pytme 0.2.1__cp311-cp311-macosx_14_0_arm64.whl → 0.2.2__cp311-cp311-macosx_14_0_arm64.whl

tme/backends/npfftw_backend.py

@@ -4,26 +4,79 @@
 
     Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
 """
-
+import os
 from typing import Tuple, Dict, List
+from contextlib import contextmanager
 from multiprocessing import shared_memory
 from multiprocessing.managers import SharedMemoryManager
-from contextlib import contextmanager
 
 import numpy as np
 from psutil import virtual_memory
-from numpy.typing import NDArray
+from scipy.ndimage import maximum_filter, affine_transform
 from pyfftw import zeros_aligned, simd_alignment, FFTW, next_fast_len
 from pyfftw.builders import rfftn as rfftn_builder, irfftn as irfftn_builder
-from scipy.ndimage import maximum_filter, affine_transform
 
-from .matching_backend import MatchingBackend
-from ..matching_utils import rigid_transform
+from ..types import NDArray, BackendArray, shm_type
+from .matching_backend import MatchingBackend, _create_metafunction
+
+os.environ["MKL_NUM_THREADS"] = "1"
+os.environ["OMP_NUM_THREADS"] = "1"
+os.environ["PYFFTW_NUM_THREADS"] = "1"
+os.environ["OPENBLAS_NUM_THREADS"] = "1"
+
+
+def create_ufuncs(obj):
+    ufuncs = [
+        "add",
+        "subtract",
+        "multiply",
+        "divide",
+        "mod",
+        "sum",
+        "where",
+        "einsum",
+        "mean",
+        "einsum",
+        "std",
+        "max",
+        "min",
+        "maximum",
+        "minimum",
+        "sqrt",
+        "square",
+        "abs",
+        "power",
+        "full",
+        "clip",
+        "arange",
+        "stack",
+        "concatenate",
+        "repeat",
+        "indices",
+        "unique",
+        "argsort",
+        "tril_indices",
+        "reshape",
+        "identity",
+        "dot",
+    ]
+    for ufunc in ufuncs:
+        setattr(obj, ufunc, _create_metafunction(ufunc))
+    return obj
+
+
+@create_ufuncs
+class _NumpyWrapper:
+    """
+    MatchingBackend prohibits using create_ufuncs on NumpyFFTWBackend directly.
+    """
+
+    pass
 
 
-class NumpyFFTWBackend(MatchingBackend):
+class NumpyFFTWBackend(_NumpyWrapper, MatchingBackend):
     """
-    A numpy and pyfftw based backend for template matching.
+    A numpy and pyfftw-based matching backend.
     """
 
     def __init__(
@@ -50,7 +103,7 @@ class NumpyFFTWBackend(MatchingBackend):
         return self._array_backend.asarray(arr)
 
     def to_numpy_array(self, arr: NDArray) -> NDArray:
-        return arr
+        return np.array(arr)
 
     def to_cpu_array(self, arr: NDArray) -> NDArray:
         return arr
@@ -68,147 +121,30 @@ class NumpyFFTWBackend(MatchingBackend):
     def free_cache(self):
         pass
 
