""" Backend using cupy for template matching.
Copyright (c) 2023 European Molecular Biology Laboratory
Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
"""
import warnings
from importlib.util import find_spec
from contextlib import contextmanager
from typing import Tuple, Callable, List
import numpy as np
from .npfftw_backend import NumpyFFTWBackend
from ..types import CupyArray, NDArray, shm_type
PLAN_CACHE = {}
TEXTURE_CACHE = {}
[docs]
class CupyBackend(NumpyFFTWBackend):
"""
A cupy-based matching backend.
"""
def __init__(
self,
float_dtype: type = None,
complex_dtype: type = None,
int_dtype: type = None,
overflow_safe_dtype: type = None,
**kwargs,
):
import cupy as cp
import cupyx.scipy.fft as cufft
from cupyx.scipy.ndimage import affine_transform, maximum_filter
from ._cupy_utils import affine_transform_batch
float_dtype = cp.float32 if float_dtype is None else float_dtype
complex_dtype = cp.complex64 if complex_dtype is None else complex_dtype
int_dtype = cp.int32 if int_dtype is None else int_dtype
if overflow_safe_dtype is None:
overflow_safe_dtype = cp.float32
super().__init__(
array_backend=cp,
float_dtype=float_dtype,
complex_dtype=complex_dtype,
int_dtype=int_dtype,
overflow_safe_dtype=overflow_safe_dtype,
)
self._cufft = cufft
self.maximum_filter = maximum_filter
self.affine_transform = affine_transform
self.affine_transform_batch = affine_transform_batch
itype = f"int{self.datatype_bytes(int_dtype) * 8}"
ftype = f"float{self.datatype_bytes(float_dtype) * 8}"
self._max_score_over_rotations = self._array_backend.ElementwiseKernel(
f"{ftype} internal_scores, {ftype} scores, {itype} rot_index",
f"{ftype} out1, {itype} rotations",
"if (internal_scores < scores) {out1 = scores; rotations = rot_index;}",
"max_score_over_rotations",
)
self.norm_scores = cp.ElementwiseKernel(
f"{ftype} arr, {ftype} exp_sq, {ftype} sq_exp, {ftype} n_obs, {ftype} eps",
f"{ftype} out",
"""
// tmp1 = E(X)^2; tmp2 = E(X^2)
float tmp1 = sq_exp / n_obs;
float tmp2 = exp_sq / n_obs;
tmp1 *= tmp1;
tmp2 = sqrt(max(tmp2 - tmp1, 0.0));
// out = (tmp2 < eps) ? 0.0 : arr / (tmp2 * n_obs);
tmp1 = arr;
if (tmp2 < eps){
tmp1 = 0;
}
tmp2 *= n_obs;
out = tmp1 / tmp2;
""",
"norm_scores",
)
self.texture_available = find_spec("voltools") is not None
[docs]
def to_backend_array(self, arr: NDArray) -> CupyArray:
current_device = self._array_backend.cuda.device.get_device_id()
if (
isinstance(arr, self._array_backend.ndarray)
and arr.device.id == current_device
):
return arr
return self._array_backend.asarray(arr)
[docs]
def to_numpy_array(self, arr: CupyArray) -> NDArray:
return self._array_backend.asnumpy(arr)
[docs]
def to_cpu_array(self, arr: NDArray) -> NDArray:
return self.to_numpy_array(arr)
[docs]
def from_sharedarr(self, arr: CupyArray) -> CupyArray:
return arr
[docs]
@staticmethod
def to_sharedarr(arr: CupyArray, shared_memory_handler: type = None) -> shm_type:
return arr
[docs]
def zeros(self, *args, **kwargs):
return self._array_backend.zeros(*args, **kwargs)
[docs]
def unravel_index(self, indices, shape):
return self._array_backend.unravel_index(indices=indices, dims=shape)
[docs]
def unique(self, ar, axis=None, *args, **kwargs):
if axis is None:
return self._array_backend.unique(ar=ar, axis=axis, *args, **kwargs)
warnings.warn("Axis argument not yet supported in CupY, falling back to NumPy.")
