nabu 2024.1.1__py3-none-any.whl → 2024.1.3__py3-none-any.whl

build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/build/lib/nabu/estimation/cor.py

@@ -1,1621 +0,0 @@
-import math
-import numpy as np
-from scipy.fftpack import rfft
-from numbers import Real
-from ..misc import fourier_filters
-from .alignment import AlignmentBase, plt, progress_bar, local_fftn, local_ifftn
-from ..resources.utils import extract_parameters
-
-# three possible  values for the validity check, which can optionally be returned by the find_shifts methods
-cor_result_validity = {
-    "unknown": "unknown",
-    "sound": "sound",
-    "correct": "sound",
-    "questionable": "questionable",
-}
-
-
-class CenterOfRotation(AlignmentBase):
-    def find_shift(
-        self,
-        img_1: np.ndarray,
-        img_2: np.ndarray,
-        shift_axis: int = -1,
-        roi_yxhw=None,
-        median_filt_shape=None,
-        padding_mode=None,
-        peak_fit_radius=1,
-        high_pass=None,
-        low_pass=None,
-        return_validity=False,
-        cor_options=None,
-    ):
-        """Find the Center of Rotation (CoR), given two images.
-
-        This method finds the half-shift between two opposite images, by
-        means of correlation computed in Fourier space.
-
-        The output of this function, allows to compute motor movements for
-        aligning the sample rotation axis. Given the following values:
-
-           - L1: distance from source to motor
-           - L2: distance from source to detector
-           - ps: physical pixel size
-           - v: output of this function
-
-        displacement of motor = (L1 / L2 * ps) * v
-
-        Parameters
-        ----------
-        img_1: numpy.ndarray
-            First image
-        img_2: numpy.ndarray
-            Second image, it needs to have been flipped already (e.g. using numpy.fliplr).
-        shift_axis: int
-            Axis along which we want the shift to be computed. Default is -1 (horizontal).
-        roi_yxhw: (2, ) or (4, ) numpy.ndarray, tuple, or array, optional
-            4 elements vector containing: vertical and horizontal coordinates
-            of first pixel, plus height and width of the Region of Interest (RoI).
-            Or a 2 elements vector containing: plus height and width of the
-            centered Region of Interest (RoI).
-            Default is None -> deactivated.
-        median_filt_shape: (2, ) numpy.ndarray, tuple, or array, optional
-            Shape of the median filter window. Default is None -> deactivated.
-        padding_mode: str in numpy.pad's mode list, optional
-            Padding mode, which determines the type of convolution. If None or
-            'wrap' are passed, this resorts to the traditional circular convolution.
-            If 'edge' or 'constant' are passed, it results in a linear convolution.
-            Default is the circular convolution.
-            All options are:
-                None | 'constant' | 'edge' | 'linear_ramp' | 'maximum' | 'mean'
-                | 'median' | 'minimum' | 'reflect' | 'symmetric' |'wrap'
-        peak_fit_radius: int, optional
-            Radius size around the max correlation pixel, for sub-pixel fitting.
-            Minimum and default value is 1.
-        low_pass: float or sequence of two floats
-            Low-pass filter properties, as described in `nabu.misc.fourier_filters`
-        high_pass: float or sequence of two floats
-            High-pass filter properties, as described in `nabu.misc.fourier_filters`
-        return_validity: a boolean, defaults to false
-            if set to True adds a second return value which may have three string values.
-            These values are "unknown", "sound", "questionable".
-            It will be "uknown" if the  validation method is not implemented
-            and it will be "sound" or "questionable" if it is implemented.
-
-
-        Raises
-        ------
-        ValueError
-            In case images are not 2-dimensional or have different sizes.
-
-        Returns
-        -------
-        float
-            Estimated center of rotation position from the center of the RoI in pixels.
-
-        Examples
-        --------
-        The following code computes the center of rotation position for two
-        given images in a tomography scan, where the second image is taken at
-        180 degrees from the first.
-
-        >>> radio1 = data[0, :, :]
-        ... radio2 = np.fliplr(data[1, :, :])
-        ... CoR_calc = CenterOfRotation()
-        ... cor_position = CoR_calc.find_shift(radio1, radio2)
-
-        Or for noisy images:
-
-        >>> cor_position = CoR_calc.find_shift(radio1, radio2, median_filt_shape=(3, 3))
-        """
-
-        self._check_img_pair_sizes(img_1, img_2)
-
-        if peak_fit_radius < 1:
-            self.logger.warning("Parameter peak_fit_radius should be at least 1, given: %d instead." % peak_fit_radius)
-            peak_fit_radius = 1
-
-        img_shape = img_2.shape
-        roi_yxhw = self._determine_roi(img_shape, roi_yxhw)
-
-        img_1 = self._prepare_image(img_1, roi_yxhw=roi_yxhw, median_filt_shape=median_filt_shape)
-        img_2 = self._prepare_image(img_2, roi_yxhw=roi_yxhw, median_filt_shape=median_filt_shape)
-
-        cc = self._compute_correlation_fft(img_1, img_2, padding_mode, high_pass=high_pass, low_pass=low_pass)
-        img_shape = img_2.shape
-        cc_vs = np.fft.fftfreq(img_shape[-2], 1 / img_shape[-2])
-        cc_hs = np.fft.fftfreq(img_shape[-1], 1 / img_shape[-1])
-
-        (f_vals, fv, fh) = self.extract_peak_region_2d(cc, peak_radius=peak_fit_radius, cc_vs=cc_vs, cc_hs=cc_hs)
-        fitted_shifts_vh = self.refine_max_position_2d(f_vals, fv, fh)
-
-        estimated_cor = fitted_shifts_vh[shift_axis] / 2.0
-
-        if isinstance(self.cor_options.get("near_pos", None), (int, float)):
-            near_pos = self.cor_options["near_pos"]
-            if (
-                np.abs(near_pos - estimated_cor) / near_pos > 0.2
-            ):  # For comparison, near_pos is RELATIVE (as estimated_cor is).
-                validity_check_result = cor_result_validity["questionable"]
-            else:
-                validity_check_result = cor_result_validity["sound"]
-        else:
-            validity_check_result = cor_result_validity["unknown"]
-
-        if return_validity:
-            return estimated_cor, validity_check_result
-        else:
-            return estimated_cor
-
-
-class CenterOfRotationSlidingWindow(CenterOfRotation):
-    def find_shift(
-        self,
-        img_1: np.ndarray,
-        img_2: np.ndarray,
-        side,
-        window_width=None,
-        roi_yxhw=None,
-        median_filt_shape=None,
-        padding_mode=None,
-        peak_fit_radius=1,
-        high_pass=None,
-        low_pass=None,
-        return_validity=False,
-        cor_options=None,
-    ):
-        """Semi-automatically find the Center of Rotation (CoR), given two images
-        or sinograms. Suitable for half-aquisition scan.
-
-        This method finds the half-shift between two opposite images,  by
-        minimizing difference over a moving window.
-
-        The output of this function, allows to compute motor movements for
-        aligning the sample rotation axis. Given the following values:
-
-        - L1: distance from source to motor
-        - L2: distance from source to detector
-        - ps: physical pixel size
-        - v: output of this function
-
-        displacement of motor = (L1 / L2 * ps) * v
-
-        Parameters
-        ----------
-        img_1: numpy.ndarray
-            First image
-        img_2: numpy.ndarray
-            Second image, it needs to have been flipped already (e.g. using numpy.fliplr).
-        side: string
-            Expected region of the CoR. Allowed values: 'left', 'center' or 'right'.
-        window_width: int, optional
-            Width of window that will slide on the other image / part of the
-            sinogram. Default is None.
-        roi_yxhw: (2, ) or (4, ) numpy.ndarray, tuple, or array, optional
-            4 elements vector containing: vertical and horizontal coordinates
-            of first pixel, plus height and width of the Region of Interest (RoI).
-            Or a 2 elements vector containing: plus height and width of the
-            centered Region of Interest (RoI).
-            Default is None -> deactivated.
-        median_filt_shape: (2, ) numpy.ndarray, tuple, or array, optional
-            Shape of the median filter window. Default is None -> deactivated.
-        padding_mode: str in numpy.pad's mode list, optional
-            Padding mode, which determines the type of convolution. If None or
-            'wrap' are passed, this resorts to the traditional circular convolution.
-            If 'edge' or 'constant' are passed, it results in a linear convolution.
-            Default is the circular convolution.