-    def add(self, x1, x2, *args, **kwargs) -> NDArray:
-        x1 = self.to_backend_array(x1)
-        x2 = self.to_backend_array(x2)
-        return self._array_backend.add(x1, x2, *args, **kwargs)
-
-    def subtract(self, x1, x2, *args, **kwargs) -> NDArray:
-        x1 = self.to_backend_array(x1)
-        x2 = self.to_backend_array(x2)
-        return self._array_backend.subtract(x1, x2, *args, **kwargs)
-
-    def multiply(self, x1, x2, *args, **kwargs) -> NDArray:
-        x1 = self.to_backend_array(x1)
-        x2 = self.to_backend_array(x2)
-        return self._array_backend.multiply(x1, x2, *args, **kwargs)
-
-    def divide(self, x1, x2, *args, **kwargs) -> NDArray:
-        x1 = self.to_backend_array(x1)
-        x2 = self.to_backend_array(x2)
-        return self._array_backend.divide(x1, x2, *args, **kwargs)
-
-    def mod(self, x1, x2, *args, **kwargs):
-        x1 = self.to_backend_array(x1)
-        x2 = self.to_backend_array(x2)
-        return self._array_backend.mod(x1, x2, *args, **kwargs)
-
-    def sum(self, *args, **kwargs) -> NDArray:
-        return self._array_backend.sum(*args, **kwargs)
-
-    def einsum(self, *args, **kwargs) -> NDArray:
-        return self._array_backend.einsum(*args, **kwargs)
-
-    def mean(self, *args, **kwargs) -> NDArray:
-        return self._array_backend.mean(*args, **kwargs)
-
-    def std(self, *args, **kwargs) -> NDArray:
-        return self._array_backend.std(*args, **kwargs)
-
-    def max(self, *args, **kwargs) -> NDArray:
-        return self._array_backend.max(*args, **kwargs)
-
-    def min(self, *args, **kwargs) -> NDArray:
-        return self._array_backend.min(*args, **kwargs)
-
-    def maximum(self, x1, x2, *args, **kwargs) -> NDArray:
-        x1 = self.to_backend_array(x1)
-        x2 = self.to_backend_array(x2)
-        return self._array_backend.maximum(x1, x2, *args, **kwargs)
-
-    def minimum(self, x1, x2, *args, **kwargs) -> NDArray:
-        x1 = self.to_backend_array(x1)
-        x2 = self.to_backend_array(x2)
-        return self._array_backend.minimum(x1, x2, *args, **kwargs)
-
-    def sqrt(self, *args, **kwargs) -> NDArray:
-        return self._array_backend.sqrt(*args, **kwargs)
-
-    def square(self, *args, **kwargs) -> NDArray:
-        return self._array_backend.square(*args, **kwargs)
-
-    def abs(self, *args, **kwargs) -> NDArray:
-        return self._array_backend.abs(*args, **kwargs)
-
     def transpose(self, arr):
         return arr.T
 
-    def power(self, *args, **kwargs):
-        return self._array_backend.power(*args, **kwargs)
-
     def tobytes(self, arr):
         return arr.tobytes()
 
     def size(self, arr):
         return arr.size
 
-    def fill(self, arr: NDArray, value: float) -> None:
+    def fill(self, arr: NDArray, value: float) -> NDArray:
         arr.fill(value)
-
-    def zeros(self, shape, dtype=np.float64) -> NDArray:
-        return self._array_backend.zeros(shape=shape, dtype=dtype)
-
-    def full(self, shape, fill_value, dtype=None, **kwargs) -> NDArray:
-        return self._array_backend.full(
-            shape, dtype=dtype, fill_value=fill_value, **kwargs
-        )
+        return arr
 
     def eps(self, dtype: type) -> NDArray:
-        """
-        Returns the eps defined as diffeerence between 1.0 and the next
-        representable floating point value larger than 1.0.
-
-        Parameters
-        ----------
-        dtype : type
-            Data type for which eps should be returned.
-
-        Returns
-        -------
-        Scalar
-            The eps for the given data type
-        """
         return self._array_backend.finfo(dtype).eps
 
     def datatype_bytes(self, dtype: type) -> NDArray:
-        """
-        Return the number of bytes occupied by a given datatype.
-
-        Parameters
-        ----------
-        dtype : type
-            Datatype for which the number of bytes is to be determined.
-
-        Returns
-        -------
-        int
-            Number of bytes occupied by the datatype.
-        """
         temp = self._array_backend.zeros(1, dtype=dtype)
         return temp.nbytes
 
-    def clip(self, *args, **kwargs) -> NDArray:
-        return self._array_backend.clip(*args, **kwargs)
-
-    def flip(self, a, axis, **kwargs):
-        return self._array_backend.flip(a, axis, **kwargs)
-
     @staticmethod
     def astype(arr, dtype):
         return arr.astype(dtype)
 
-    def arange(self, *args, **kwargs):
-        return self._array_backend.arange(*args, **kwargs)
-
-    def stack(self, *args, **kwargs):
-        return self._array_backend.stack(*args, **kwargs)
-
-    def concatenate(self, *args, **kwargs):
-        return self._array_backend.concatenate(*args, **kwargs)
-
-    def repeat(self, *args, **kwargs):
-        return self._array_backend.repeat(*args, **kwargs)
-
     def topk_indices(self, arr: NDArray, k: int):
         temp = arr.reshape(-1)
         indices = self._array_backend.argpartition(temp, -k)[-k:][:k]
@@ -227,18 +163,9 @@ class NumpyFFTWBackend(MatchingBackend):
             **kwargs,
         )
 
