            dxy = 0.07).
+        fine_dphi: Convergence tolerance for rotations (in degrees) (default:\
+            dphi = 0.21).
+        dprefix: Write files containing the registration parameters for each\
+            slice in chronological order.
+        dmm: Change dx and dy output format from pixels to mm.
+        rprefix: Write files containing the volume RMS error for the original\
+            and the registered datasets.
+        debug: Lots of additional output to screen.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V2dImRegOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_2D_IM_REG_METADATA)
+    params = v_2d_im_reg_params(
+        input_file=input_file,
+        base_file=base_file,
+        base=base,
+        nofine=nofine,
+        fine_blur=fine_blur,
+        fine_dxy=fine_dxy,
+        fine_dphi=fine_dphi,
+        prefix=prefix,
+        dprefix=dprefix,
+        dmm=dmm,
+        rprefix=rprefix,
+        debug=debug,
+    )
+    return v_2d_im_reg_execute(params, execution)
+
+
+__all__ = [
+    "V2dImRegOutputs",
+    "V2dImRegParameters",
+    "V_2D_IM_REG_METADATA",
+    "v_2d_im_reg",
+    "v_2d_im_reg_params",
+]