pytme 0.2.9__cp311-cp311-macosx_15_0_arm64.whl

tme/backends/pytorch_backend.py

@@ -0,0 +1,430 @@
+""" Backend using pytorch and optionally GPU acceleration for
+    template matching.
+
+    Copyright (c) 2023 European Molecular Biology Laboratory
+
+    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+"""
+
+from typing import Tuple, Callable
+from contextlib import contextmanager
+from multiprocessing import shared_memory
+from multiprocessing.managers import SharedMemoryManager
+
+import numpy as np
+from .npfftw_backend import NumpyFFTWBackend
+from ..types import NDArray, TorchTensor, shm_type
+
+
+class PytorchBackend(NumpyFFTWBackend):
+    """
+    A pytorch-based matching backend.
+    """
+
+    def __init__(
+        self,
+        device="cuda",
+        float_dtype=None,
+        complex_dtype=None,
+        int_dtype=None,
+        overflow_safe_dtype=None,
+        **kwargs,
+    ):
+        import torch
+        import torch.nn.functional as F
+
+        float_dtype = torch.float32 if float_dtype is None else float_dtype
+        complex_dtype = torch.complex64 if complex_dtype is None else complex_dtype
+        int_dtype = torch.int32 if int_dtype is None else int_dtype
+        if overflow_safe_dtype is None:
+            overflow_safe_dtype = torch.float32
+
+        super().__init__(
+            array_backend=torch,
+            float_dtype=float_dtype,
+            complex_dtype=complex_dtype,
+            int_dtype=int_dtype,
+            overflow_safe_dtype=overflow_safe_dtype,
+        )
+        self.device = device
+        self.F = F
+
+    def to_backend_array(self, arr: NDArray, check_device: bool = True) -> TorchTensor:
+        if isinstance(arr, self._array_backend.Tensor):
+            if arr.device == self.device or not check_device:
+                return arr
+            return arr.to(self.device)
+        return self.tensor(arr, device=self.device)
+
+    def to_numpy_array(self, arr: TorchTensor) -> NDArray:
+        if isinstance(arr, np.ndarray):
+            return arr
+        elif isinstance(arr, self._array_backend.Tensor):
+            return arr.cpu().numpy()
+        return np.array(arr)
+
+    def to_cpu_array(self, arr: TorchTensor) -> NDArray:
+        return arr.cpu()
+
+    def get_fundamental_dtype(self, arr):
+        if self._array_backend.is_floating_point(arr):
+            return float
+        elif self._array_backend.is_complex(arr):
+            return complex
+        return int
+
+    def free_cache(self):
+        self._array_backend.cuda.empty_cache()
+
+    def mod(self, x1, x2, *args, **kwargs):
+        return self._array_backend.remainder(x1, x2, *args, **kwargs)
+
+    def max(self, *args, **kwargs) -> NDArray:
+        ret = self._array_backend.amax(*args, **kwargs)
+        if isinstance(ret, self._array_backend.Tensor):
+            return ret
+        return ret[0]
+
+    def min(self, *args, **kwargs) -> NDArray:
+        ret = self._array_backend.amin(*args, **kwargs)
+        if isinstance(ret, self._array_backend.Tensor):
+            return ret
+        return ret[0]
+
+    def maximum(self, x1, x2, *args, **kwargs) -> NDArray:
+        x1 = self.to_backend_array(x1, check_device=False)
+        x2 = self.to_backend_array(x2, check_device=False).to(x1.device)
+        return self._array_backend.maximum(input=x1, other=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(input=x1, other=x2, *args, **kwargs)
+
+    def tobytes(self, arr):
+        return arr.cpu().numpy().tobytes()
+
+    def size(self, arr):
+        return arr.numel()
+
+    def zeros(self, shape, dtype=None):
+        return self._array_backend.zeros(shape, dtype=dtype, device=self.device)
+
+    def copy(self, arr: TorchTensor) -> TorchTensor:
+        return self._array_backend.clone(arr)
+
+    def full(self, shape, fill_value, dtype=None):
+        if isinstance(shape, int):
+            shape = (shape,)
+        return self._array_backend.full(
+            size=shape, dtype=dtype, fill_value=fill_value, device=self.device
+        )
+
+    def arange(self, *args, **kwargs):
+        return self._array_backend.arange(*args, **kwargs, device=self.device)
+
+    def datatype_bytes(self, dtype: type) -> int:
+        temp = self.zeros(1, dtype=dtype)
+        return temp.element_size()
+
+    def fill(self, arr: TorchTensor, value: float) -> TorchTensor:
+        arr.fill_(value)
+        return arr
+
+    def astype(self, arr: TorchTensor, dtype: type) -> TorchTensor:
+        return arr.to(dtype)
+
+    def flip(self, a, axis, **kwargs):
+        return self._array_backend.flip(input=a, dims=axis, **kwargs)
+
+    def topk_indices(self, arr, k):
+        temp = arr.reshape(-1)
+        values, indices = self._array_backend.topk(temp, k)
+        indices = self.unravel_index(indices=indices, shape=arr.shape)
+        return indices
+
+    def indices(self, shape: Tuple[int], dtype: type = int) -> TorchTensor:
+        grids = [self.arange(x, dtype=dtype) for x in shape]
+        mesh = self._array_backend.meshgrid(*grids, indexing="ij")
+        return self._array_backend.stack(mesh)
+
+    def unravel_index(self, indices, shape):
+        indices = self.to_backend_array(indices)
+        shape = self.to_backend_array(shape)
+        strides = self._array_backend.cumprod(shape.flip(0), dim=0).flip(0)
+        strides = self._array_backend.cat(
+            (strides[1:], self.to_backend_array([1])),
+        )
+        unraveled_coords = (indices.view(-1, 1) // strides.view(1, -1)) % shape.view(
+            1, -1
+        )
+        if unraveled_coords.size(0) == 1:
+            return (unraveled_coords[0, :],)
+
+        else:
+            return tuple(unraveled_coords.T)
+
+    def roll(self, a, shift, axis, **kwargs):
+        shift = tuple(shift)
+        return self._array_backend.roll(input=a, shifts=shift, dims=axis, **kwargs)
+
+    def unique(
+        self,
+        ar,
+        return_index: bool = False,
+        return_inverse: bool = False,
+        return_counts: bool = False,
+        axis: int = None,
+        sorted: bool = True,
+    ):
+        # https://github.com/pytorch/pytorch/issues/36748#issuecomment-1478913448
+        unique, inverse, counts = self._array_backend.unique(
+            ar, return_inverse=True, return_counts=True, dim=axis, sorted=sorted
+        )
+        inverse = inverse.reshape(-1)
+
+        if return_index:
+            inv_sorted = inverse.argsort(stable=True)
+            tot_counts = self._array_backend.cat(
+                (counts.new_zeros(1), counts.cumsum(dim=0))
+            )[:-1]
+            index = inv_sorted[tot_counts]
+
+        ret = unique
+        if return_index or return_inverse or return_counts:
+            ret = [unique]
+
+        if return_index:
+            ret.append(index)
+        if return_inverse:
+            ret.append(inverse)
+        if return_counts:
+            ret.append(counts)
+
+        return ret
+
+    def max_filter_coordinates(self, score_space, min_distance: Tuple[int]):
+        if score_space.ndim == 3:
+            func = self._array_backend.nn.MaxPool3d
+        elif score_space.ndim == 2:
+            func = self._array_backend.nn.MaxPool2d
+        else:
+            raise NotImplementedError("Operation only implemented for 2 and 3D inputs.")
+
+        pool = func(
+            kernel_size=min_distance, padding=min_distance // 2, return_indices=True
+        )
+        _, indices = pool(score_space.reshape(1, 1, *score_space.shape))
+        coordinates = self.unravel_index(indices.reshape(-1), score_space.shape)
+        coordinates = self.transpose(self.stack(coordinates))
+        return coordinates
+
+    def repeat(self, *args, **kwargs):
+        return self._array_backend.repeat_interleave(*args, **kwargs)
+
+    def from_sharedarr(self, args) -> TorchTensor:
+        if self.device == "cuda":
+            return args
+
+        shm, shape, dtype = args
+        required_size = int(self._array_backend.prod(self.to_backend_array(shape)))
+
+        ret = self._array_backend.frombuffer(shm.buf, dtype=dtype)[
+            :required_size
+        ].reshape(shape)
+        return ret
+
+    def to_sharedarr(
+        self, arr: TorchTensor, shared_memory_handler: type = None
+    ) -> shm_type:
+        if self.device == "cuda":
+            return arr
+
+        nbytes = arr.numel() * arr.element_size()
+
+        if isinstance(shared_memory_handler, SharedMemoryManager):
+            shm = shared_memory_handler.SharedMemory(size=nbytes)
+        else:
+            shm = shared_memory.SharedMemory(create=True, size=nbytes)
+
+        shm.buf[:nbytes] = arr.numpy().tobytes()
+        return shm, arr.shape, arr.dtype