-    def unique(self, *args, **kwargs):
-        return self._array_backend.unique(*args, **kwargs)
-
-    def argsort(self, *args, **kwargs):
-        return self._array_backend.argsort(*args, **kwargs)
-
     def unravel_index(self, indices, shape):
         return self._array_backend.unravel_index(indices=indices, shape=shape)
 
-    def tril_indices(self, *args, **kwargs):
-        return self._array_backend.tril_indices(*args, **kwargs)
-
     def max_filter_coordinates(self, score_space, min_distance: Tuple[int]):
         score_box = tuple(min_distance for _ in range(score_space.ndim))
         max_filter = maximum_filter(score_space, size=score_box, mode="constant")
@@ -248,93 +175,27 @@ class NumpyFFTWBackend(MatchingBackend):
         return peaks
 
     @staticmethod
-    def preallocate_array(shape: Tuple[int], dtype: type) -> NDArray:
-        """
-        Returns a byte-aligned array of zeros with specified shape and dtype.
-
-        Parameters
-        ----------
-        shape : Tuple[int]
-            Desired shape for the array.
-        dtype : type
-            Desired data type for the array.
-
-        Returns
-        -------
-        NDArray
-            Byte-aligned array of zeros with specified shape and dtype.
-        """
+    def zeros(shape: Tuple[int], dtype: type = None) -> NDArray:
         arr = zeros_aligned(shape, dtype=dtype, n=simd_alignment)
         return arr
 
-    def sharedarr_to_arr(
-        self, shm: shared_memory.SharedMemory, shape: Tuple[int], dtype: str
-    ) -> NDArray:
-        """
-        Returns an array of given shape and dtype from shared memory location.
-
-        Parameters
-        ----------
-        shape : tuple
-            Tuple of integers specifying the shape of the array.
-        dtype : str
-            String specifying the dtype of the array.
-        shm : shared_memory.SharedMemory
-            Shared memory object where the array is stored.
-
-        Returns
-        -------
-        NDArray
-            Array of the specified shape and dtype from the shared memory location.
-        """
+    def from_sharedarr(self, args) -> NDArray:
+        shm, shape, dtype = args
         return self.ndarray(shape, dtype, shm.buf)
 
-    def arr_to_sharedarr(
+    def to_sharedarr(
         self, arr: NDArray, shared_memory_handler: type = None
-    ) -> shared_memory.SharedMemory:
-        """
-        Converts a numpy array to an object shared in memory.
-
-        Parameters
-        ----------
-        arr : NDArray
-            Numpy array to convert.
-        shared_memory_handler : type, optional
-            The type of shared memory handler. Default is None.
-
-        Returns
-        -------
-        shared_memory.SharedMemory
-            The shared memory object containing the numpy array.
-        """
+    ) -> shm_type:
         if type(shared_memory_handler) == SharedMemoryManager:
             shm = shared_memory_handler.SharedMemory(size=arr.nbytes)
         else:
             shm = shared_memory.SharedMemory(create=True, size=arr.nbytes)
         np_array = self.ndarray(arr.shape, dtype=arr.dtype, buffer=shm.buf)
         np_array[:] = arr[:].copy()
-        return shm
+        return shm, arr.shape, arr.dtype
 
