nabu 2024.1.0rc4__py3-none-any.whl → 2024.1.1__py3-none-any.whl

build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/stitching/utils.py

@@ -0,0 +1,563 @@
+from distutils.version import StrictVersion
+from typing import Optional, Union
+import logging
+import functools
+import numpy
+from scipy.ndimage import affine_transform
+from tomoscan.scanbase import TomoScanBase
+from tomoscan.volumebase import VolumeBase
+from nxtomo.utils.transformation import build_matrix, UDDetTransformation
+from silx.utils.enum import Enum as _Enum
+from scipy.fft import rfftn as local_fftn
+from scipy.fft import irfftn as local_ifftn
+from silx.utils.enum import Enum as _Enum
+from nxtomo.utils.transformation import build_matrix, UDDetTransformation
+from tomoscan.scanbase import TomoScanBase
+from .overlap import OverlapStitchingStrategy, ZStichOverlapKernel
+from .alignment import AlignmentAxis1, AlignmentAxis2, PaddedRawData
+from ..misc import fourier_filters
+from ..estimation.alignment import AlignmentBase
+from ..resources.dataset_analyzer import HDF5DatasetAnalyzer
+from ..resources.nxflatfield import update_dataset_info_flats_darks
+
+try:
+    import itk
+except ImportError:
+    has_itk = False
+else:
+    has_itk = True
+
+_logger = logging.getLogger(__name__)
+
+
+try:
+    from skimage.registration import phase_cross_correlation
+except ImportError:
+    _logger.warning(
+        "Unable to load skimage. Please install it if you want to use it for finding shifts from `find_relative_shifts`"
+    )
+    __has_sk_phase_correlation__ = False
+else:
+    __has_sk_phase_correlation__ = True
+
+
+class ShiftAlgorithm(_Enum):
+    """All generic shift search algorithm"""
+
+    NABU_FFT = "nabu-fft"
+    SKIMAGE = "skimage"
+    ITK_IMG_REG_V4 = "itk-img-reg-v4"
+    NONE = "None"
+
+    # In the case of shift search on radio along axis 2 (or axis x in image space) we can benefit from the existing
+    # nabu algorithm such as growing-window or sliding-window
+    CENTERED = "centered"
+    GLOBAL = "global"
+    SLIDING_WINDOW = "sliding-window"
+    GROWING_WINDOW = "growing-window"
+    SINO_COARSE_TO_FINE = "sino-coarse-to-fine"
+    COMPOSITE_COARSE_TO_FINE = "composite-coarse-to-fine"
+
+    @classmethod
+    def from_value(cls, value):
+        if value in ("", None):
+            return ShiftAlgorithm.NONE
+        else:
+            return super().from_value(value=value)
+
+
+def test_overlap_stitching_strategy(overlap_1, overlap_2, stitching_strategies):
+    """
+    stitch the two ovrelap with all the requested strategies.
+    Return a dictionary with stitching strategy as key and a result dict as value.
+    result dict keys are: 'weights_overlap_1', 'weights_overlap_2', 'stiching'
+    """
+    res = {}
+    for strategy in stitching_strategies:
+        s = OverlapStitchingStrategy.from_value(strategy)
+        stitcher = ZStichOverlapKernel(
+            stitching_strategy=s,
+            frame_width=overlap_1.shape[1],
+        )
+        stiched_overlap, w1, w2 = stitcher.stitch(overlap_1, overlap_2, check_input=True)
+        res[s.value] = {
+            "stitching": stiched_overlap,
+            "weights_overlap_1": w1,
+            "weights_overlap_2": w2,
+        }
+    return res
+
+
+def find_frame_relative_shifts(
+    overlap_upper_frame: numpy.ndarray,
+    overlap_lower_frame: numpy.ndarray,
+    estimated_shifts,
+    x_cross_correlation_function=None,
+    y_cross_correlation_function=None,
+    x_shifts_params: Optional[dict] = None,
+    y_shifts_params: Optional[dict] = None,
+):
+    from nabu.stitching.config import (
+        KEY_WINDOW_SIZE,
+        KEY_LOW_PASS_FILTER,
+        KEY_HIGH_PASS_FILTER,
+    )  # avoid cyclic import
+
+    x_cross_correlation_function = ShiftAlgorithm.from_value(x_cross_correlation_function)
+    y_cross_correlation_function = ShiftAlgorithm.from_value(y_cross_correlation_function)
+
+    if x_shifts_params is None:
+        x_shifts_params = {}
+
+    if y_shifts_params is None:
+        y_shifts_params = {}
+