-            All options are:
-                None | 'constant' | 'edge' | 'linear_ramp' | 'maximum' | 'mean'
-                | 'median' | 'minimum' | 'reflect' | 'symmetric' |'wrap'
-        peak_fit_radius: int, optional
-            Radius size around the max correlation pixel, for sub-pixel fitting.
-            Minimum and default value is 1.
-        low_pass: float or sequence of two floats
-            Low-pass filter properties, as described in `nabu.misc.fourier_filters`
-        high_pass: float or sequence of two floats
-            High-pass filter properties, as described in `nabu.misc.fourier_filters`
-        return_validity: a boolean, defaults to false
-            if set to True adds a second return value which may have three string values.
-            These values are "unknown", "sound", "questionable".
-            It will be "uknown" if the  validation method is not implemented
-            and it will be "sound" or "questionable" if it is implemented.
-
-        Raises
-        ------
-        ValueError
-            In case images are not 2-dimensional or have different sizes.
-
-        Returns
-        -------
-        float
-            Estimated center of rotation position from the center of the RoI in pixels.
-
-        Examples
-        --------
-        The following code computes the center of rotation position for two
-        given images in a tomography scan, where the second image is taken at
-        180 degrees from the first.
-
-        >>> radio1 = data[0, :, :]
-        ... radio2 = np.fliplr(data[1, :, :])
-        ... CoR_calc = CenterOfRotationSlidingWindow()
-        ... cor_position = CoR_calc.find_shift(radio1, radio2)
-
-        Or for noisy images:
-
-        >>> cor_position = CoR_calc.find_shift(radio1, radio2, median_filt_shape=(3, 3))
-        """
-
-        validity_check_result = cor_result_validity["unknown"]
-
-        if side is None:
-            raise ValueError("Side should be one of 'left', 'right', or 'center'. 'None' was given instead")
-
-        self._check_img_pair_sizes(img_1, img_2)
-
-        if peak_fit_radius < 1:
-            self.logger.warning("Parameter peak_fit_radius should be at least 1, given: %d instead." % peak_fit_radius)
-            peak_fit_radius = 1
-
-        img_shape = img_2.shape
-        roi_yxhw = self._determine_roi(img_shape, roi_yxhw)
-
-        img_1 = self._prepare_image(
-            img_1, roi_yxhw=roi_yxhw, median_filt_shape=median_filt_shape, high_pass=high_pass, low_pass=low_pass
-        )
-        img_2 = self._prepare_image(
-            img_2, roi_yxhw=roi_yxhw, median_filt_shape=median_filt_shape, high_pass=high_pass, low_pass=low_pass
-        )
-        img_shape = img_2.shape
-
-        near_pos = self.cor_options.get("near_pos", None)
-        if near_pos is None:
-            if window_width is None:
-                if side.lower() == "center":
-                    window_width = round(img_shape[-1] / 4.0 * 3.0)
-                else:
-                    window_width = round(img_shape[-1] / 10)
-            window_shift = window_width // 2
-            window_width = window_shift * 2 + 1
-
-            win_1_start_seed = 0
-            # number of pixels where the window will "slide".
-            n = img_shape[-1] - window_width
-        else:
-            abs_pos = near_pos + img_shape[-1] // 2
-            offset = min(img_shape[-1] - abs_pos, abs_pos)  # distance to closest edge.
-
-            window_fraction = 0.4  # Hard-coded ?
-            window_shift = int(np.floor(offset * window_fraction))
-            window_width = 2 * window_shift + 1
-
-            sliding_shift = int(np.floor(offset * (1 - window_fraction))) - 1
-            n = 2 * sliding_shift + 1
-            win_1_start_seed = 2 * near_pos - sliding_shift
-
-        if side.lower() == "right":
-            win_2_start = 0
-        elif side.lower() == "left":
-            win_2_start = img_shape[-1] - window_width
-        elif side.lower() == "center":
-            win_2_start = img_shape[-1] // 2 - window_shift
-        else:
-            raise ValueError(
-                "Side should be one of 'left', 'right', or 'center'. '%s' was given instead" % side.lower()
-            )
-
-        win_2_end = win_2_start + window_width
-
-        diffs_mean = np.zeros((n,), dtype=img_1.dtype)
-        diffs_std = np.zeros((n,), dtype=img_1.dtype)
-
-        for ii in progress_bar(range(n), verbose=self.verbose):
-            win_1_start = win_1_start_seed + ii
-            win_1_end = win_1_start + window_width
-            img_diff = img_1[:, win_1_start:win_1_end] - img_2[:, win_2_start:win_2_end]
-            diffs_abs = np.abs(img_diff)
-            diffs_mean[ii] = diffs_abs.mean()
-            diffs_std[ii] = diffs_abs.std()
-
-        diffs_mean = diffs_mean.min() - diffs_mean
-        win_ind_max = np.argmax(diffs_mean)
-
-        diffs_std = diffs_std.min() - diffs_std
-        if not win_ind_max == np.argmax(diffs_std):
-            self.logger.warning(
-                "Minimum mean difference and minimum std-dev of differences do not coincide. "
-                + "This means that the validity of the found solution might be questionable."
-            )
-            validity_check_result = cor_result_validity["questionable"]
-        else:
-            validity_check_result = cor_result_validity["sound"]
-
-        (f_vals, f_pos) = self.extract_peak_regions_1d(diffs_mean, peak_radius=peak_fit_radius)
-        win_pos_max, win_val_max = self.refine_max_position_1d(f_vals, return_vertex_val=True)
-
-        # Derive the COR
-        if isinstance(near_pos, Real):
-            cor_h = -(win_2_start - (win_1_start_seed + win_ind_max + win_pos_max)) / 2.0
-            cor_pos = -(win_2_start - (win_1_start_seed + np.arange(n))) / 2.0
-        else:
-            cor_h = -(win_2_start - (win_ind_max + win_pos_max)) / 2.0
-            cor_pos = -(win_2_start - np.arange(n)) / 2.0
-
-        if (side.lower() == "right" and win_ind_max == 0) or (side.lower() == "left" and win_ind_max == n):
-            self.logger.warning("Sliding window width %d might be too large!" % window_width)
-
-        if self.verbose:
-            print("Lowest difference window: index=%d, range=[0, %d]" % (win_ind_max, n))
-            print("CoR tested for='%s', found at voxel=%g (from center)" % (side, cor_h))
-
-            f, ax = plt.subplots(1, 1)
-            self._add_plot_window(f, ax=ax)
-            ax.stem(cor_pos, diffs_mean, label="Mean difference")
-            ax.stem(cor_h, win_val_max, linefmt="C1-", markerfmt="C1o", label="Best mean difference")
-            ax.stem(cor_pos, -diffs_std, linefmt="C2-", markerfmt="C2o", label="Std-dev difference")
-            ax.set_title("Window dispersions")
-            plt.legend()
-            plt.show(block=False)
-
-        if return_validity:
-            return cor_h, validity_check_result
-        else:
-            return cor_h
-
-
-class CenterOfRotationGrowingWindow(CenterOfRotation):
-    def find_shift(
-        self,
-        img_1: np.ndarray,
-        img_2: np.ndarray,
-        side="all",
-        min_window_width=11,
-        roi_yxhw=None,
-        median_filt_shape=None,
-        padding_mode=None,
-        peak_fit_radius=1,
-        high_pass=None,
-        low_pass=None,
-        return_validity=False,
-    ):
-        """Automatically find the Center of Rotation (CoR), given two images or
-        sinograms. Suitable for half-aquisition scan.
-
-        This method finds the half-shift between two opposite images,  by
-        minimizing difference over a moving window.
-
-        The output of this function, allows to compute motor movements for
-        aligning the sample rotation axis. Given the following values:
-
-        - L1: distance from source to motor
-        - L2: distance from source to detector
-        - ps: physical pixel size
-        - v: output of this function
-
-        displacement of motor = (L1 / L2 * ps) * v
-
-        Parameters
-        ----------
-        img_1: numpy.ndarray
-            First image
-        img_2: numpy.ndarray
-            Second image, it needs to have been flipped already (e.g. using numpy.fliplr).
-        side: string, optional
-            Expected region of the CoR. Allowed values: 'left', 'center', 'right', or 'all'.
-            Default is 'all'.
-        min_window_width: int, optional
-            Minimum window width that covers the common region of the two images /
-            sinograms. Default is 11.
-        roi_yxhw: (2, ) or (4, ) numpy.ndarray, tuple, or array, optional
-            4 elements vector containing: vertical and horizontal coordinates
-            of first pixel, plus height and width of the Region of Interest (RoI).