     def topleft_pad(self, arr: NDArray, shape: Tuple[int], padval: int = 0) -> NDArray:
-        """
-        Returns an array that has been padded to a specified shape with a padding
-        value at the top-left corner.
-
-        Parameters
-        ----------
-        arr : NDArray
-            Input array to be padded.
-        shape : Tuple[int]
-            Desired shape for the output array.
-        padval : int, optional
-            Value to use for padding, default is 0.
-
-        Returns
-        -------
-        NDArray
-            Array that has been padded to the specified shape.
-        """
-        b = self.preallocate_array(shape, arr.dtype)
+        b = self.zeros(shape, arr.dtype)
         self.add(b, padval, out=b)
         aind = [slice(None, None)] * arr.ndim
         bind = [slice(None, None)] * arr.ndim
@@ -357,40 +218,10 @@ class NumpyFFTWBackend(MatchingBackend):
         temp_real: NDArray = None,
         temp_fft: NDArray = None,
     ) -> Tuple[FFTW, FFTW]:
-        """
-        Build pyFFTW builder functions.
-
-        Parameters
-        ----------
-        fast_shape : tuple
-            Tuple of integers corresponding to fast convolution shape
-            (see `compute_convolution_shapes`).
-        fast_ft_shape : tuple
-            Tuple of integers corresponding to the shape of the fourier
-            transform array (see `compute_convolution_shapes`).
-        real_dtype : dtype
-            Numpy dtype of the inverse fourier transform.
-        complex_dtype : dtype
-            Numpy dtype of the fourier transform.
-        inverse_fast_shape : tuple, optional
-            Output shape of the inverse Fourier transform. By default fast_shape.
-        fftargs : dict, optional
-            Dictionary passed to pyFFTW builders.
-        temp_real : NDArray, optional
-            Temporary real numpy array, by default None.
-        temp_fft : NDArray, optional
-            Temporary fft numpy array, by default None.
-
-        Returns
-        -------
-        tuple
-            Tuple containing callable pyFFTW objects for forward and inverse
-            fourier transform.
-        """
         if temp_real is None:
-            temp_real = self.preallocate_array(fast_shape, real_dtype)
+            temp_real = self.zeros(fast_shape, real_dtype)
         if temp_fft is None:
-            temp_fft = self.preallocate_array(fast_ft_shape, complex_dtype)
+            temp_fft = self.zeros(fast_ft_shape, complex_dtype)
         if inverse_fast_shape is None:
             inverse_fast_shape = fast_shape
 
@@ -419,30 +250,11 @@ class NumpyFFTWBackend(MatchingBackend):
         return rfftn, irfftn
 
     def extract_center(self, arr: NDArray, newshape: Tuple[int]) -> NDArray:
-        """
-        Extract the centered portion of an array based on a new shape.
-
-        Parameters
-        ----------
-        arr : NDArray
-            Input array.
-        newshape : tuple
-            Desired shape for the central portion.
-
-        Returns
-        -------
-        NDArray
-            Central portion of the array with shape `newshape`.
-
-        References
-        ----------
-        .. [1] https://github.com/scipy/scipy/blob/v1.11.2/scipy/signal/_signaltools.py
-        """
         new_shape = self.to_backend_array(newshape)
         current_shape = self.to_backend_array(arr.shape)
         starts = self.subtract(current_shape, new_shape)
         starts = self.astype(self.divide(starts, 2), self._int_dtype)
-        stops = self.astype(self.add(starts, newshape), self._int_dtype)
+        stops = self.astype(self.add(starts, new_shape), self._int_dtype)
         box = tuple(slice(start, stop) for start, stop in zip(starts, stops))
         return arr[box]
 
@@ -466,252 +278,110 @@ class NumpyFFTWBackend(MatchingBackend):
             fourier transform, shape of the forward fourier transform
             (see :py:meth:`build_fft`).
         """
-        convolution_shape = [
-            int(x) + int(y) - 1 for x, y in zip(arr1_shape, arr2_shape)
-        ]
+        convolution_shape = [int(x + y - 1) for x, y in zip(arr1_shape, arr2_shape)]
         fast_shape = [next_fast_len(x) for x in convolution_shape]
         fast_ft_shape = list(fast_shape[:-1]) + [fast_shape[-1] // 2 + 1]
 