+    # apply filtering if any
+    def _str_to_int(value):
+        if isinstance(value, str):
+            value = value.lstrip("'").lstrip('"')
+            value = value.rstrip("'").rstrip('"')
+            value = int(value)
+        return value
+
+    low_pass = _str_to_int(x_shifts_params.get(KEY_LOW_PASS_FILTER, y_shifts_params.get(KEY_LOW_PASS_FILTER, None)))
+    high_pass = _str_to_int(x_shifts_params.get(KEY_HIGH_PASS_FILTER, y_shifts_params.get(KEY_HIGH_PASS_FILTER, None)))
+    if high_pass is None and low_pass is None:
+        pass
+    else:
+        if low_pass is None:
+            low_pass = 1
+        if high_pass is None:
+            high_pass = 20
+        _logger.info(f"filter image for shift search (low_pass={low_pass}, high_pass={high_pass})")
+        img_filter = fourier_filters.get_bandpass_filter(
+            overlap_upper_frame.shape[-2:],
+            cutoff_lowpass=low_pass,
+            cutoff_highpass=high_pass,
+            use_rfft=True,
+            data_type=overlap_upper_frame.dtype,
+        )
+        overlap_upper_frame = local_ifftn(
+            local_fftn(overlap_upper_frame, axes=(-2, -1)) * img_filter, axes=(-2, -1)
+        ).real
+        overlap_lower_frame = local_ifftn(
+            local_fftn(overlap_lower_frame, axes=(-2, -1)) * img_filter, axes=(-2, -1)
+        ).real
+
+    # compute shifts
+    initial_shifts = numpy.array(estimated_shifts).copy()
+    extra_shifts = numpy.array([0.0, 0.0])
+
+    def skimage_proxy(img1, img2):
+        if not __has_sk_phase_correlation__:
+            raise ValueError("scikit-image not installed. Cannot do phase correlation from it")
+        else:
+            found_shift, _, _ = phase_cross_correlation(reference_image=img1, moving_image=img2, space="real")
+            return -found_shift
+
+    shift_methods = {
+        ShiftAlgorithm.NABU_FFT: functools.partial(
+            find_shift_correlate, img1=overlap_upper_frame, img2=overlap_lower_frame
+        ),
+        ShiftAlgorithm.SKIMAGE: functools.partial(skimage_proxy, img1=overlap_upper_frame, img2=overlap_lower_frame),
+        ShiftAlgorithm.ITK_IMG_REG_V4: functools.partial(
+            find_shift_with_itk, img1=overlap_upper_frame, img2=overlap_lower_frame
+        ),
+        ShiftAlgorithm.NONE: functools.partial(lambda: (0.0, 0.0)),
+    }
+
+    res_algo = {}
+    for shift_alg in set((x_cross_correlation_function, y_cross_correlation_function)):
+        if shift_alg not in shift_methods:
+            raise ValueError(f"requested image alignment function not handled ({shift_alg})")
+        try:
+            res_algo[shift_alg] = shift_methods[shift_alg]()
+        except Exception as e:
+            _logger.error(f"Failed to find shift from {shift_alg.value}. Error is {e}")
+            res_algo[shift_alg] = (0, 0)
+
+    extra_shifts = (
+        res_algo[y_cross_correlation_function][0],
+        res_algo[x_cross_correlation_function][1],
+    )
+
+    final_rel_shifts = numpy.array(extra_shifts) + initial_shifts
+    return tuple([int(shift) for shift in final_rel_shifts])
+
+
+def find_volumes_relative_shifts(
+    upper_volume: VolumeBase,
+    lower_volume: VolumeBase,
+    estimated_shifts,
+    dim_axis_1: int,
+    dtype,
+    flip_ud_upper_frame: bool = False,
+    flip_ud_lower_frame: bool = False,
+    slice_for_shift: Union[int, str] = "middle",
+    x_cross_correlation_function=None,
+    y_cross_correlation_function=None,
+    x_shifts_params: Optional[dict] = None,
+    y_shifts_params: Optional[dict] = None,
+    alignment_axis_2="center",
+    alignment_axis_1="center",
+):
+    """
+
+    :param int dim_axis_1: axis 1 dimension (to handle axis 1 alignment)
+    """
+    if y_shifts_params is None:
+        y_shifts_params = {}
+
+    if x_shifts_params is None:
+        x_shifts_params = {}
+
+    alignment_axis_2 = AlignmentAxis2.from_value(alignment_axis_2)
+    alignment_axis_1 = AlignmentAxis1.from_value(alignment_axis_1)
+    assert dim_axis_1 > 0, "dim_axis_1 <= 0"
+
+    if isinstance(slice_for_shift, str):