-            Or a 2 elements vector containing: plus height and width of the
-            centered Region of Interest (RoI).
-            Default is None -> deactivated.
-        median_filt_shape: (2, ) numpy.ndarray, tuple, or array, optional
-            Shape of the median filter window. Default is None -> deactivated.
-        padding_mode: str in numpy.pad's mode list, optional
-            Padding mode, which determines the type of convolution. If None or
-            'wrap' are passed, this resorts to the traditional circular convolution.
-            If 'edge' or 'constant' are passed, it results in a linear convolution.
-            Default is the circular convolution.
-            All options are:
-                None | 'constant' | 'edge' | 'linear_ramp' | 'maximum' | 'mean'
-                | 'median' | 'minimum' | 'reflect' | 'symmetric' |'wrap'
-        peak_fit_radius: int, optional
-            Radius size around the max correlation pixel, for sub-pixel fitting.
-            Minimum and default value is 1.
-        low_pass: float or sequence of two floats
-            Low-pass filter properties, as described in `nabu.misc.fourier_filters`
-        high_pass: float or sequence of two floats
-            High-pass filter properties, as described in `nabu.misc.fourier_filters`
-        return_validity: a boolean, defaults to false
-            if set to True adds a second return value which may have three string values.
-            These values are "unknown", "sound", "questionable".
-            It will be "uknown" if the  validation method is not implemented
-            and it will be "sound" or "questionable" if it is implemented.
-
-
-
-        Raises
-        ------
-        ValueError
-            In case images are not 2-dimensional or have different sizes.
-
-        Returns
-        -------
-        float
-            Estimated center of rotation position from the center of the RoI in pixels.
-
-        Examples
-        --------
-        The following code computes the center of rotation position for two
-        given images in a tomography scan, where the second image is taken at
-        180 degrees from the first.
-
-        >>> radio1 = data[0, :, :]
-        ... radio2 = np.fliplr(data[1, :, :])
-        ... CoR_calc = CenterOfRotationGrowingWindow()
-        ... cor_position = CoR_calc.find_shift(radio1, radio2)
-
-        Or for noisy images:
-
-        >>> cor_position = CoR_calc.find_shift(radio1, radio2, median_filt_shape=(3, 3))
-        """
-
-        validity_check_result = cor_result_validity["unknown"]
-
-        self._check_img_pair_sizes(img_1, img_2)
-
-        if peak_fit_radius < 1:
-            self.logger.warning("Parameter peak_fit_radius should be at least 1, given: %d instead." % peak_fit_radius)
-            peak_fit_radius = 1
-
-        img_shape = img_2.shape
-        roi_yxhw = self._determine_roi(img_shape, roi_yxhw)
-
-        img_1 = self._prepare_image(
-            img_1, roi_yxhw=roi_yxhw, median_filt_shape=median_filt_shape, high_pass=high_pass, low_pass=low_pass
-        )
-        img_2 = self._prepare_image(
-            img_2, roi_yxhw=roi_yxhw, median_filt_shape=median_filt_shape, high_pass=high_pass, low_pass=low_pass
-        )
-        img_shape = img_2.shape
-
-        def window_bounds(mid_point, window_max_width=img_shape[-1]):
-            return (
-                np.fmax(np.ceil(mid_point - window_max_width / 2), 0).astype(np.intp),
-                np.fmin(np.ceil(mid_point + window_max_width / 2), img_shape[-1]).astype(np.intp),
-            )
-
-        img_lower_half_size = np.floor(img_shape[-1] / 2).astype(np.intp)
-        img_upper_half_size = np.ceil(img_shape[-1] / 2).astype(np.intp)
-
-        use_estimate_from_motor = "near_pos" in self.cor_options.keys() and isinstance(
-            self.cor_options["near_pos"], (int, float)
-        )
-        use_estimate_from_motor = False  # Not yet implemented.
-        if use_estimate_from_motor:
-            near_pos = self.cor_options["near_pos"]
-
-        else:
-            if side.lower() == "right":
-                win_1_mid_start = img_lower_half_size
-                win_1_mid_end = np.floor(img_shape[-1] * 3 / 2).astype(np.intp) - min_window_width
-                win_2_mid_start = -img_upper_half_size + min_window_width
-                win_2_mid_end = img_upper_half_size
-            elif side.lower() == "left":
-                win_1_mid_start = -img_lower_half_size + min_window_width
-                win_1_mid_end = img_lower_half_size
-                win_2_mid_start = img_upper_half_size
-                win_2_mid_end = np.ceil(img_shape[-1] * 3 / 2).astype(np.intp) - min_window_width
-            elif side.lower() == "center":
-                win_1_mid_start = 0
-                win_1_mid_end = img_shape[-1]
-                win_2_mid_start = 0
-                win_2_mid_end = img_shape[-1]
-            elif side.lower() == "all":
-                win_1_mid_start = -img_lower_half_size + min_window_width
-                win_1_mid_end = np.floor(img_shape[-1] * 3 / 2).astype(np.intp) - min_window_width
-                win_2_mid_start = -img_upper_half_size + min_window_width
-                win_2_mid_end = np.ceil(img_shape[-1] * 3 / 2).astype(np.intp) - min_window_width
-            else:
-                raise ValueError(
-                    "Side should be one of 'left', 'right', or 'center'. '%s' was given instead" % side.lower()
-                )
-
-        n1 = win_1_mid_end - win_1_mid_start
-        n2 = win_2_mid_end - win_2_mid_start
-
-        if not n1 == n2:
-            raise ValueError(
-                "Internal error: the number of window steps for the two images should be the same."
-                + "Found the following configuration instead => Side: %s, #1: %d, #2: %d" % (side, n1, n2)
-            )
-
-        diffs_mean = np.zeros((n1,), dtype=img_1.dtype)
-        diffs_std = np.zeros((n1,), dtype=img_1.dtype)
-
-        for ii in progress_bar(range(n1), verbose=self.verbose):
-            win_1 = window_bounds(win_1_mid_start + ii)
-            win_2 = window_bounds(win_2_mid_end - ii)
-            img_diff = img_1[:, win_1[0] : win_1[1]] - img_2[:, win_2[0] : win_2[1]]
-            diffs_abs = np.abs(img_diff)
-            diffs_mean[ii] = diffs_abs.mean()
-            diffs_std[ii] = diffs_abs.std()
-
-        diffs_mean = diffs_mean.min() - diffs_mean
-        win_ind_max = np.argmax(diffs_mean)
-
-        diffs_std = diffs_std.min() - diffs_std
-        if not win_ind_max == np.argmax(diffs_std):
-            self.logger.warning(
-                "Minimum mean difference and minimum std-dev of differences do not coincide. "
-                + "This means that the validity of the found solution might be questionable."
-            )
-            validity_check_result = cor_result_validity["questionable"]
-        else:
-            validity_check_result = cor_result_validity["sound"]
-
-        (f_vals, f_pos) = self.extract_peak_regions_1d(diffs_mean, peak_radius=peak_fit_radius)
-        win_pos_max, win_val_max = self.refine_max_position_1d(f_vals, return_vertex_val=True)
-
-        cor_h = (win_1_mid_start + (win_ind_max + win_pos_max) - img_upper_half_size) / 2.0
-
-        if (side.lower() == "right" and win_ind_max == 0) or (side.lower() == "left" and win_ind_max == n1):
-            self.logger.warning("Minimum growing window width %d might be too large!" % min_window_width)
-
-        if self.verbose:
-            cor_pos = (win_1_mid_start + np.arange(n1) - img_upper_half_size) / 2.0
-
-            self.logger.info("Lowest difference window: index=%d, range=[0, %d]" % (win_ind_max, n1))
-            self.logger.info("CoR tested for='%s', found at voxel=%g (from center)" % (side, cor_h))
-
-            f, ax = plt.subplots(1, 1)
-            self._add_plot_window(f, ax=ax)
-            ax.stem(cor_pos, diffs_mean, label="Mean difference")
-            ax.stem(cor_h, win_val_max, linefmt="C1-", markerfmt="C1o", label="Best mean difference")
-            ax.stem(cor_pos, -diffs_std, linefmt="C2-", markerfmt="C2o", label="Std-dev difference")
-            ax.set_title("Window dispersions")
-            plt.show(block=False)
-
-        if return_validity:
-            return cor_h, validity_check_result
-        else:
-            return cor_h
-
-
-class CenterOfRotationAdaptiveSearch(CenterOfRotation):
-    """This adaptive method works by applying a gaussian which highlights, by apodisation, a region
-    which can possibly contain the good center of rotation.