         return convolution_shape, fast_shape, fast_ft_shape
 
-    def rotate_array(
+    def _rigid_transform_matrix(
         self,
-        arr: NDArray,
-        rotation_matrix: NDArray,
-        arr_mask: NDArray = None,
+        rotation_matrix: NDArray = None,
         translation: NDArray = None,
-        use_geometric_center: bool = False,
-        out: NDArray = None,
-        out_mask: NDArray = None,
-        order: int = 3,
-    ) -> None:
-        """
-        Rotates coordinates of arr according to rotation_matrix.
-
-        If no output array is provided, this method will compute an array with
-        sufficient space to hold all elements. If both `arr` and `arr_mask`
-        are provided, `arr_mask` will be centered according to arr.
-
-        Parameters
-        ----------
-        arr : NDArray
-            The input array to be rotated.
-        arr_mask : NDArray, optional
-            The mask of `arr` that will be equivalently rotated.
-        rotation_matrix : NDArray
-            The rotation matrix to apply [d x d].
-        translation : NDArray
-            The translation to apply [d].
-        use_geometric_center : bool, optional
-            Whether the rotation should be centered around the geometric
-            or mass center. Default is mass center.
-        out : NDArray, optional
-            The output array to write the rotation of `arr` to.
-        out_mask : NDArray, optional
-            The output array to write the rotation of `arr_mask` to.
-        order : int, optional
-            Spline interpolation order. Has to be in the range 0-5. Non-zero
-            elements will be converted into a point-cloud and rotated according
-            to ``rotation_matrix`` if order is None.
-        """
+        center: NDArray = None,
+    ) -> NDArray:
+        ndim = rotation_matrix.shape[0]
+        matrix = self.identity(ndim + 1, dtype=self._float_dtype)
 
-        if order is None:
-            mask_coordinates = None
-            if arr_mask is not None:
-                mask_coordinates = np.array(np.where(arr_mask > 0))
-            return self.rotate_array_coordinates(
-                arr=arr,
-                arr_mask=arr_mask,
-                coordinates=np.array(np.where(arr > 0)),
-                mask_coordinates=mask_coordinates,
-                out=out,
-                out_mask=out_mask,
-                rotation_matrix=rotation_matrix,
-                translation=translation,
-                use_geometric_center=use_geometric_center,
-            )
+        if translation is not None:
+            translation_matrix = self.identity(ndim + 1, dtype=self._float_dtype)
+            translation_matrix[:ndim, ndim] = -translation
+            self.dot(matrix, translation_matrix, out=matrix)
 
-        rotate_mask = arr_mask is not None
-        return_type = (out is None) + 2 * rotate_mask * (out_mask is None)
-        translation = np.zeros(arr.ndim) if translation is None else translation
+        if center is not None:
+            center_matrix = self.identity(ndim + 1, dtype=self._float_dtype)
+            center_matrix[:ndim, ndim] = center
+            self.dot(matrix, center_matrix, out=matrix)
 
-        center = np.divide(arr.shape, 2)
-        if not use_geometric_center:
-            center = self.center_of_mass(arr, cutoff=0)
+        if rotation_matrix is not None:
+            rmat = self.identity(ndim + 1, dtype=self._float_dtype)
+            rmat[:ndim, :ndim] = self._array_backend.linalg.inv(rotation_matrix)
+            self.dot(matrix, rmat, out=matrix)
 
-        rotation_matrix_inverted = np.linalg.inv(rotation_matrix)
-        transformed_center = rotation_matrix_inverted @ center.reshape(-1, 1)
-        transformed_center = transformed_center.reshape(-1)
-        base_offset = np.subtract(center, transformed_center)
-        offset = np.subtract(base_offset, translation)
+        if center is not None:
+            center_matrix[:ndim, ndim] = -center_matrix[:ndim, ndim]
+            self.dot(matrix, center_matrix, out=matrix)
 
-        out = np.zeros_like(arr) if out is None else out
-        out_slice = tuple(slice(0, stop) for stop in arr.shape)
+        matrix /= matrix[ndim, ndim]
+        return matrix
 
-        # Applying the prefilter can cause artifacts in the mask
-        affine_transform(
-            input=arr,
-            matrix=rotation_matrix_inverted,
-            offset=offset,
+    def _rigid_transform(
+        self,
+        data: NDArray,
+        matrix: NDArray,
+        output: NDArray,
+        prefilter: bool,
+        order: int,
+        cache: bool = False,
+    ) -> None:
+        out_slice = tuple(slice(0, stop) for stop in data.shape)
+        self.affine_transform(
+            input=data,
+            matrix=matrix,
             mode="constant",
-            output=out[out_slice],
+            output=output[out_slice],
             order=order,
-            prefilter=True,
+            prefilter=prefilter,
         )
 