+        if slice_for_shift == "first":
+            slice_for_shift = 0
+        elif slice_for_shift == "last":
+            slice_for_shift = dim_axis_1
+        elif slice_for_shift == "middle":
+            slice_for_shift = dim_axis_1 // 2
+        else:
+            raise ValueError("invalid slice provided to search shift", slice_for_shift)
+
+    def get_slice_along_axis_1(volume: VolumeBase, index: int):
+        assert isinstance(index, int), f"index should be an int, {type(index)} provided"
+        volume_shape = volume.get_volume_shape()
+        if alignment_axis_1 is AlignmentAxis1.BACK:
+            front_empty_width = dim_axis_1 - volume_shape[1]
+            if index < front_empty_width:
+                return PaddedRawData.get_empty_frame(shape=(volume_shape[0], volume_shape[2]), dtype=dtype)
+            else:
+                return volume.get_slice(index=index - front_empty_width, axis=1)
+        elif alignment_axis_1 is AlignmentAxis1.FRONT:
+            if index >= volume_shape[1]:
+                return PaddedRawData.get_empty_frame(shape=(volume_shape[0], volume_shape[2]), dtype=dtype)
+            else:
+                return volume.get_slice(index=index, axis=1)
+        elif alignment_axis_1 is AlignmentAxis1.CENTER:
+            front_empty_width = (dim_axis_1 - volume_shape[1]) // 2
+            back_empty_width = dim_axis_1 - front_empty_width
+            if index < front_empty_width or index > back_empty_width:
+                return PaddedRawData.get_empty_frame(shape=(volume_shape[0], volume_shape[2]), dtype=dtype)
+            else:
+                return volume.get_slice(index=index - front_empty_width, axis=1)
+        else:
+            raise TypeError(f"unmanaged alignment mode {alignment_axis_1.value}")
+
+    upper_frame = get_slice_along_axis_1(upper_volume, index=slice_for_shift)
+    lower_frame = get_slice_along_axis_1(lower_volume, index=slice_for_shift)
+    if flip_ud_upper_frame:
+        upper_frame = numpy.flipud(upper_frame.copy())
+    if flip_ud_lower_frame:
+        lower_frame = numpy.flipud(lower_frame.copy())
+
+    from nabu.stitching.config import KEY_WINDOW_SIZE  # avoid cyclic import
+
+    w_window_size = int(y_shifts_params.get(KEY_WINDOW_SIZE, 400))
+    start_overlap = max(estimated_shifts[0] // 2 - w_window_size // 2, 0)
+    end_overlap = min(estimated_shifts[0] // 2 + w_window_size // 2, min(upper_frame.shape[0], lower_frame.shape[0]))
+
+    if start_overlap == 0:
+        overlap_upper_frame = upper_frame[-end_overlap:]
+    else:
+        overlap_upper_frame = upper_frame[-end_overlap:-start_overlap]
+    overlap_lower_frame = lower_frame[start_overlap:end_overlap]
+
+    # align if necessary
+    if overlap_upper_frame.shape[1] != overlap_lower_frame.shape[1]:
+        overlap_frame_width = min(overlap_upper_frame.shape[1], overlap_lower_frame.shape[1])
+        if alignment_axis_2 is AlignmentAxis2.CENTER:
+            upper_frame_left_pos = overlap_upper_frame.shape[1] // 2 - overlap_frame_width // 2
+            upper_frame_right_pos = upper_frame_left_pos + overlap_frame_width
+            overlap_upper_frame = overlap_upper_frame[:, upper_frame_left_pos:upper_frame_right_pos]
+
+            lower_frame_left_pos = overlap_lower_frame.shape[1] // 2 - overlap_frame_width // 2
+            lower_frame_right_pos = lower_frame_left_pos + overlap_frame_width
+            overlap_lower_frame = overlap_lower_frame[:, lower_frame_left_pos:lower_frame_right_pos]
+        elif alignment_axis_2 is AlignmentAxis2.LEFT:
+            overlap_upper_frame = overlap_upper_frame[:, :overlap_frame_width]
+            overlap_lower_frame = overlap_lower_frame[:, :overlap_frame_width]
+        elif alignment_axis_2 is AlignmentAxis2.RIGTH:
+            overlap_upper_frame = overlap_upper_frame[:, -overlap_frame_width:]
+            overlap_lower_frame = overlap_lower_frame[:, -overlap_frame_width:]
+        else:
+            raise ValueError(f"Alignement {alignment_axis_2.value} is not handled")
+