+
+    def transpose(self, arr, axes=None):
+        if axes is None:
+            axes = tuple(range(arr.ndim - 1, -1, -1))
+        return arr.permute(axes)
+
+    def power(self, *args, **kwargs):
+        return self._array_backend.pow(*args, **kwargs)
+
+    def eye(self, *args, **kwargs):
+        if "device" not in kwargs:
+            kwargs["device"] = self.device
+        return self._array_backend.eye(*args, **kwargs)
+
+    def build_fft(
+        self,
+        fwd_shape: Tuple[int],
+        inv_shape: Tuple[int],
+        inv_output_shape: Tuple[int] = None,
+        fwd_axes: Tuple[int] = None,
+        inv_axes: Tuple[int] = None,
+        **kwargs,
+    ) -> Tuple[Callable, Callable]:
+        rfft_shape = self._format_fft_shape(fwd_shape, fwd_axes)
+        irfft_shape = fwd_shape if inv_output_shape is None else inv_output_shape
+        irfft_shape = self._format_fft_shape(irfft_shape, inv_axes)
+
+        def rfftn(
+            arr: TorchTensor, out: TorchTensor, s=rfft_shape, axes=fwd_axes
+        ) -> TorchTensor:
+            return self._array_backend.fft.rfftn(arr, s=s, out=out, dim=axes)
+
+        def irfftn(
+            arr: TorchTensor, out: TorchTensor = None, s=irfft_shape, axes=inv_axes
+        ) -> TorchTensor:
+            return self._array_backend.fft.irfftn(arr, s=s, out=out, dim=axes)
+
+        return rfftn, irfftn
+
+    def rfftn(self, arr: NDArray, *args, **kwargs) -> NDArray:
+        kwargs["dim"] = kwargs.pop("axes", None)
+        return self._array_backend.fft.rfftn(arr, **kwargs)
+
+    def irfftn(self, arr: NDArray, *args, **kwargs) -> NDArray:
+        kwargs["dim"] = kwargs.pop("axes", None)
+        return self._array_backend.fft.irfftn(arr, **kwargs)
+
+    def rigid_transform(
+        self,
+        arr: TorchTensor,
+        rotation_matrix: TorchTensor,
+        arr_mask: TorchTensor = None,
+        translation: TorchTensor = None,
+        use_geometric_center: bool = False,
+        out: TorchTensor = None,
+        out_mask: TorchTensor = None,
+        order: int = 1,
+        cache: bool = False,
+    ):
+        _mode_mapping = {0: "nearest", 1: "bilinear", 3: "bicubic"}
+        mode = _mode_mapping.get(order, None)
+        if mode is None:
+            modes = ", ".join([str(x) for x in _mode_mapping.keys()])
+            raise ValueError(
+                f"Got {order} but supported interpolation orders are: {modes}."
+            )
+
+        out = self.zeros_like(arr) if out is None else out
+
+        if translation is None:
+            translation = self._array_backend.zeros(arr.ndim, device=arr.device)
+
+        normalized_translation = self.divide(
+            -2.0 * translation, self.tensor(arr.shape, device=arr.device)
+        )
+        rotation_matrix_pull = self.linalg.inv(self.flip(rotation_matrix, [0, 1]))
+
+        out_slice = tuple(slice(0, x) for x in arr.shape)
+        subset = tuple(slice(None) for _ in range(arr.ndim))
+        offset = max(int(arr.ndim - rotation_matrix.shape[0]) - 1, 0)
+        if offset > 0:
+            normalized_translation = normalized_translation[offset:]
+            subset = tuple(0 if i < offset else slice(None) for i in range(arr.ndim))
+            out_slice = tuple(
+                slice(0, 1) if i < offset else slice(0, x)
+                for i, x in enumerate(arr.shape)
+            )
+
+        out[out_slice] = self._affine_transform(
+            arr=arr[subset],
+            rotation_matrix=rotation_matrix_pull,
+            translation=normalized_translation,
+            mode=mode,
+        )
+
+        if arr_mask is not None:
+            out_mask_slice = tuple(slice(0, x) for x in arr_mask.shape)
+            if out_mask is None:
+                out_mask = self._array_backend.zeros_like(arr_mask)
+            out_mask[out_mask_slice] = self._affine_transform(
+                arr=arr_mask[subset],
+                rotation_matrix=rotation_matrix_pull,
+                translation=normalized_translation,
+                mode=mode,
+            )
+
+        return out, out_mask
+
+    def _affine_transform(
+        self,
+        arr: TorchTensor,
+        rotation_matrix: TorchTensor,
+        translation: TorchTensor,
+        mode,
+    ) -> TorchTensor:
+        batched = arr.ndim != rotation_matrix.shape[0]
+
