"""
Backend using numpy and pyFFTW for template matching.
Copyright (c) 2023 European Molecular Biology Laboratory
Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
"""
import os
from psutil import virtual_memory
from contextlib import contextmanager
from typing import Tuple, List, Type
import scipy
import numpy as np
from scipy.ndimage import maximum_filter, affine_transform
from pyfftw import (
zeros_aligned,
simd_alignment,
next_fast_len,
interfaces,
config,
)
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",
"copy",
]
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
[docs]
class NumpyFFTWBackend(_NumpyWrapper, MatchingBackend):
"""
A numpy and pyfftw-based matching backend.
"""
def __init__(
self,
array_backend=np,
float_dtype=np.float32,
complex_dtype=np.complex64,
int_dtype=np.int32,
overflow_safe_dtype=np.float32,
**kwargs,
):
super().__init__(
array_backend=array_backend,
float_dtype=float_dtype,
complex_dtype=complex_dtype,
int_dtype=int_dtype,
overflow_safe_dtype=overflow_safe_dtype,
)
self.affine_transform = affine_transform
self.cholesky = self._linalg_cholesky
self.solve_triangular = self._solve_triangular
self.linalg.solve_triangular = scipy.linalg.solve_triangular
try:
from ._numpyfftw_utils import rfftn as rfftn_cache
from ._numpyfftw_utils import irfftn as irfftn_cache
self._rfftn = rfftn_cache
self._irfftn = irfftn_cache
except Exception as e:
print(e)
config.NUM_THREADS = 1
config.PLANNER_EFFORT = "FFTW_MEASURE"
interfaces.cache.enable()
interfaces.cache.set_keepalive_time(360)
def _linalg_cholesky(self, arr, lower=False, *args, **kwargs):
# Upper argument is not supported until numpy 2.0
ret = self._array_backend.linalg.cholesky(arr, *args, **kwargs)
if not lower:
axes = list(range(ret.ndim))
axes[-2:] = (ret.ndim - 1, ret.ndim - 2)
ret = self._array_backend.transpose(ret, axes)
return ret
def _solve_triangular(self, a, b, lower=True, *args, **kwargs):
mask = self._array_backend.tril if lower else self._array_backend.triu
return self._array_backend.linalg.solve(mask(a), b, *args, **kwargs)
[docs]
def to_backend_array(self, arr: NDArray) -> NDArray:
if isinstance(arr, self._array_backend.ndarray):
return arr
return self._array_backend.asarray(arr)
[docs]
def to_numpy_array(self, arr: NDArray) -> NDArray:
return np.array(arr)
[docs]
def to_cpu_array(self, arr: NDArray) -> NDArray:
return arr
[docs]
def get_fundamental_dtype(self, arr: NDArray) -> Type:
dt = arr.dtype
if self._array_backend.issubdtype(dt, self._array_backend.integer):
return int
elif self._array_backend.issubdtype(dt, self._array_backend.floating):
return float
elif self._array_backend.issubdtype(dt, self._array_backend.complexfloating):
return complex
return float
[docs]
def free_cache(self):
interfaces.cache.disable()
[docs]
def transpose(self, arr: NDArray, *args, **kwargs) -> NDArray:
return self._array_backend.transpose(arr, *args, **kwargs)
[docs]
def tobytes(self, arr: NDArray) -> str:
return arr.tobytes()
[docs]
def size(self, arr: NDArray) -> int:
return arr.size
[docs]
def fill(self, arr: NDArray, value: float) -> NDArray:
arr.fill(value)
return arr
[docs]
def eps(self, dtype: type) -> NDArray:
return self._array_backend.finfo(dtype).eps
[docs]
def datatype_bytes(self, dtype: type) -> NDArray:
temp = self._array_backend.zeros(1, dtype=dtype)
return temp.nbytes
[docs]
def astype(self, arr, dtype: Type) -> NDArray:
if self._array_backend.iscomplexobj(arr):
arr = arr.real
return arr.astype(dtype)
[docs]
@staticmethod
def at(arr, idx, value) -> NDArray:
arr[idx] = value
return arr
[docs]
def addat(self, arr, indices, *args, **kwargs) -> NDArray:
self._array_backend.add.at(arr, indices, *args, **kwargs)
return arr
[docs]
def topk_indices(self, arr: NDArray, k: int):
temp = arr.reshape(-1)
indices = self._array_backend.argpartition(temp, -k)[-k:][:k]
sorted_indices = indices[self._array_backend.argsort(temp[indices])][::-1]
sorted_indices = self.unravel_index(indices=sorted_indices, shape=arr.shape)
return sorted_indices
[docs]
def ssum(self, arr, *args, **kwargs):
return self.sum(self.square(arr), *args, **kwargs)
[docs]
def indices(self, *args, **kwargs) -> NDArray:
return self._array_backend.indices(*args, **kwargs)
[docs]
def roll(
self, a: NDArray, shift: Tuple[int], axis: Tuple[int], **kwargs
) -> NDArray:
return self._array_backend.roll(
a,
shift=shift,
axis=axis,
**kwargs,
)
[docs]
def unravel_index(self, indices: NDArray, shape: Tuple[int]) -> NDArray:
return self._array_backend.unravel_index(indices=indices, shape=shape)
[docs]
def max_filter_coordinates(self, score_space: NDArray, 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")
max_filter = max_filter == score_space