-        if rotate_mask:
-            out_mask = np.zeros_like(arr_mask) if out_mask is None else out_mask
-            out_mask_slice = tuple(slice(0, stop) for stop in arr_mask.shape)
-            affine_transform(
-                input=arr_mask,
-                matrix=rotation_matrix_inverted,
-                offset=offset,
-                mode="constant",
-                output=out_mask[out_mask_slice],
-                order=order,
-                prefilter=False,
-            )
-
-        match return_type:
-            case 0:
-                return None
-            case 1:
-                return out
-            case 2:
-                return out_mask
-            case 3:
-                return out, out_mask
-
-    @staticmethod
-    def rotate_array_coordinates(
+    def rigid_transform(
+        self,
         arr: NDArray,
-        coordinates: NDArray,
         rotation_matrix: NDArray,
+        arr_mask: NDArray = None,
         translation: NDArray = None,
+        use_geometric_center: bool = False,
         out: NDArray = None,
-        use_geometric_center: bool = True,
-        arr_mask: NDArray = None,
-        mask_coordinates: NDArray = None,
         out_mask: NDArray = None,
-    ) -> None:
-        """
-        Rotates coordinates of arr according to rotation_matrix.
-
-        If no output array is provided, this method will compute an array with
-        sufficient space to hold all elements. If both `arr` and `arr_mask`
-        are provided, `arr_mask` will be centered according to arr.
-
-        No centering will be performed if the rotation matrix is the identity matrix.
-
-        Parameters
-        ----------
-        arr : NDArray
-            The input array to be rotated.
-        coordinates : NDArray
-            The pointcloud [d x N] containing elements of `arr` that should be rotated.
-            See :py:meth:`Density.to_pointcloud` on how to obtain the coordinates.
-        rotation_matrix : NDArray
-            The rotation matrix to apply [d x d].
-        rotation_matrix : NDArray
-            The translation to apply [d].
-        out : NDArray, optional
-            The output array to write the rotation of `arr` to.
-        use_geometric_center : bool, optional
-            Whether the rotation should be centered around the geometric
-            or mass center.
-        arr_mask : NDArray, optional
-            The mask of `arr` that will be equivalently rotated.
-        mask_coordinates : NDArray, optional
-            Equivalent to `coordinates`, but containing elements of `arr_mask`
-            that should be rotated.
-        out_mask : NDArray, optional
-            The output array to write the rotation of `arr_mask` to.
-        """
-        rotate_mask = arr_mask is not None and mask_coordinates is not None
-        return_type = (out is None) + 2 * rotate_mask * (out_mask is None)
-
-        coordinates_rotated = np.empty(coordinates.shape, dtype=rotation_matrix.dtype)
-        mask_rotated = (
-            np.empty(mask_coordinates.shape, dtype=rotation_matrix.dtype)
-            if rotate_mask
-            else None
-        )
-
-        center = np.array(arr.shape) // 2 if use_geometric_center else None
-        if translation is None:
-            translation = np.zeros(coordinates_rotated.shape[0])
+        order: int = 3,
+        cache: bool = False,
+    ) -> Tuple[NDArray, NDArray]:
+        translation = self.zeros(arr.ndim) if translation is None else translation
+        center = self.divide(self.to_backend_array(arr.shape), 2)
+        if not use_geometric_center:
+            center = self.center_of_mass(arr, cutoff=0)
 
-        rigid_transform(
-            coordinates=coordinates,
-            coordinates_mask=mask_coordinates,
-            out=coordinates_rotated,
-            out_mask=mask_rotated,
+        matrix = self._rigid_transform_matrix(
             rotation_matrix=rotation_matrix,
             translation=translation,
-            use_geometric_center=use_geometric_center,
             center=center,
         )
+        out = self.zeros_like(arr) if out is None else out
 