-    The whole image is spanned during several applications of the apodisation. At each application
-    the apodisation function, which is a gaussian, is moved to a new guess position.
-    The lenght of the step, by which the gaussian is moved, and its sigma are
-    obtained by multiplying the shortest distance from the left or right border with
-    a self.step_fraction and  self.sigma_fraction factors which ensure global overlapping.
-    for each step a region around the CoR  of each image is selected, and the regions of the two images
-    are compared to  calculate a cost function. The value of the cost function, at its minimum
-    is used to select the best step at which the CoR is taken as final result.
-    The option filtered_cost= True (default) triggers the filtering (according to low_pass and high_pass)
-    of the two images which are used for he cost function. ( Note: the low_pass and high_pass options
-    are used, if given, also without the filtered_cost option, by being passed to the base class
-    CenterOfRotation )
-    """
-
-    sigma_fraction = 1.0 / 4.0
-    step_fraction = 1.0 / 6.0
-
-    def find_shift(
-        self,
-        img_1: np.ndarray,
-        img_2: np.ndarray,
-        roi_yxhw=None,
-        median_filt_shape=None,
-        padding_mode=None,
-        high_pass=None,
-        low_pass=None,
-        margins=None,
-        filtered_cost=True,
-        return_validity=False,
-    ):
-        """Find the Center of Rotation (CoR), given two images.
-
-        This method finds the half-shift between two opposite images, by
-        means of correlation computed in Fourier space.
-        A global search is done on on the detector span (minus a margin) without assuming centered scan conditions.
-
-        The output of this function, allows to compute motor movements for
-        aligning the sample rotation axis. Given the following values:
-
-        - L1: distance from source to motor
-        - L2: distance from source to detector
-        - ps: physical pixel size
-        - v: output of this function
-
-        displacement of motor = (L1 / L2 * ps) * v
-
-        Parameters
-        ----------
-        img_1: numpy.ndarray
-            First image
-        img_2: numpy.ndarray
-            Second image, it needs to have been flipped already (e.g. using numpy.fliplr).
-        roi_yxhw: (2, ) or (4, ) numpy.ndarray, tuple, or array, optional
-            4 elements vector containing: vertical and horizontal coordinates
-            of first pixel, plus height and width of the Region of Interest (RoI).
-            Or a 2 elements vector containing: plus height and width of the
-            centered Region of Interest (RoI).
-            Default is None -> deactivated.
-        median_filt_shape: (2, ) numpy.ndarray, tuple, or array, optional
-            Shape of the median filter window. Default is None -> deactivated.
-        padding_mode: str in numpy.pad's mode list, optional
-            Padding mode, which determines the type of convolution. If None or
-            'wrap' are passed, this resorts to the traditional circular convolution.
-            If 'edge' or 'constant' are passed, it results in a linear convolution.
-            Default is the circular convolution.
-            All options are:
-                None | 'constant' | 'edge' | 'linear_ramp' | 'maximum' | 'mean'
-                | 'median' | 'minimum' | 'reflect' | 'symmetric' |'wrap'
-        low_pass: float or sequence of two floats.
-            Low-pass filter properties, as described in `nabu.misc.fourier_filters`
-        high_pass: float or sequence of two floats
-            High-pass filter properties, as described in `nabu.misc.fourier_filters`.
-        margins:  None or a couple of floats or ints
-            if margins is None or in the form of  (margin1,margin2) the search is done between margin1 and  dim_x-1-margin2.
-            If left to None then by default (margin1,margin2)  = ( 10, 10 ).
-        filtered_cost: boolean.
-            True by default. It triggers the use of filtered images in the calculation of the cost function.
-        return_validity: a boolean, defaults to false
-            if set to True adds a second return value which may have three string values.
-            These values are "unknown", "sound", "questionable".
-            It will be "uknown" if the  validation method is not implemented
-            and it will be "sound" or "questionable" if it is implemented.
-
-        Raises
-        ------
-        ValueError
-            In case images are not 2-dimensional or have different sizes.
-
-        Returns
-        -------
-        float
-            Estimated center of rotation position from the center of the RoI in pixels.
-
-        Examples
-        --------
-        The following code computes the center of rotation position for two
-        given images in a tomography scan, where the second image is taken at
-        180 degrees from the first.
-
-        >>> radio1 = data[0, :, :]
-        ... radio2 = np.fliplr(data[1, :, :])
-        ... CoR_calc = CenterOfRotationAdaptiveSearch()
-        ... cor_position = CoR_calc.find_shift(radio1, radio2)
-
-        Or for noisy images:
-
-        >>> cor_position = CoR_calc.find_shift(radio1, radio2, median_filt_shape=(3, 3), high_pass=20, low_pass=1   )
-        """
-
-        validity_check_result = cor_result_validity["unknown"]
-
-        self._check_img_pair_sizes(img_1, img_2)
-
-        used_type = img_1.dtype
-
-        roi_yxhw = self._determine_roi(img_1.shape, roi_yxhw)
-
-        if filtered_cost and (low_pass is not None or high_pass is not None):
-            img_filter = fourier_filters.get_bandpass_filter(
-                img_1.shape[-2:],
-                cutoff_lowpass=low_pass,
-                cutoff_highpass=high_pass,
-                use_rfft=True,
-                data_type=self.data_type,
-            )
-            # fft2 and iff2 use axes=(-2, -1) by default
-            img_filtered_1 = local_ifftn(local_fftn(img_1, axes=(-2, -1)) * img_filter, axes=(-2, -1)).real
-            img_filtered_2 = local_ifftn(local_fftn(img_2, axes=(-2, -1)) * img_filter, axes=(-2, -1)).real
-        else:
-            img_filtered_1 = img_1
-            img_filtered_2 = img_2
-
-        img_1 = self._prepare_image(img_1, roi_yxhw=roi_yxhw, median_filt_shape=median_filt_shape)
-        img_2 = self._prepare_image(img_2, roi_yxhw=roi_yxhw, median_filt_shape=median_filt_shape)
-
-        img_filtered_1 = self._prepare_image(img_filtered_1, roi_yxhw=roi_yxhw, median_filt_shape=median_filt_shape)
-        img_filtered_2 = self._prepare_image(img_filtered_2, roi_yxhw=roi_yxhw, median_filt_shape=median_filt_shape)
-
-        dim_radio = img_1.shape[1]
-
-        if margins is None:
-            lim_1, lim_2 = 10, dim_radio - 1 - 10
-        else:
-            lim_1, lim_2 = margins
-            lim_2 = dim_radio - 1 - lim_2
-
-        if lim_1 < 1:
-            lim_1 = 1
-        if lim_2 > dim_radio - 2:
-            lim_2 = dim_radio - 2
-
-        if lim_2 <= lim_1:
-            message = (
-                "Image shape or cropped selection too small for global search."
-                + " After removal of the margins the search limits collide."