+        batch_size, spatial_dims = 1, arr.shape
+        if batched:
+            translation = translation[1:]
+            batch_size, *spatial_dims = arr.shape
+
+        n_dims = len(spatial_dims)
+        transformation_matrix = self._array_backend.zeros(
+            n_dims, n_dims + 1, device=arr.device, dtype=arr.dtype
+        )
+
+        transformation_matrix[:, :n_dims] = rotation_matrix
+        transformation_matrix[:, n_dims] = translation
+        transformation_matrix = transformation_matrix.unsqueeze(0).expand(
+            batch_size, -1, -1
+        )
+
+        if not batched:
+            arr = arr.unsqueeze(0)
+
+        size = self.Size([batch_size, 1, *spatial_dims])
+        grid = self.F.affine_grid(
+            theta=transformation_matrix, size=size, align_corners=False
+        )
+        output = self.F.grid_sample(
+            input=arr.unsqueeze(1),
+            grid=grid,
+            mode=mode,
+            align_corners=False,
+        )
+
+        if not batched:
+            output = output.squeeze(0)
+
+        return output.squeeze(1)
+
+    def get_available_memory(self) -> int:
+        if self.device == "cpu":
+            return super().get_available_memory()
+        return self._array_backend.cuda.mem_get_info()[0]
+
+    @contextmanager
+    def set_device(self, device_index: int):
+        if self.device == "cuda":
+            with self._array_backend.cuda.device(device_index):
+                yield
+        else:
+            yield None
+
+    def device_count(self) -> int:
+        if self.device == "cpu":
+            return 1
+        return self._array_backend.cuda.device_count()
+
+    def reverse(self, arr: TorchTensor, axis: Tuple[int] = None) -> TorchTensor:
+        if axis is None:
+            axis = tuple(range(arr.ndim))
+        return self._array_backend.flip(arr, [i for i in range(arr.ndim) if i in axis])
+
+    def triu_indices(self, n: int, k: int = 0, m: int = None) -> TorchTensor:
+        if m is None:
+            m = n
+        return self._array_backend.triu_indices(n, m, k)

tme/data/metadata.yaml

@@ -0,0 +1,80 @@
+c48n309.npy:
+- 7416
+- 9.72
+- 1.91567
+c48n527.npy:
+- 12648
+- 8.17
+- 1.94334
+c48n9.npy:
+- 216
+- 36.47
+- 2.89689
+c48u1.npy:
+- 24
+- 62.8
+- 1.57514
+c48u1153.npy:
+- 27672
+- 6.6
+- 2.23735
+c48u1201.npy:
+- 28824
+- 6.48
+- 2.20918
+c48u1641.npy:
+- 39384
+- 5.75
+- 2.10646
+c48u181.npy:
+- 4344
+- 12.29
+- 2.27013
+c48u2219.npy:
+- 53256
+- 5.27
+- 2.20117
+c48u27.npy:
+- 648
+- 20.83
+- 1.64091
+c48u2947.npy:
+- 70728
+- 4.71
+- 2.07843
+c48u3733.npy:
+- 89592
+- 4.37
+- 2.11197
+c48u4749.npy:
+- 113976
+- 4.0
+- 2.053
+c48u5879.npy:
+- 141096
+- 3.74
+- 2.07325
+c48u7111.npy:
+- 170664
+- 3.53
+- 2.11481
+c48u815.npy:
+- 19560
+- 7.4
+- 2.23719
+c48u83.npy:
+- 1992
+- 16.29
+- 2.42065
+c48u8649.npy:
+- 207576
+- 3.26
+- 2.02898
+c600v.npy:
+- 60
+- 44.48
+- 1.4448
+c600vc.npy:
+- 360
+- 27.78
+- 2.15246

tme/data/quat_to_numpy.py

@@ -0,0 +1,42 @@
+#!python3
+
+from os import listdir
+from os.path import dirname, join, basename
+
+import numpy as np
+import yaml
+
+
+def quat_to_numpy(filepath):
+    data = []
+    with open(join(filepath, filepath), "r", encoding="utf-8") as ifile:
+        for line in ifile:
+            if line.startswith("#") or line.startswith("format quaternion"):
+                continue
+            line_split = line.strip().split()
+            if len(line_split) == 3:
+                n, angle, c = line_split
+                continue
+            data.append(line_split)
+
+    data = np.array(data).astype(float)
+    return data, int(n), float(angle), float(c)
+
+
+if __name__ == "__main__":
+    current_directory = dirname(__file__)
+    files = listdir(current_directory)
+
+    files = [file for file in files if file.endswith(".quat")]
+    files = [join(current_directory, file) for file in files]
+    numpy_names = [
+        join(current_directory, file.replace("quat", "npy")) for file in files
+    ]
+
+    metadata = {}
+    for file, np_out in zip(files, numpy_names):
+        quaternions, n, angle, c = quat_to_numpy(file)
+        np.save(np_out, quaternions)
+        metadata[basename(np_out)] = [n, angle, c]
+    with open(join(current_directory, "metadata.yaml"), "w", encoding="utf-8") as ofile:
+        yaml.dump(metadata, ofile, default_flow_style=False)