-        coordinates_rotated = coordinates_rotated.astype(int)
-        offset = coordinates_rotated.min(axis=1)
-        np.multiply(offset, offset < 0, out=offset)
-        coordinates_rotated -= offset[:, None]
-
-        out_offset = np.zeros(
-            coordinates_rotated.shape[0], dtype=coordinates_rotated.dtype
+        self._rigid_transform(
+            data=arr,
+            matrix=matrix,
+            output=out,
+            order=order,
+            prefilter=True,
+            cache=cache,
         )
-        if out is None:
-            out_offset = coordinates_rotated.min(axis=1)
-            coordinates_rotated -= out_offset[:, None]
-            out = np.zeros(coordinates_rotated.max(axis=1) + 1, dtype=arr.dtype)
-
-        if rotate_mask:
-            mask_rotated = mask_rotated.astype(int)
-            if out_mask is None:
-                # mask_rotated -= out_offset[:, None]
-                out_mask = np.zeros(mask_rotated.max(axis=1) + 1, dtype=arr.dtype)
-
-            in_box = np.logical_and(
-                mask_rotated < np.array(out_mask.shape)[:, None],
-                mask_rotated >= 0,
-            ).min(axis=0)
-            out_of_box = np.invert(in_box).sum()
-            if out_of_box != 0:
-                print(
-                    f"{out_of_box} elements out of bounds. Perhaps increase"
-                    " *arr_mask* size."
-                )
-
-            mask_coordinates = tuple(mask_coordinates[:, in_box])
-            mask_rotated = tuple(mask_rotated[:, in_box])
-            np.add.at(out_mask, mask_rotated, arr_mask[mask_coordinates])
-
-        # Negative coordinates would be (mis)interpreted as reverse index
-        in_box = np.logical_and(
-            coordinates_rotated < np.array(out.shape)[:, None], coordinates_rotated >= 0
-        ).min(axis=0)
-        out_of_box = np.invert(in_box).sum()
-        if out_of_box != 0:
-            print(f"{out_of_box} elements out of bounds. Perhaps increase *out* size.")
-
-        coordinates = coordinates[:, in_box]
-        coordinates_rotated = coordinates_rotated[:, in_box]
-
-        coordinates = tuple(coordinates)
-        coordinates_rotated = tuple(coordinates_rotated)
-        np.add.at(out, coordinates_rotated, arr[coordinates])
-
-        match return_type:
-            case 0:
-                return None
-            case 1:
-                return out
-            case 2:
-                return out_mask
-            case 3:
-                return out, out_mask
-
-    def center_of_mass(self, arr: NDArray, cutoff: float = None) -> NDArray:
+
+        # Applying the prefilter leads to artifacts in the mask.
+        if arr_mask is not None:
+            out_mask = self.zeros_like(arr_mask) if out_mask is None else out_mask
+            self._rigid_transform(
+                data=arr_mask,
+                matrix=matrix,
+                output=out_mask,
+                order=order,
+                prefilter=False,
+                cache=cache,
+            )
+
+        return out, out_mask
+
+    def center_of_mass(self, arr: BackendArray, cutoff: float = None) -> BackendArray:
         """
         Computes the center of mass of a numpy ndarray instance using all available
         elements. For template matching it typically makes sense to only input
@@ -719,7 +389,7 @@ class NumpyFFTWBackend(MatchingBackend):
 
         Parameters
         ----------
-        arr : NDArray
+        arr : BackendArray
             Array to compute the center of mass of.
         cutoff : float, optional
             Densities less than or equal to cutoff are nullified for center
@@ -727,23 +397,24 @@ class NumpyFFTWBackend(MatchingBackend):
 
         Returns
         -------
-        NDArray
+        BackendArray
             Center of mass with shape (arr.ndim).
         """
-        cutoff = arr.min() - 1 if cutoff is None else cutoff
-        arr = self._array_backend.where(arr > cutoff, arr, 0)
+        cutoff = self.min(arr) - 1 if cutoff is None else cutoff
+
+        arr = self.where(arr > cutoff, arr, 0)
         denominator = self.sum(arr)
-        grids = self._array_backend.ogrid[tuple(slice(0, i) for i in arr.shape)]
-        grids = [grid.astype(self._float_dtype) for grid in grids]
-
-        center_of_mass = self.array(
-            [
-                self.sum(self.multiply(arr, grids[dim]) / denominator)
-                for dim in range(arr.ndim)
-            ]
-        )
 