-                + " The cropped size is %d\n" % (dim_radio)
-            )
-            raise ValueError(message)
-
-        found_centers = []
-        x_cor = lim_1
-        while x_cor < lim_2:
-            tmp_sigma = (
-                min(
-                    (img_1.shape[1] - x_cor),
-                    (x_cor),
-                )
-                * self.sigma_fraction
-            )
-
-            tmp_x = (np.arange(img_1.shape[1]) - x_cor) / tmp_sigma
-            apodis = np.exp(-tmp_x * tmp_x / 2.0)
-
-            x_cor_rel = x_cor - (img_1.shape[1] // 2)
-
-            img_1_apodised = img_1 * apodis
-
-            try:
-                cor_position = CenterOfRotation.find_shift(
-                    self,
-                    img_1_apodised.astype(used_type),
-                    img_2.astype(used_type),
-                    low_pass=low_pass,
-                    high_pass=high_pass,
-                    roi_yxhw=roi_yxhw,
-                )
-            except ValueError as err:
-                if "positions are outside the input margins" in str(err):
-                    x_cor = min(x_cor + x_cor * self.step_fraction, x_cor + (dim_radio - x_cor) * self.step_fraction)
-                    continue
-            except:
-                message = "Unexpected error from base class CenterOfRotation.find_shift in CenterOfRotationAdaptiveSearch.find_shift  : {err}".format(
-                    err=err
-                )
-                self.logger.error(message)
-                raise
-
-            p_1 = cor_position * 2
-            if cor_position < 0:
-                p_2 = img_2.shape[1] + cor_position * 2
-            else:
-                p_2 = -img_2.shape[1] + cor_position * 2
-
-            if abs(x_cor_rel - p_1 / 2) < abs(x_cor_rel - p_2 / 2):
-                cor_position = p_1 / 2
-            else:
-                cor_position = p_2 / 2
-
-            cor_in_img = img_1.shape[1] // 2 + cor_position
-            tmp_sigma = (
-                min(
-                    (img_1.shape[1] - cor_in_img),
-                    (cor_in_img),
-                )
-                * self.sigma_fraction
-            )
-
-            M1 = int(round(cor_position + img_1.shape[1] // 2)) - int(round(tmp_sigma))
-            M2 = int(round(cor_position + img_1.shape[1] // 2)) + int(round(tmp_sigma))
-
-            piece_1 = img_filtered_1[:, M1:M2]
-            piece_2 = img_filtered_2[:, img_1.shape[1] - M2 : img_1.shape[1] - M1]
-
-            if piece_1.size and piece_2.size:
-                piece_1 = piece_1 - piece_1.mean()
-                piece_2 = piece_2 - piece_2.mean()
-                energy = np.array(piece_1 * piece_1 + piece_2 * piece_2, "d").sum()
-                diff_energy = np.array((piece_1 - piece_2) * (piece_1 - piece_2), "d").sum()
-                cost = diff_energy / energy
-
-                if not np.isnan(cost):
-                    if tmp_sigma * 2 > abs(x_cor_rel - cor_position):
-                        found_centers.append([cost, abs(x_cor_rel - cor_position), cor_position, energy])
-
-            x_cor = min(x_cor + x_cor * self.step_fraction, x_cor + (dim_radio - x_cor) * self.step_fraction)
-
-        if len(found_centers) == 0:
-            message = "Unable to find any valid CoR candidate in {my_class}.find_shift ".format(
-                my_class=self.__class__.__name__
-            )
-            raise ValueError(message)
-
-        # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-        # Now build the neigborhood of the minimum as a list of five elements:
-        # the minimum in the middle of the two before, and the two after
-
-        filtered_found_centers = []
-        for i in range(len(found_centers)):
-            if i > 0:
-                if abs(found_centers[i][2] - found_centers[i - 1][2]) < 0.5:
-                    filtered_found_centers.append(found_centers[i])
-                    continue
-            if i + 1 < len(found_centers):
-                if abs(found_centers[i][2] - found_centers[i + 1][2]) < 0.5:
-                    filtered_found_centers.append(found_centers[i])
-                    continue
-
-        if len(filtered_found_centers):
-            found_centers = filtered_found_centers
-
-        min_choice = min(found_centers)
-        index_min_choice = found_centers.index(min_choice)
-        min_neighborood = [
-            found_centers[i][2] if (i >= 0 and i < len(found_centers)) else math.nan
-            for i in range(index_min_choice - 2, index_min_choice + 2 + 1)
-        ]
-
-        score_right = 0
-        for i_pos in [3, 4]:
-            if abs(min_neighborood[i_pos] - min_neighborood[2]) < 0.5:
-                score_right += 1
-            else:
-                break
-
-        score_left = 0
-        for i_pos in [1, 0]:
-            if abs(min_neighborood[i_pos] - min_neighborood[2]) < 0.5:
-                score_left += 1
-            else:
-                break
-
-        if score_left + score_right >= 2:
-            validity_check_result = cor_result_validity["sound"]
-        else:
-            self.logger.warning(
-                "Minimum mean difference and minimum std-dev of differences do not coincide. "
-                + "This means that the validity of the found solution might be questionable."
-            )
-            validity_check_result = cor_result_validity["questionable"]
-
-        # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-        # An informative message in case one wish to look at how it has gone
-        informative_message = " ".join(
-            ["CenterOfRotationAdaptiveSearch found this neighborood of the optimal position:"]
-            + [str(t) if not math.isnan(t) else "N.A." for t in min_neighborood]
-        )
-        self.logger.debug(informative_message)
-
-        # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-        # The return value is the optimum which had been placed in the middle of the neighborood
-        cor_position = min_neighborood[2]
-
-        if return_validity:
-            return cor_position, validity_check_result
-        else:
-            return cor_position
-
-    __call__ = find_shift
-
-
-class CenterOfRotationFourierAngles(CenterOfRotation):
-    """This CoR estimation algo is proposed by V. Valls (BCU). It is based on the Fourier
-    transform of the columns on the sinogram.
-    It requires an initial guesss of the CoR wich is retrieved from
-    dataset_info.dataset_scanner.estimated_cor_from_motor. It is assumed in mm and pixel size in um.
-    Options are (for the moment) hard-coded in the SinoCORFinder.cor_finder.extra_options dict.
-    """
-
-    _default_cor_options = {
-        "crop_around_cor": False,
-        "side": "center",
-        "near_pos": None,
-        "near_std": 100,
-        "near_width": 20,
-        "near_shape": "tukey",
-        "near_weight": 0.1,
-        "near_alpha": 0.5,
-        "shift_sino": True,
-        "near_step": 0.5,
-        "refine": False,
-    }
-
-    def _freq_radio(self, sinos, ifrom, ito):
-        size = (sinos.shape[0] + sinos.shape[0] % 2) // 2
-        fs = np.empty((size, sinos.shape[1]))
-        for i in range(ifrom, ito):
-            line = sinos[:, i]
-            f_signal = rfft(line)
-            f = np.abs(f_signal[: (f_signal.size - 1) // 2 + 1])
-            f2 = np.abs(f_signal[(f_signal.size - 1) // 2 + 1 :][::-1])
-            if len(f) > len(f2):
-                f[1:] += f2
-            else:
-                f[0:] += f2
-            fs[:, i] = f
-        with np.errstate(divide="ignore", invalid="ignore", under="ignore"):
-            fs = np.log(fs)
-        return fs
-
-    def gaussian(self, p, x):
-        return p[3] + p[2] * np.exp(-((x - p[0]) ** 2) / (2 * p[1] ** 2))
-
-    def tukey(self, p, x):
-        pos, std, alpha, height, background = p
-        alpha = np.clip(alpha, 0, 1)
-        pi = np.pi
-        inv_alpha = 1 - alpha
-        width = std / (1 - alpha * 0.5)
-        xx = (np.abs(x - pos) - (width * 0.5 * inv_alpha)) / (width * 0.5 * alpha)
-        xx = np.clip(xx, 0, 1)
-        return (0.5 + np.cos(pi * xx) * 0.5) * height + background
-
-    def sinlet(self, p, x):
-        std = p[1] * 2.5
-        lin = np.maximum(0, std - np.abs(p[0] - x)) * 0.5 * np.pi / std
-        return p[3] + p[2] * np.sin(lin)
-
-    def _px(self, detector_width, abs_pos, near_std):
-        sym_range = None
-        if abs_pos is not None:
-            if self.cor_options["crop_around_cor"]:
-                sym_range = int(abs_pos - near_std * 2), int(abs_pos + near_std * 2)
-
-        window = self.cor_options["near_width"]
-        if sym_range is not None:
-            xx_from = max(window, sym_range[0])
-            xx_to = max(xx_from, min(detector_width - window, sym_range[1]))
-            if xx_from == xx_to:
-                sym_range = None
-        if sym_range is None:
-            xx_from = window
-            xx_to = detector_width - window
-
-        xx = np.arange(xx_from, xx_to, self.cor_options["near_step"])
-
-        return xx
-
-    def _symmetry_correlation(self, px, array, angles):
-        window = self.cor_options["near_width"]
-        if self.cor_options["shift_sino"]:
-            shift_index = np.argmin(np.abs(angles - np.pi)) - np.argmin(np.abs(angles - 0))
-        else:
-            shift_index = None
-        px_from = int(px[0])
-        px_to = int(np.ceil(px[-1]))
-        f_coef = np.empty(len(px))
-        f_array = self._freq_radio(array, px_from - window, px_to + window)
-        if shift_index is not None:
-            shift_array = np.empty(array.shape, dtype=array.dtype)
-            shift_array[0 : len(shift_array) - shift_index, :] = array[shift_index:, :]
-            shift_array[len(shift_array) - shift_index :, :] = array[:shift_index, :]
-            f_shift_array = self._freq_radio(shift_array, px_from - window, px_to + window)
-        else:
-            f_shift_array = f_array
-
-        for j, x in enumerate(px):
-            i = int(np.floor(x))
-            if x - i > 0.4:  # TO DO : Specific to near_step = 0.5?