ret = np.unique(ar=self.to_numpy_array(ar), axis=axis, *args, **kwargs)
if not isinstance(ret, tuple):
return self.to_backend_array(ret)
return tuple(self.to_backend_array(k) for k in ret)
[docs]
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]:
cache = self._array_backend.fft.config.get_plan_cache()
current_device = self._array_backend.cuda.device.get_device_id()
previous_transform = [fwd_shape, inv_shape]
if current_device in PLAN_CACHE:
previous_transform = PLAN_CACHE[current_device]
real_diff, cmplx_diff = True, True
if len(fwd_shape) == len(previous_transform[0]):
real_diff = fwd_shape == previous_transform[0]
if len(inv_shape) == len(previous_transform[1]):
cmplx_diff = inv_shape == previous_transform[1]
if real_diff or cmplx_diff:
cache.clear()
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: CupyArray, out: CupyArray = None, s=rfft_shape, axes=fwd_axes
) -> CupyArray:
return self.rfftn(arr, s=s, axes=fwd_axes)
def irfftn(
arr: CupyArray, out: CupyArray = None, s=irfft_shape, axes=inv_axes
) -> CupyArray:
return self.irfftn(arr, s=s, axes=inv_axes)
PLAN_CACHE[current_device] = [fwd_shape, inv_shape]
return rfftn, irfftn
[docs]
def rfftn(self, arr: CupyArray, out: CupyArray = None, **kwargs) -> CupyArray:
return self._cufft.rfftn(arr, **kwargs)
[docs]
def irfftn(self, arr: CupyArray, out: CupyArray = None, **kwargs) -> CupyArray:
return self._cufft.irfftn(arr, **kwargs)
[docs]
def compute_convolution_shapes(
self, arr1_shape: Tuple[int], arr2_shape: Tuple[int]
) -> Tuple[List[int], List[int], List[int]]:
from cupyx.scipy.fft import next_fast_len
convolution_shape = [int(x + y - 1) for x, y in zip(arr1_shape, arr2_shape)]
fast_shape = [next_fast_len(x, real=True) 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
[docs]
def max_filter_coordinates(self, score_space, min_distance: Tuple[int]):
score_box = tuple(min_distance for _ in range(score_space.ndim))
max_filter = self.maximum_filter(score_space, size=score_box, mode="constant")
max_filter = max_filter == score_space
peaks = self._array_backend.array(self._array_backend.nonzero(max_filter)).T
return peaks
# The default methods in Cupy were oddly slow
[docs]
def var(self, a, *args, **kwargs):
out = a - self._array_backend.mean(a, *args, **kwargs)
self._array_backend.square(out, out)
out = self._array_backend.mean(out, *args, **kwargs)
return out
[docs]
def std(self, a, *args, **kwargs):
out = self.var(a, *args, **kwargs)
return self._array_backend.sqrt(out)
def _get_texture(self, arr: CupyArray, order: int = 3, prefilter: bool = False):
key = id(arr)
if key in TEXTURE_CACHE:
return TEXTURE_CACHE[key]
from voltools import StaticVolume
# Only keep template and potential corresponding mask in cache
if len(TEXTURE_CACHE) >= 2:
TEXTURE_CACHE.clear()
interpolation = "filt_bspline"
if order == 1:
interpolation = "linear"
elif order == 3 and not prefilter:
interpolation = "bspline"
current_device = self._array_backend.cuda.device.get_device_id()
TEXTURE_CACHE[key] = StaticVolume(
arr, interpolation=interpolation, device=f"gpu:{current_device}"
)
return TEXTURE_CACHE[key]
def _rigid_transform(
self,
data: CupyArray,
matrix: CupyArray,
output: CupyArray,
prefilter: bool,
order: int,
cache: bool = False,
batched: bool = False,
) -> None:
out_slice = tuple(slice(0, stop) for stop in data.shape)
if batched:
self.affine_transform_batch(
input=data,
matrix=matrix,
mode="constant",
output=output[out_slice],
order=order,
prefilter=prefilter,
)
return None
# if data.ndim == 3 and cache and self.texture_available:
# # Device memory pool (should) come to rescue performance
# temp = self.zeros(data.shape, data.dtype)
# texture = self._get_texture(data, order=order, prefilter=prefilter)
# texture.affine(transform_m=matrix, profile=False, output=temp)
# output[out_slice] = temp
# return None
self.affine_transform(
input=data,
matrix=matrix,
mode="constant",
output=output[out_slice],
order=order,
prefilter=prefilter,
)
[docs]
def get_available_memory(self) -> int:
with self._array_backend.cuda.Device():
free_memory, _ = self._array_backend.cuda.runtime.memGetInfo()
return free_memory
[docs]
@contextmanager
def set_device(self, device_index: int):
with self._array_backend.cuda.Device(device_index):
yield
[docs]
def device_count(self) -> int:
return self._array_backend.cuda.runtime.getDeviceCount()
[docs]
def max_score_over_rotations(
self,
scores: CupyArray,
max_scores: CupyArray,
rotations: CupyArray,
rotation_index: int,
) -> Tuple[CupyArray, CupyArray]:
return self._max_score_over_rotations(
max_scores,
scores,
rotation_index,
max_scores,
rotations,
)