-        return center_of_mass
+        grids = []
+        for i, x in enumerate(arr.shape):
+            baseline_dims = tuple(1 if i != t else x for t in range(len(arr.shape)))
+            grids.append(
+                self.reshape(self.arange(x, dtype=self._float_dtype), baseline_dims)
+            )
+
+        center_of_mass = [self.sum((arr * grid) / denominator) for grid in grids]
+
+        return self.to_backend_array(center_of_mass)
 
     def get_available_memory(self) -> int:
         return virtual_memory().available
@@ -753,6 +424,7 @@ class NumpyFFTWBackend(MatchingBackend):
         yield None
 
     def device_count(self) -> int:
+        """Returns the number of available GPU devices."""
         return 1
 
     @staticmethod
@@ -774,26 +446,86 @@ class NumpyFFTWBackend(MatchingBackend):
 
     def max_score_over_rotations(
         self,
-        score_space: NDArray,
-        internal_scores: NDArray,
-        internal_rotations: NDArray,
+        scores: BackendArray,
+        max_scores: BackendArray,
+        rotations: BackendArray,
         rotation_index: int,
     ) -> None:
         """
-        Modify internal_scores and internal_rotations inplace with scores and rotation
-        index respectively, wherever score_sapce is larger than internal scores.
+        Update elements in ``max_scores`` and ``rotations`` where scores is larger than
+        max_scores with score and rotation_index, respectivelty.
+
+        .. warning:: ``max_scores`` and ``rotations`` are modified in-place.
 
         Parameters
         ----------
-        score_space : numpy.ndarray
-            The score space to compare against internal_scores.
-        internal_scores : numpy.ndarray
-            The internal scores to update with maximum scores.
-        internal_rotations : numpy.ndarray
-            The internal rotations corresponding to the maximum scores.
+        scores : BackendArray
+            The score space to compare against max_scores.
+        max_scores : BackendArray
+            Maximum score observed for each element in an array.
+        rotations : BackendArray
+            Rotation used to achieve a given max_score.
         rotation_index : int
             The index representing the current rotation.
+
+        Returns
+        -------
+        Tuple[BackendArray, BackendArray]
+            Updated ``max_scores`` and ``rotations``.
+        """
+        indices = scores > max_scores
+        max_scores[indices] = scores[indices]
+        rotations[indices] = rotation_index
+        return max_scores, rotations
+
+    def norm_scores(
+        self,
+        arr: BackendArray,
+        exp_sq: BackendArray,
+        sq_exp: BackendArray,
+        n_obs: int,
+        eps: float,
+        out: BackendArray,
+    ) -> BackendArray:
+        """
+        Normalizes ``arr`` by the standard deviation ensuring numerical stability.
+
+        Parameters
+        ----------
+        arr : BackendArray
+            The input array to be normalized.
+        exp_sq : BackendArray
+            Non-normalized expectation square.
+        sq_exp : BackendArray
+            Non-normalized expectation.
+        n_obs : int
+            Number of observations for normalization.
+        eps : float
+            Numbers below this threshold will be ignored in division.
+        out : BackendArray
+            Output array to write the result to.
+
+        Returns
+        -------
+        BackendArray
+            The normalized array with the same shape as `arr`.
+
+        See Also
+        --------
+        :py:meth:`tme.matching_exhaustive.flc_scoring`
         """
-        indices = score_space > internal_scores
-        internal_scores[indices] = score_space[indices]
-        internal_rotations[indices] = rotation_index
+        # Squared expected value (E(X)^2)
+        sq_exp = self.divide(sq_exp, n_obs, out=sq_exp)
+        sq_exp = self.square(sq_exp, out=sq_exp)
+        # Expected squared value (E(X^2))
+        exp_sq = self.divide(exp_sq, n_obs, out=exp_sq)
+        # Variance
+        sq_exp = self.subtract(exp_sq, sq_exp, out=sq_exp)
+        sq_exp = self.maximum(sq_exp, 0.0, out=sq_exp)
+        sq_exp = self.sqrt(sq_exp, out=sq_exp)
+
+        # Assume that low stdev regions also have low scores
+        # See :py:meth:`tme.matching_exhaustive.flcSphericalMask_setup` for correct norm
+        sq_exp[sq_exp < eps] = 1
+        sq_exp = self.multiply(sq_exp, n_obs, out=sq_exp)
+        return self.divide(arr, sq_exp, out=out)