-                f_left = f_array[:, i - window : i]
-                f_right = f_shift_array[:, i + 1 : i + window + 1][:, ::-1]
-            else:
-                f_left = f_array[:, i - window : i]
-                f_right = f_shift_array[:, i : i + window][:, ::-1]
-            with np.errstate(divide="ignore", invalid="ignore"):
-                f_coef[j] = np.sum(np.abs(f_left - f_right))
-        return f_coef
-
-    def _cor_correlation(self, px, abs_pos, near_std):
-        if abs_pos is not None:
-            signal = self.cor_options["near_shape"]
-            weight = self.cor_options["near_weight"]
-            alpha = self.cor_options["near_alpha"]
-            if signal == "sinlet":
-                coef = self.sinlet((abs_pos, near_std, -weight, 1), px)
-            elif signal == "gaussian":
-                coef = self.gaussian((abs_pos, near_std, -weight, 1), px)
-            elif signal == "tukey":
-                coef = self.tukey((abs_pos, near_std * 2, alpha, -weight, 1), px)
-            else:
-                raise ValueError("Shape unsupported")
-        else:
-            coef = np.ones_like(px)
-        return coef
-
-    def find_shift(
-        self,
-        img_1,
-        img_2,
-        angles,
-        side,
-        roi_yxhw=None,
-        median_filt_shape=None,
-        padding_mode=None,
-        peak_fit_radius=1,
-        high_pass=None,
-        low_pass=None,
-    ):
-        sinos = np.vstack([img_1, np.fliplr(img_2).copy()])
-        detector_width = sinos.shape[1]
-
-        increment = np.abs(angles[0] - angles[1])
-        if np.abs(angles[0] - angles[-1]) < (360 - 0.5) * np.pi / 180 - increment:
-            self.logger.warning("Not enough angles, estimator skipped")
-            return None
-
-        near_pos = self.cor_options.get("near_pos", None)  # A RELATIVE estimation of the COR
-
-        # Default coarse estimate to center of detector
-        # if no one is given either in NX or by user.
-        if near_pos is None:
-            self.logger.warning("No initial guess was found (from metadata or user) for CoR")
-            self.logger.warning("Setting initial guess to center of detector.")
-            if side == "center":
-                abs_pos = detector_width // 2
-            elif side == "left":
-                abs_pos = detector_width // 4
-            elif side == "right":
-                abs_pos = detector_width * 3 // 4
-            elif side == "near":
-                abs_pos = detector_width // 2
-            else:
-                raise ValueError(f"side '{side}' is not handled")
-        elif isinstance(near_pos, (int, float)):  # Convert RELATIVE to ABSOLUTE position
-            abs_pos = near_pos + detector_width / 2
-
-        near_std = None
-        if abs_pos is not None:
-            near_std = self.cor_options["near_std"]
-
-        px = self._px(detector_width, abs_pos, near_std)
-
-        coef_f = self._symmetry_correlation(
-            px,
-            sinos,
-            angles,
-        )
-        coef_p = self._cor_correlation(px, abs_pos, near_std)
-        coef = coef_f * coef_p
-
-        if len(px) > 0:
-            if self.cor_options["refine"]:
-                f_vals, f_pos = self.extract_peak_regions_1d(-coef, peak_radius=20, cc_coords=px)
-                cor, _ = self.refine_max_position_1d(f_vals, fx=f_pos, return_vertex_val=True)
-            else:
-                cor = px[np.argmin(coef)]
-            cor = cor - detector_width / 2
-        else:
-            cor = None
-
-        return cor
-
-    __call__ = find_shift
-
-
-class CenterOfRotationOctaveAccurate(AlignmentBase):
-    """This is a Python implementation of Octave/fastomo3/accurate COR estimator.
-    The Octave 'accurate' function is renamed `local_correlation`.
-    The Nabu standard `find_shift` has the same API as the other COR estimators (sliding, growing...)
-
-    The class inherits directly from AlignmentBase.
-    """
-
-    _default_cor_options = {
-        "maxsize": [5, 5],
-        "refine": None,
-        "pmcc": False,
-        "normalize": True,
-        "low_pass": 0.01,
-        "limz": 0.5,
-    }
-
-    def _cut(self, im, nrows, ncols, new_center_row=None, new_center_col=None):
-        """Cuts a sub-matrix out of a larger matrix.
-        Cuts in the center of the original matrix, except if new center is specified
-        NO CHECKING of validity indices sub-matrix!
-
-        Parameters
-        ----------
-        im : array.
-            Original matrix
-        nrows : int
-            Number of rows in the output matrix.
-        ncols : int
-            Number of columns in the output matrix.
-        new_center_row : int
-            Index of center row around which to cut (default: None, i.e. center)
-        new_center_col : int
-            Index of center column around which to cut (default: None, i.e. center)
-
-        Returns
-        -------
-        nrows x ncols array.
-
-        Examples
-        --------
-        im_roi = cut(im, 1024, 1024)                -> cut center 1024x1024 pixels
-        im_roi = cut(im, 1024, 1024, 600.5, 700.5)  -> cut 1024x1024 pixels around pixels (600-601, 700-701)
-
-        Author: P. Cloetens <cloetens@esrf.eu>
-        2023-11-06 J. Lesaint <jerome.lesaint@esrf.fr>
-
-        * See octave-archive for the original Octave code.
-        * 2023-11-06: Python implementation. Comparison seems OK.
-        """
-        [n, m] = im.shape
-        if new_center_row is None:
-            new_center_row = (n + 1) / 2
-        if new_center_col is None:
-            new_center_col = (m + 1) / 2
-
-        rb = int(np.round(0.5 + new_center_row - nrows / 2))
-        rb = int(np.round(new_center_row - nrows / 2))
-        re = int(nrows + rb)
-        cb = int(np.round(0.5 + new_center_col - ncols / 2))
-        cb = int(np.round(new_center_col - ncols / 2))
-        ce = int(ncols + cb)
-
-        return im[rb:re, cb:ce]
-
-    def _checkifpart(self, rapp, rapp_hist):
-        res = 0
-        for k in range(rapp_hist.shape[0]):
-            if np.allclose(rapp, rapp_hist[k, :]):
-                res = 1
-                return res
-        return res
-
-    def _interpolate(self, input, shift, mode="mean", interpolation_method="linear"):
-        """Applies to the input a translation by a vector `shift`. Based on
-        `scipy.ndimage.affine_transform` function.
-        JL: This Octave function was initially used in the refine clause of the local_correlation (Octave find_shift).
-        Since find_shift is always called with refine=False in Octave, refine is not implemented (see local_interpolation())
-        and this function becomes useless.
-
-        Parameters
-        ----------
-        input : array
-            Array to which the translation is applied.
-        shift : tuple, list or array of length 2.
-        mode : str
-            Type of padding applied to the unapplicable areas of the output image.
-            Default `mean` is a constant padding with the mean of the input array.
-            `mode` must belong to 'reflect', 'grid-mirror', 'constant', 'grid-constant', 'nearest', 'mirror', 'grid-wrap', 'wrap'
-            See `scipy.ndimage.affine_transform` for details.
-        interpolation_method : str or int.
-            The interpolation is based on spline interpolation.
-            Either 0, 1, 2, 3, 4 or 5: order of the spline interpolation functions.
-            Or one among 'linear','cubic','pchip','nearest','spline' (Octave legacy).
-                'nearest' is equivalent to 0
-                'linear' is equivalent to 1
-                'cubic','pchip','spline' are equivalent to 3.
-        """
-        admissible_modes = (
-            "reflect",
-            "grid-mirror",
-            "constant",
-            "grid-constant",
-            "nearest",
-            "mirror",
-            "grid-wrap",
-            "wrap",
-        )
-        admissible_interpolation_methods = ("linear", "cubic", "pchip", "nearest", "spline")
-
-        from scipy.ndimage import affine_transform
-
-        [s0, s1] = shift
-        matrix = np.zeros([2, 3], dtype=float)
-        matrix[0, 0] = 1.0
-        matrix[1, 1] = 1.0
-        matrix[:, 2] = [-s0, -s1]  # JL: due to transf. convention diff in Octave and scipy (push fwd vs pull back)
-
-        if interpolation_method == "nearest":
-            order = 0
-        elif interpolation_method == "linear":
-            order = 1
-        elif interpolation_method in ("pchip", "cubic", "spline"):
-            order = 3
-        elif interpolation_method in (0, 1, 2, 3, 4, 5):
-            order = interpolation_method
-        else:
-            raise ValueError(
-                f"Interpolation method is {interpolation_method} and should either an integer between 0 (inc.) and 5 (inc.) or in {admissible_interpolation_methods}."