+    if not overlap_upper_frame.shape == overlap_lower_frame.shape:
+        raise ValueError(f"Fail to get consistant overlap ({overlap_upper_frame.shape} vs {overlap_lower_frame.shape})")
+
+    return find_frame_relative_shifts(
+        overlap_upper_frame=overlap_upper_frame,
+        overlap_lower_frame=overlap_lower_frame,
+        estimated_shifts=estimated_shifts,
+        x_cross_correlation_function=x_cross_correlation_function,
+        y_cross_correlation_function=y_cross_correlation_function,
+        x_shifts_params=x_shifts_params,
+        y_shifts_params=y_shifts_params,
+    )
+
+
+from nabu.pipeline.estimators import estimate_cor
+
+
+def find_projections_relative_shifts(
+    upper_scan: TomoScanBase,
+    lower_scan: TomoScanBase,
+    estimated_shifts,
+    flip_ud_upper_frame: bool = False,
+    flip_ud_lower_frame: bool = False,
+    projection_for_shift: Union[int, str] = "middle",
+    invert_order: bool = False,
+    x_cross_correlation_function=None,
+    y_cross_correlation_function=None,
+    x_shifts_params: Optional[dict] = None,
+    y_shifts_params: Optional[dict] = None,
+) -> tuple:
+    """
+    deduce the relative shift between the two scans.
+    Expected behavior:
+    * compute expected overlap area from z_translations and (sample) pixel size
+    * call an (optional) cross correlation function from the overlap area to compute the x shift and polish the y shift from `projection_for_shift`
+
+    :param TomoScanBase scan_0:
+    :param TomoScanBase scan_1:
+    :param int axis_0_overlap_px: overlap between the two scans in pixel
+    :param Union[int,str] projection_for_shift: index fo the projection to use (in projection space or in scan space ?. For now in projection) or str. If str must be in (`middle`, `first`, `last`)
+    :param str x_cross_correlation_function: optional method to refine x shift from computing cross correlation. For now valid values are: ("skimage", "nabu-fft")
+    :param str y_cross_correlation_function: optional method to refine y shift from computing cross correlation. For now valid values are: ("skimage", "nabu-fft")
+    :param int minimal_overlap_area_for_cross_correlation: if first approximated overlap shift found from z_translation is lower than this value will fall back on taking the full image for the cross correlation and log a warning
+    :param bool invert_order: are projections inverted between the two scans (case if rotation angle are inverted)
+    :param tuple estimated_shifts: 'a priori' shift estimation
+    :return: relative shift of scan_1 with scan_0 as reference: (y_shift, x_shift)
+    :rtype: tuple
+
+    :warning: this function will flip left-right and up-down frames by default. So it will return shift according to this information
+    """
+    if x_shifts_params is None:
+        x_shifts_params = {}
+    if y_shifts_params is None:
+        y_shifts_params = {}
+    if estimated_shifts[0] < 0:
+        raise ValueError("y_overlap_px is expected to be stricktly positive")
+
+    x_cross_correlation_function = ShiftAlgorithm.from_value(x_cross_correlation_function)
+    y_cross_correlation_function = ShiftAlgorithm.from_value(y_cross_correlation_function)
+
+    # { handle specific use case (finding shift on scan) - when using nabu COR algorithms (for axis 2)
+    if x_cross_correlation_function in (
+        ShiftAlgorithm.SINO_COARSE_TO_FINE,
+        ShiftAlgorithm.COMPOSITE_COARSE_TO_FINE,
+        ShiftAlgorithm.CENTERED,
+        ShiftAlgorithm.GLOBAL,
+        ShiftAlgorithm.GROWING_WINDOW,
+        ShiftAlgorithm.SLIDING_WINDOW,
+    ):
+        cor_options = x_shifts_params.copy()
+        cor_options.pop("img_reg_method", None)
+        # remove all none numeric options because estimate_cor will call 'literal_eval' on them
+
+        upper_scan_dataset_info = HDF5DatasetAnalyzer(
+            location=upper_scan.master_file, extra_options={"hdf5_entry": upper_scan.entry}
+        )
+        update_dataset_info_flats_darks(upper_scan_dataset_info, flatfield_mode=1)
+
+        upper_scan_pos = estimate_cor(
