pytme 0.2.1__cp311-cp311-macosx_14_0_arm64.whl → 0.2.3__cp311-cp311-macosx_14_0_arm64.whl

tme/matching_constrained.py

@@ -1,195 +0,0 @@
-import numpy as np
-from typing import Tuple, Dict
-
-from scipy.ndimage import map_coordinates
-
-from tme.types import ArrayLike
-from tme.backends import backend
-from tme.matching_data import MatchingData
-from tme.matching_exhaustive import _normalize_under_mask
-
-
-class MatchDensityToDensity:
-    def __init__(
-        self,
-        matching_data: "MatchingData",
-        pad_target_edges: bool = False,
-        pad_fourier: bool = False,
-        rotate_mask: bool = True,
-        interpolation_order: int = 1,
-        negate_score: bool = False,
-    ):
-        self.rotate_mask = rotate_mask
-        self.interpolation_order = interpolation_order
-
-        target_pad = matching_data.target_padding(pad_target=pad_target_edges)
-        matching_data = matching_data.subset_by_slice(target_pad=target_pad)
-
-        fast_shape, fast_ft_shape, fourier_shift = matching_data.fourier_padding(
-            pad_fourier=pad_fourier
-        )
-
-        self.target = backend.topleft_pad(matching_data.target, fast_shape)
-        self.target_mask = matching_data.target_mask
-
-        self.template = matching_data.template
-        self.template_rot = backend.preallocate_array(
-            fast_shape, backend._default_dtype
-        )
-
-        self.template_mask, self.template_mask_rot = 1, 1
-        rotate_mask = False if matching_data.template_mask is None else rotate_mask
-        if matching_data.template_mask is not None:
-            self.template_mask = matching_data.template_mask
-            self.template_mask_rot = backend.topleft_pad(
-                matching_data.template_mask, fast_shape
-            )
-
-        self.score_sign = -1 if negate_score else 1
-
-    @staticmethod
-    def rigid_transform(
-        arr,
-        rotation_matrix,
-        translation,
-        arr_mask=None,
-        out=None,
-        out_mask=None,
-        order: int = 1,
-        use_geometric_center: bool = False,
-    ):
-        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
-
-        center = np.floor(np.array(arr.shape) / 2)[:, None]
-        grid = np.indices(arr.shape, dtype=np.float32).reshape(arr.ndim, -1)
-        np.subtract(grid, center, out=grid)
-        np.matmul(rotation_matrix.T, grid, out=grid)
-        np.add(grid, center, out=grid)
-
-        if out is None:
-            out = np.zeros_like(arr)
-
-        map_coordinates(arr, grid, order=order, output=out.ravel())
-
-        if out_mask is None and arr_mask is not None:
-            out_mask = np.zeros_like(arr_mask)
-
-        if arr_mask is not None:
-            map_coordinates(arr_mask, grid, order=order, output=out_mask.ravel())
-
-        match return_type:
-            case 0:
-                return None
-            case 1:
-                return out
-            case 2:
-                return out_mask
-            case 3:
-                return out, out_mask
-
-    @staticmethod
-    def angles_to_rotationmatrix(angles: Tuple[float]) -> ArrayLike:
-        angles = backend.to_numpy_array(angles)
-        rotation_matrix = euler_to_rotationmatrix(angles)
-        return backend.to_backend_array(rotation_matrix)
-
-    def format_translation(self, translation: Tuple[float] = None) -> ArrayLike:
-        if translation is None:
-            return backend.zeros(self.template.ndim, backend._default_dtype)
-
-        return backend.to_backend_array(translation)
-
-    def score_translation(self, x: Tuple[float]) -> float:
-        translation = self.format_translation(x)
-        rotation_matrix = self.angles_to_rotationmatrix((0, 0, 0))
-
-        return self(translation=translation, rotation_matrix=rotation_matrix)
-
-    def score_angles(self, x: Tuple[float]) -> float:
-        translation = self.format_translation(None)
-        rotation_matrix = self.angles_to_rotationmatrix(x)
-
-        return self(translation=translation, rotation_matrix=rotation_matrix)
-
-    def score(self, x: Tuple[float]) -> float:
-        split = len(x) // 2
-        translation, angles = x[:split], x[split:]
-
-        translation = self.format_translation(translation)
-        rotation_matrix = self.angles_to_rotationmatrix(angles)
-
-        return self(translation=translation, rotation_matrix=rotation_matrix)
-
-
-class FLC(MatchDensityToDensity):
-    def __init__(self, **kwargs: Dict):
-        super().__init__(**kwargs)
-
-        if self.target_mask is not None:
-            backend.multiply(self.target, self.target_mask, out=self.target)
-
-        self.target_square = backend.square(self.target)
-
-        _normalize_under_mask(
-            template=self.template,
-            mask=self.template_mask,
-            mask_intensity=backend.sum(self.template_mask),
-        )
-
-        self.template = backend.reverse(self.template)
-        self.template_mask = backend.reverse(self.template_mask)
-
-    def __call__(self, translation: ArrayLike, rotation_matrix: ArrayLike) -> float:
-        if self.rotate_mask:
-            self.rigid_transform(
-                arr=self.template,
-                arr_mask=self.template_mask,
-                rotation_matrix=rotation_matrix,
-                translation=translation,
-                out=self.template_rot,
-                out_mask=self.template_mask_rot,
-                use_geometric_center=False,
-                order=self.interpolation_order,
-            )
-        else:
-            self.rigid_transform(
-                arr=self.template,
-                rotation_matrix=rotation_matrix,
-                translation=translation,
-                out=self.template_rot,
-                use_geometric_center=False,
-                order=self.interpolation_order,
-            )
-        n_observations = backend.sum(self.template_mask_rot)
-
-        _normalize_under_mask(
-            template=self.template_rot,
-            mask=self.template_mask_rot,
-            mask_intensity=n_observations,
-        )
-
-        ex2 = backend.sum(
-            backend.divide(
-                backend.sum(
-                    backend.multiply(self.target_square, self.template_mask_rot),
-                ),
-                n_observations,
-            )
-        )
-        e2x = backend.square(
-            backend.divide(
-                backend.sum(backend.multiply(self.target, self.template_mask_rot)),
-                n_observations,
-            )
-        )
-
-        denominator = backend.maximum(backend.subtract(ex2, e2x), 0.0)
-        denominator = backend.sqrt(denominator)
-        denominator = backend.multiply(denominator, n_observations)
-
-        overlap = backend.sum(backend.multiply(self.template_rot, self.target))
-
-        score = backend.divide(overlap, denominator) * self.score_sign
-        return score