-            )
-
-        if mode == "mean":
-            mode = "constant"
-            cval = input.mean()
-            return affine_transform(input, matrix, mode=mode, order=order, cval=cval)
-        elif mode not in admissible_modes:
-            raise ValueError(f"Pad method is {mode} and should be in {admissible_modes}.")
-
-        return affine_transform(input, matrix, mode=mode, order=order)
-
-    def _local_correlation(
-        self,
-        z1,
-        z2,
-        maxsize=[5, 5],
-        cor_estimate=[0, 0],
-        refine=None,
-        pmcc=False,
-        normalize=True,
-    ):
-        """Returns the 2D shift in pixels between two images.
-        It looks for a local optimum around the initial shift cor_estimate
-        and within a window 'maxsize'.
-        It uses variance of the difference of the normalized images or PMCC
-        It adapts the shift estimate in case optimum is at the edge of the window
-        If 'maxsize' is set to 0, it will only use approximate shift (+ refine possibly)
-        Set 'cor_estimate' to allow for the use of any initial shift estimation.
-
-        When not successful (stuck in loop or edge reached), returns [nan nan]
-        Positive values corresponds to moving z2 to higher values of the index
-        to compensate drift: interpolate(f)(z2, row, column)
-
-        Parameters
-        ----------
-        z1,z2 : 2D arrays.
-            The two (sub)images to be compared.
-
-        maxsize : 2-list. Default [5,5]
-            Size of the search window.
-
-        cor_estimate:
-            Initial guess of the center of rotation.
-
-        refine: Boolean or None (default is None)
-            Wether the initial guess should be refined of not.
-
-        pmcc: Boolean (default is False)
-            Use Pearson correlation coefficient  i.o. variance.
-
-        normalize: Boolean (default is True)
-            Set mean of each image to 1 if True.
-
-        Returns
-        -------
-        c = [row,column] (or [NaN,NaN] if unsuccessful.)
-
-        2007-01-05 P. Cloetens cloetens@esrf.eu
-        * Initial revision
-        2023-11-10 J. Lesaint jerome.lesaint@esrf.fr
-        * Python conversion.
-        """
-
-        if type(maxsize) in (float, int):
-            maxsize = [int(maxsize), int(maxsize)]
-        elif type(maxsize) in (tuple, list):
-            maxsize = [int(maxsize[0]), int(maxsize[1])]
-        elif maxsize in ([], None, ""):
-            maxsize = [5, 5]
-
-        if refine is None:
-            refine = np.allclose(maxsize, 0.0)
-
-        if normalize:
-            z1 /= np.mean(z1)
-            z2 /= np.mean(z2)
-
-        #####################################
-        # JL : seems useless since func is always called with a first approximate.
-        ## determination of approximative shift (manually or Fourier correlation)
-        # if isinstance(cor_estimate,str):
-        #    if cor_estimate in ('fft','auto','fourier'):
-        #        padding_mode = None
-        #        cor_estimate = self._compute_correlation_fft(
-        #            z1,
-        #            z2,
-        #            padding_mode,
-        #            high_pass=self.high_pass,
-        #            low_pass=self.low_pass
-        #        )
-        #    elif cor_estimate in ('manual','man','m'):
-        #        cor_estimate = None
-        #        # No ImageJ plugin here :
-        #        # rapp = ij_align(z1,z2)
-
-        ####################################
-        # check if refinement with realspace correlation is required
-        # otherwise keep result as it is
-        if np.allclose(maxsize, 0):
-            shiftfound = 1
-            if refine:
-                c = np.round(np.array(cor_estimate, dtype=int))
-            else:
-                c = np.array(cor_estimate, dtype=int)
-        else:
-            shiftfound = 0
-            cor_estimate = np.round(np.array(cor_estimate, dtype=int))
-
-        rapp_hist = []
-        if np.sum(np.abs(cor_estimate) + 1 >= z1.shape):
-            self.logger.info(f"Approximate shift of [{cor_estimate[0]},{cor_estimate[1]}] is too large, setting [0 0]")
-            cor_estimate = np.array([0, 0])
-        maxsize = np.minimum(maxsize, np.floor((np.array(z1.shape) - 1) / 2)).astype(int)
-        maxsize = np.minimum(maxsize, np.array(z1.shape) - np.abs(cor_estimate) - 1).astype(int)
-
-        while not shiftfound:
-            # Set z1 region
-            # Rationale: the (shift[0]+maxsize[0]:,shift[1]+maxsize[1]:) block of z1 should match
-            # the (maxsize[0]:,maxisze[1]:)-upper-left corner of z2.
-            # We first extract this z1 block.
-            # Then, take moving z2-block according to maxsize.
-            # Of course, care must be taken with borders, hence the various max,min calls.
-
-            # Extract the reference block
-            shape_ar = np.array(z1.shape)
-            cor_ar = np.array(cor_estimate)
-            maxsize_ar = np.array(maxsize)
-
-            z1beg = np.maximum(cor_ar + maxsize_ar, np.zeros(2, dtype=int))
-            z1end = shape_ar + np.minimum(cor_ar - maxsize_ar, np.zeros(2, dtype=int))
-
-            z1p = z1[z1beg[0] : z1end[0], z1beg[1] : z1end[1]].flatten()
-
-            # Build local correlations array.
-            window_shape = (2 * int(maxsize[0]) + 1, 2 * int(maxsize[1]) + 1)
-            cc = np.zeros(window_shape)
-
-            # Prepare second block indices
-            z2beg = (cor_ar + maxsize_ar > 0) * cc.shape + (cor_ar + maxsize_ar <= 0) * (shape_ar - z1end + z1beg) - 1
-            z2end = z2beg + z1end - z1beg
-
-            if pmcc:
-                std_z1p = z1p.std()
-            if normalize == 2:
-                z1p /= z1p.mean()
-
-            for k in range(cc.shape[0]):
-                for l in range(cc.shape[1]):
-                    if pmcc:
-                        z2p = z2[z2beg[0] - k : z2end[0] - k, z2beg[1] - l : z2end[1] - l].flatten()
-                        std_z2p = z2p.std()
-                        cc[k, l] = -np.cov(z1p, z2p, rowvar=True)[1, 0] / (std_z1p * std_z2p)
-                    else:
-                        if normalize == 2:
-                            z2p = z2[z2beg[0] - k : z2end[0] - k, z2beg[1] - l : z2end[1] - l].flatten()
-                            z2p /= z2p.mean()
-                            z2p -= z1p
-                        else:
-                            z2p = z2[z2beg[0] - k : z2end[0] - k, z2beg[1] - l : z2end[1] - l].flatten()
-                            z2p -= z1p
-                        cc[k, l] = ((z2p - z2p.mean()) ** 2).sum()
-                        # cc(k,l) = std(z1p./z2(z2beg(1)-k:z2end(1)-k,z2beg(2)-l:z2end(2)-l)(:));
-
-            c = np.unravel_index(np.argmin(cc, axis=None), shape=cc.shape)
-
-            if not np.sum((c == 0) + (c == np.array(cc.shape) - 1)):
-                # check that we are not at the edge of the region that was sampled
-                x = np.array([-1, 0, 1])
-                tmp = self.refine_max_position_2d(cc[c[0] - 1 : c[0] + 2, c[1] - 1 : c[1] + 2], x, x)
-                c += tmp
-            shiftfound = True
-
-            c += z1beg - z2beg
-
-            rapp_hist = []
-            if not shiftfound:
-                cor_estimate = c
-                # Check that new shift estimate was not already done (avoid eternal loop)
-                if self._checkifpart(cor_estimate, rapp_hist):
-                    if self.verbose:
-                        self.logger.info(f"Stuck in loop?")
-                    refine = True
-                    shiftfound = True
-                    c = np.array([np.nan, np.nan])
-                else:
-                    rapp_hist.append(cor_estimate)
-                    if self.verbose:
-                        self.logger.info(f"Changing shift estimate: {cor_estimate}")
-                    maxsize = np.minimum(maxsize, np.array(z1.shape) - np.abs(cor_estimate) - 1).astype(int)
-                    if (maxsize == 0).sum():
-                        if self.verbose:
-                            self.logger.info(f"Edge of image reached")
-                        refine = False
-                        shiftfound = True
-                        c = np.array([np.nan, np.nan])
-            elif len(rapp_hist) > 0:
-                if self.verbose:
-                    self.logger.info("\n")
-
-        ####################################
-        # refine result; useful when shifts are not integer values
-        # JL: I don't understand why this refine step should be useful.