+            method=x_cross_correlation_function.value,
+            dataset_info=upper_scan_dataset_info,
+            cor_options=cor_options,
+        )
+        lower_scan_dataset_info = HDF5DatasetAnalyzer(
+            location=lower_scan.master_file, extra_options={"hdf5_entry": lower_scan.entry}
+        )
+        update_dataset_info_flats_darks(lower_scan_dataset_info, flatfield_mode=1)
+        lower_scan_pos = estimate_cor(
+            method=x_cross_correlation_function.value,
+            dataset_info=lower_scan_dataset_info,
+            cor_options=cor_options,
+        )
+
+        estimated_shifts = tuple(
+            [
+                estimated_shifts[0],
+                (lower_scan_pos - upper_scan_pos),
+            ]
+        )
+        x_cross_correlation_function = ShiftAlgorithm.NONE
+
+    # } else we will compute shift from the flat projections
+
+    def get_flat_fielded_proj(
+        scan: TomoScanBase, proj_index: int, reverse: bool, transformation_matrix: Optional[numpy.ndarray]
+    ):
+        first_proj_idx = sorted(lower_scan.projections.keys(), reverse=reverse)[proj_index]
+        ff = scan.flat_field_correction(
+            (scan.projections[first_proj_idx],),
+            (first_proj_idx,),
+        )[0]
+        assert ff.ndim == 2, f"expects a single 2D frame. Get something with {ff.ndim} dimensions"
+        if transformation_matrix is not None:
+            assert (
+                transformation_matrix.ndim == 2
+            ), f"expects a 2D transformation matrix. Get a {transformation_matrix.ndim} D"
+            if numpy.isclose(transformation_matrix[2, 2], -1):
+                transformation_matrix[2, :] = 0
+                transformation_matrix[0, 2] = 0
+                transformation_matrix[2, 2] = 1
+                ff = numpy.flipud(ff)
+        return ff
+
+    if isinstance(projection_for_shift, str):
+        if projection_for_shift.lower() == "first":
+            projection_for_shift = 0
+        elif projection_for_shift.lower() == "last":
+            projection_for_shift = -1
+        elif projection_for_shift.lower() == "middle":
+            projection_for_shift = len(upper_scan.projections) // 2
+        else:
+            try:
+                projection_for_shift = int(projection_for_shift)
+            except ValueError:
+                raise ValueError(
+                    f"{projection_for_shift} cannot be cast to an int and is not one of the possible ('first', 'last', 'middle')"
+                )
+    elif not isinstance(projection_for_shift, (int, numpy.number)):
+        raise TypeError(
+            f"projection_for_shift is expected to be an int. Not {type(projection_for_shift)} - {projection_for_shift}"
+        )
+
+    upper_scan_transformations = list(upper_scan.get_detector_transformations(tuple()))
+    if flip_ud_upper_frame:
+        upper_scan_transformations.append(UDDetTransformation())
+    upper_scan_trans_matrix = build_matrix(upper_scan_transformations)
+    lower_scan_transformations = list(lower_scan.get_detector_transformations(tuple()))
+    if flip_ud_lower_frame:
+        lower_scan_transformations.append(UDDetTransformation())
+    lower_scan_trans_matrix = build_matrix(lower_scan_transformations)
+    upper_proj = get_flat_fielded_proj(
+        upper_scan,
+        projection_for_shift,
+        reverse=False,
+        transformation_matrix=upper_scan_trans_matrix,
+    )
+    lower_proj = get_flat_fielded_proj(
+        lower_scan,
+        projection_for_shift,
+        reverse=invert_order,
+        transformation_matrix=lower_scan_trans_matrix,
+    )
+
+    from nabu.stitching.config import KEY_WINDOW_SIZE  # avoid cyclic import
+
+    w_window_size = int(y_shifts_params.get(KEY_WINDOW_SIZE, 400))
+    start_overlap = max(estimated_shifts[0] // 2 - w_window_size // 2, 0)
+    end_overlap = min(estimated_shifts[0] // 2 + w_window_size // 2, min(upper_proj.shape[0], lower_proj.shape[0]))
+    if start_overlap == 0:
+        overlap_upper_frame = upper_proj[-end_overlap:]
+    else:
+        overlap_upper_frame = upper_proj[-end_overlap:-start_overlap]
+    overlap_lower_frame = lower_proj[start_overlap:end_overlap]
+    if not overlap_upper_frame.shape == overlap_lower_frame.shape:
+        raise ValueError(f"Fail to get consistant overlap ({overlap_upper_frame.shape} vs {overlap_lower_frame.shape})")
+
+    return find_frame_relative_shifts(
+        overlap_upper_frame=overlap_upper_frame,
+        overlap_lower_frame=overlap_lower_frame,
+        estimated_shifts=estimated_shifts,
+        x_cross_correlation_function=x_cross_correlation_function,
+        y_cross_correlation_function=y_cross_correlation_function,
+        x_shifts_params=x_shifts_params,
+        y_shifts_params=y_shifts_params,
+    )
+
+
+def find_shift_correlate(img1, img2, padding_mode="reflect"):
+    alignment = AlignmentBase()
+    cc = alignment._compute_correlation_fft(
+        img1,
+        img2,
+        padding_mode,
+    )
+
+    img_shape = img1.shape[-2:]
+    cc_vs = numpy.fft.fftfreq(img_shape[-2], 1 / img_shape[-2])
+    cc_hs = numpy.fft.fftfreq(img_shape[-1], 1 / img_shape[-1])
+
+    (f_vals, fv, fh) = alignment.extract_peak_region_2d(cc, cc_vs=cc_vs, cc_hs=cc_hs)
+    shifts_vh = alignment.refine_max_position_2d(f_vals, fv, fh)
+    return -shifts_vh
+
+
+def find_shift_with_itk(img1: numpy.ndarray, img2: numpy.ndarray) -> tuple:
+    # created from https://examples.itk.org/src/registration/common/perform2dtranslationregistrationwithmeansquares/documentation
+    # return (y_shift, x_shift). For now shift are integers as only integer shift are handled.
+    if not img1.dtype == img2.dtype:
+        raise ValueError("the two images are expected to have the same type")
+    if not img1.ndim == img2.ndim == 2:
+        raise ValueError("the two images are expected to 2D numpy arrays")
+
+    if not has_itk:
+        _logger.warning("itk is not installed. Please install it to find shift with it")
+        return (0, 0)
+
+    if StrictVersion(itk.Version.GetITKVersion()) < StrictVersion("4.9.0"):
+        _logger.error("ITK 4.9.0 is required to find shift with it.")
+        return (0, 0)
+
+    pixel_type = itk.ctype("float")
+    img1 = numpy.ascontiguousarray(img1, dtype=numpy.float32)
+    img2 = numpy.ascontiguousarray(img2, dtype=numpy.float32)
+
+    dimension = 2
+    image_type = itk.Image[pixel_type, dimension]
+
+    fixed_image = itk.PyBuffer[image_type].GetImageFromArray(img1)
+    moving_image = itk.PyBuffer[image_type].GetImageFromArray(img2)
+
+    transform_type = itk.TranslationTransform[itk.D, dimension]
+    initial_transform = transform_type.New()
+
+    optimizer = itk.RegularStepGradientDescentOptimizerv4.New(
+        LearningRate=4,
+        MinimumStepLength=0.001,
+        RelaxationFactor=0.5,
+        NumberOfIterations=200,
+    )
+
+    metric = itk.MeanSquaresImageToImageMetricv4[image_type, image_type].New()
+
+    registration = itk.ImageRegistrationMethodv4.New(
+        FixedImage=fixed_image,
+        MovingImage=moving_image,
+        Metric=metric,
+        Optimizer=optimizer,
+        InitialTransform=initial_transform,
+    )
+
+    moving_initial_transform = transform_type.New()
+    initial_parameters = moving_initial_transform.GetParameters()
+    initial_parameters[0] = 0
+    initial_parameters[1] = 0
+    moving_initial_transform.SetParameters(initial_parameters)
+    registration.SetMovingInitialTransform(moving_initial_transform)
+
+    identity_transform = transform_type.New()
+    identity_transform.SetIdentity()
+    registration.SetFixedInitialTransform(identity_transform)
+
+    registration.SetNumberOfLevels(1)
+    registration.SetSmoothingSigmasPerLevel([0])
+    registration.SetShrinkFactorsPerLevel([1])
+
+    registration.Update()
+
+    transform = registration.GetTransform()
+    final_parameters = transform.GetParameters()
+    translation_along_x = final_parameters.GetElement(0)
+    translation_along_y = final_parameters.GetElement(1)
+
+    return numpy.round(translation_along_y), numpy.round(translation_along_x)