peaks = np.array(np.nonzero(max_filter)).T
return peaks
[docs]
@staticmethod
def zeros(shape: Tuple[int], dtype: type = None) -> NDArray:
arr = zeros_aligned(shape, dtype=dtype, n=simd_alignment)
return arr
[docs]
def from_sharedarr(self, args) -> NDArray:
if len(args) == 1:
return args[0]
shm, shape, dtype = args
return self.ndarray(shape, dtype, shm.buf)
[docs]
def to_sharedarr(
self, arr: NDArray, shared_memory_handler: type = None
) -> shm_type:
if shared_memory_handler is None:
return (arr,)
shm = shared_memory_handler.SharedMemory(size=arr.nbytes)
np_array = self.ndarray(arr.shape, dtype=arr.dtype, buffer=shm.buf)
np_array[:] = arr[:].copy()
return shm, arr.shape, arr.dtype
[docs]
def topleft_pad(self, arr: NDArray, shape: Tuple[int], padval: int = 0) -> NDArray:
b = self.zeros(shape, arr.dtype)
self.add(b, padval, out=b)
aind = [slice(None, None)] * arr.ndim
bind = [slice(None, None)] * arr.ndim
for i in range(arr.ndim):
if arr.shape[i] > shape[i]:
aind[i] = slice(0, shape[i])
elif arr.shape[i] < shape[i]:
bind[i] = slice(0, arr.shape[i])
b[tuple(bind)] = arr[tuple(aind)]
return b
def _rfftn(self, arr, out=None, **kwargs):
ret = interfaces.numpy_fft.rfftn(arr, **kwargs)
if out is not None:
out[:] = ret
return out
return ret
def _irfftn(self, arr, out=None, **kwargs):
ret = interfaces.numpy_fft.irfftn(arr, **kwargs)
if out is not None:
out[:] = ret
return out
return ret
[docs]
def rfftn(
self,
arr: NDArray,
out=None,
auto_align_input: bool = False,
auto_contiguous: bool = False,
overwrite_input: bool = True,
**kwargs,
) -> NDArray:
return self._rfftn(
arr,
auto_align_input=auto_align_input,
auto_contiguous=auto_contiguous,
overwrite_input=overwrite_input,
**kwargs,
)
[docs]
def irfftn(
self,
arr: NDArray,
out=None,
auto_align_input: bool = False,
auto_contiguous: bool = False,
overwrite_input: bool = True,
**kwargs,
) -> NDArray:
return self._irfftn(
arr,
auto_align_input=auto_align_input,
auto_contiguous=auto_contiguous,
overwrite_input=overwrite_input,
**kwargs,
)
[docs]
def compute_convolution_shapes(
self, arr1_shape: Tuple[int], arr2_shape: Tuple[int]
) -> Tuple[List[int], List[int], List[int]]:
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 _rigid_transform_matrix(
self,
rotation_matrix: NDArray,
translation: NDArray = None,
center: NDArray = None,
) -> NDArray:
ndim = rotation_matrix.shape[0]
matrix = self.identity(ndim + 1, dtype=self._float_dtype)
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)
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)
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)
if center is not None:
center_matrix[:ndim, ndim] = -center_matrix[:ndim, ndim]
self.dot(matrix, center_matrix, out=matrix)
matrix /= matrix[ndim, ndim]
return matrix
def _rigid_transform(
self,
data: NDArray,
matrix: NDArray,
output: NDArray,
prefilter: bool,
order: int,
cache: bool = False,
batched=False,
) -> None:
if batched:
for i in range(data.shape[0]):
self._rigid_transform(
data=data[i],
matrix=matrix,
output=output[i],
prefilter=prefilter,
order=order,
cache=cache,
batched=False,
)
return None
out_slice = tuple(slice(0, stop) for stop in data.shape)
self.affine_transform(
input=data,
matrix=matrix,
mode="constant",
output=output[out_slice],
order=order,
prefilter=prefilter,
)
[docs]
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
positive densities.
Parameters
----------
arr : BackendArray
Array to compute the center of mass of.
cutoff : float, optional
Densities less than or equal to cutoff are nullified for center
of mass computation. By default considers all values.
Returns
-------
BackendArray
Center of mass with shape (arr.ndim).
"""
cutoff = self.min(arr) - 1 if cutoff is None else cutoff
arr = self.where(arr > cutoff, arr, 0)
denominator = self.sum(arr)
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)
[docs]
def get_available_memory(self) -> int:
return virtual_memory().available
[docs]
@contextmanager
def set_device(self, device_index: int):
yield None
[docs]
def device_count(self) -> int:
return 1
[docs]
@staticmethod
def reverse(arr: NDArray, axis: Tuple[int] = None) -> NDArray:
if axis is None:
axis = tuple(range(arr.ndim))
keep, rev = slice(None, None), slice(None, None, -1)
return arr[tuple(rev if i in axis else keep for i in range(arr.ndim))]
[docs]
def max_score_over_rotations(
self,
scores: BackendArray,
max_scores: BackendArray,
rotations: BackendArray,
rotation_index: int,
) -> None:
"""
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
----------
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
[docs]
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`
"""
# 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)