-        # In Octave, from fastomo.m, refine is always set to False.
-        # So this could be ignored.
-        # I keep it for future use if it proves useful.
-        # if refine:
-        #    if debug:
-        #        print('Refining solution ...')
-        #    z2n = self.interpolate(z2,c)
-        #    indices = np.ceil(np.abs(c)).astype(int)
-        #    z1p = np.roll(z1,((c>0) * (-1) * indices),[0,1])
-        #    z1p = z1p[1:-indices[0]-1,1:-indices[1]-1].flatten()
-        #    z2n = np.roll(z2n,((c>0) * (-1) * indices),[0,1])
-        #    z2n = z2n[:-indices[0],:-indices[1]]
-        #    ccrefine = np.zeros([3,3])
-        #    [n2,m2] = z2n.shape
-        #    for k in range(3):
-        #        for l in range(3):
-        #            z2p = z1p - z2n[2-k:n2-k,2-l:m2-l].flatten()
-        #            ccrefine[k,l] = ((z2p - z2p.mean())**2).sum()
-        #    x = np.array([-1,0,1])
-        #    crefine = self.refine_max_position_2d(ccrefine, x, x)
-        #    #crefine = min2par(ccrefine)
-
-        #    # Check if the refinement is effectively confined to subpixel
-        #    if (np.abs(crefine) >= 1).sum():
-        #        self.logger.info("Problems refining result\n")
-        #    else:
-        #        c += crefine
-
-        return c
-
-    def find_shift(
-        self,
-        img_1: np.ndarray,
-        img_2: np.ndarray,
-        side: str,
-        roi_yxhw=None,
-        median_filt_shape=None,
-        padding_mode=None,
-        low_pass=0.01,
-        high_pass=None,
-    ):
-        """Automatically finds the Center of Rotation (CoR), given two images
-        (projections/radiographs). Suitable for half-aquisition scan.
-
-        This method finds the half-shift between two opposite images,  by
-        minimizing the variance of small ROI around a global COR estimate
-        (obtained by maximizing Fourier-space computed global correlations).
-
-
-        The output of this function, allows to compute motor movements for
-        aligning the sample rotation axis. Given the following values:
-
-        - L1: distance from source to motor
-        - L2: distance from source to detector
-        - ps: physical pixel size
-        - v: output of this function
-
-        displacement of motor = (L1 / L2 * ps) * v
-
-        Parameters
-        ----------
-        img_1: numpy.ndarray
-            First image
-        img_2: numpy.ndarray
-            Second image, it needs to have been flipped already (e.g. using numpy.fliplr).
-        side: string
-            Expected region of the CoR. Must be 'center' in that case.
-        roi_yxhw: (2, ) or (4, ) numpy.ndarray, tuple, or array, optional
-            4 elements vector containing: vertical and horizontal coordinates
-            of first pixel, plus height and width of the Region of Interest (RoI).
-            Or a 2 elements vector containing: plus height and width of the
-            centered Region of Interest (RoI).
-            Default is None -> deactivated.
-            The ROI will be used for the global estimate.
-        median_filt_shape: (2, ) numpy.ndarray, tuple, or array, optional
-            Shape of the median filter window. Default is None -> deactivated.
-        padding_mode: str in numpy.pad's mode list, optional
-            Padding mode, which determines the type of convolution. If None or
-            'wrap' are passed, this resorts to the traditional circular convolution.
-            If 'edge' or 'constant' are passed, it results in a linear convolution.
-            Default is the circular convolution.
-            All options are:
-                None | 'constant' | 'edge' | 'linear_ramp' | 'maximum' | 'mean'
-                | 'median' | 'minimum' | 'reflect' | 'symmetric' |'wrap'
-        low_pass: float or sequence of two floats
-            Low-pass filter properties, as described in `nabu.misc.fourier_filters`
-        high_pass: float or sequence of two floats
-            High-pass filter properties, as described in `nabu.misc.fourier_filters`
-
-                    Raises
-        ------
-        ValueError
-            In case images are not 2-dimensional or have different sizes.
-
-        Returns
-        -------
-        float
-            Estimated center of rotation position from the center of the RoI in pixels.
-
-        Examples
-        --------
-        The following code computes the center of rotation position for two
-        given images in a tomography scan, where the second image is taken at
-        180 degrees from the first.
-
-        >>> radio1 = data[0, :, :]
-        ... radio2 = np.fliplr(data[1, :, :])
-        ... CoR_calc = CenterOfRotationOctaveAccurate()
-        ... cor_position = CoR_calc.find_shift(radio1, radio2)
-
-        Or for noisy images:
-
-        >>> cor_position = CoR_calc.find_shift(radio1, radio2, median_filt_shape=(3, 3))
-        """
-
-        self.logger.info(
-            f"Estimation of the COR with following options: high_pass={high_pass}, low_pass={low_pass}, limz={self.cor_options['limz']}."
-        )
-
-        self._check_img_pair_sizes(img_1, img_2)
-
-        if side != "center":
-            self.logger.fatal(
-                "The accurate algorithm cannot handle half acq. Use 'near', 'fourier-angles', 'sliding-window' or 'growing-window' instead."
-            )
-            raise ValueError(
-                "The accurate algorithm cannot handle half acq. Use 'near', 'fourier-angles', 'sliding-window' or 'growing-window' instead."
-            )
-
-        img_shape = img_2.shape
-        roi_yxhw = self._determine_roi(img_shape, roi_yxhw)
-
-        img_1 = self._prepare_image(img_1, roi_yxhw=roi_yxhw, median_filt_shape=median_filt_shape)
-        img_2 = self._prepare_image(img_2, roi_yxhw=roi_yxhw, median_filt_shape=median_filt_shape)
-
-        cc = self._compute_correlation_fft(
-            img_1,
-            img_2,
-            padding_mode,
-            high_pass=high_pass,
-            low_pass=low_pass,
-        )
-
-        # We use fftshift to deal more easily with negative shifts.
-        # This has a cost of subtracting half the image shape afterward.
-        shift = np.unravel_index(np.argmax(np.fft.fftshift(cc)), img_shape)
-        shift -= np.array(img_shape) // 2
-
-        # The real "accurate" starts here (i.e. the octave findshift() func).
-        if np.abs(shift[0]) > 10 * self.cor_options["limz"]:
-            # This is suspiscious. We don't trust results of correlate.
-            self.logger.info(f"Pre-correlation yields {shift[0]} pixels vertical motion")
-            self.logger.info(f"We do not consider it.")
-            shift = (0, 0)
-
-        # Limit the size of region for comparison to cutsize in both directions.
-        # Hard-coded?
-        cutsize = img_shape[1] // 2
-        oldshift = np.round(shift).astype(int)
-        if (img_shape[0] > cutsize) or (img_shape[1] > cutsize):
-            im0 = self._cut(img_1, min(img_shape[0], cutsize), min(img_shape[1], cutsize))
-            im1 = self._cut(
-                np.roll(img_2, oldshift, axis=(0, 1)), min(img_shape[0], cutsize), min(img_shape[1], cutsize)
-            )
-            shift = oldshift + self._local_correlation(
-                im0,
-                im1,
-                maxsize=self.cor_options["maxsize"],
-                refine=self.cor_options["refine"],
-                pmcc=self.cor_options["pmcc"],
-                normalize=self.cor_options["normalize"],
-            )
-        else:
-            shift = self._local_correlation(
-                img_1,
-                img_2,
-                maxsize=self.cor_options["maxsize"],
-                cor_estimate=oldshift,
-                refine=self.cor_options["refine"],
-                pmcc=self.cor_options["pmcc"],
-                normalize=self.cor_options["normalize"],
-            )
-        if ((shift - oldshift) ** 2).sum() > 4:
-            self.logger.info(f"Pre-correlation ({oldshift}) and accurate correlation ({shift}) are not consistent.")
-            self.logger.info("Please check!!!")
-
-        offset = shift[1] / 2
-
-        if np.abs(shift[0]) > self.cor_options["limz"]:
-            self.logger.info("Verify alignment or sample motion.")
-            self.logger.info(f"Verical motion: {shift[0]} pixels.")
-            self.logger.info(f"Offset?: {offset} pixels.")
-        else:
-            self.logger.info(f"Offset?: {offset} pixels.")
-
-        return offset