Old engine for Continuous Time Bayesian Networks. Superseded by reCTBN. 🐍
https://github.com/madlabunimib/PyCTBN
You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
214 lines
5.4 KiB
214 lines
5.4 KiB
4 years ago
|
from numbers import Number
|
||
|
import operator
|
||
|
import os
|
||
|
import threading
|
||
|
import contextlib
|
||
|
|
||
|
import numpy as np
|
||
|
# good_size is exposed (and used) from this import
|
||
|
from .pypocketfft import good_size
|
||
|
|
||
|
_config = threading.local()
|
||
|
_cpu_count = os.cpu_count()
|
||
|
|
||
|
|
||
|
def _iterable_of_int(x, name=None):
|
||
|
"""Convert ``x`` to an iterable sequence of int
|
||
|
|
||
|
Parameters
|
||
|
----------
|
||
|
x : value, or sequence of values, convertible to int
|
||
|
name : str, optional
|
||
|
Name of the argument being converted, only used in the error message
|
||
|
|
||
|
Returns
|
||
|
-------
|
||
|
y : ``List[int]``
|
||
|
"""
|
||
|
if isinstance(x, Number):
|
||
|
x = (x,)
|
||
|
|
||
|
try:
|
||
|
x = [operator.index(a) for a in x]
|
||
|
except TypeError as e:
|
||
|
name = name or "value"
|
||
|
raise ValueError("{} must be a scalar or iterable of integers"
|
||
|
.format(name)) from e
|
||
|
|
||
|
return x
|
||
|
|
||
|
|
||
|
def _init_nd_shape_and_axes(x, shape, axes):
|
||
|
"""Handles shape and axes arguments for nd transforms"""
|
||
|
noshape = shape is None
|
||
|
noaxes = axes is None
|
||
|
|
||
|
if not noaxes:
|
||
|
axes = _iterable_of_int(axes, 'axes')
|
||
|
axes = [a + x.ndim if a < 0 else a for a in axes]
|
||
|
|
||
|
if any(a >= x.ndim or a < 0 for a in axes):
|
||
|
raise ValueError("axes exceeds dimensionality of input")
|
||
|
if len(set(axes)) != len(axes):
|
||
|
raise ValueError("all axes must be unique")
|
||
|
|
||
|
if not noshape:
|
||
|
shape = _iterable_of_int(shape, 'shape')
|
||
|
|
||
|
if axes and len(axes) != len(shape):
|
||
|
raise ValueError("when given, axes and shape arguments"
|
||
|
" have to be of the same length")
|
||
|
if noaxes:
|
||
|
if len(shape) > x.ndim:
|
||
|
raise ValueError("shape requires more axes than are present")
|
||
|
axes = range(x.ndim - len(shape), x.ndim)
|
||
|
|
||
|
shape = [x.shape[a] if s == -1 else s for s, a in zip(shape, axes)]
|
||
|
elif noaxes:
|
||
|
shape = list(x.shape)
|
||
|
axes = range(x.ndim)
|
||
|
else:
|
||
|
shape = [x.shape[a] for a in axes]
|
||
|
|
||
|
if any(s < 1 for s in shape):
|
||
|
raise ValueError(
|
||
|
"invalid number of data points ({0}) specified".format(shape))
|
||
|
|
||
|
return shape, axes
|
||
|
|
||
|
|
||
|
def _asfarray(x):
|
||
|
"""
|
||
|
Convert to array with floating or complex dtype.
|
||
|
|
||
|
float16 values are also promoted to float32.
|
||
|
"""
|
||
|
if not hasattr(x, "dtype"):
|
||
|
x = np.asarray(x)
|
||
|
|
||
|
if x.dtype == np.float16:
|
||
|
return np.asarray(x, np.float32)
|
||
|
elif x.dtype.kind not in 'fc':
|
||
|
return np.asarray(x, np.float64)
|
||
|
|
||
|
# Require native byte order
|
||
|
dtype = x.dtype.newbyteorder('=')
|
||
|
# Always align input
|
||
|
copy = not x.flags['ALIGNED']
|
||
|
return np.array(x, dtype=dtype, copy=copy)
|
||
|
|
||
|
def _datacopied(arr, original):
|
||
|
"""
|
||
|
Strict check for `arr` not sharing any data with `original`,
|
||
|
under the assumption that arr = asarray(original)
|
||
|
"""
|
||
|
if arr is original:
|
||
|
return False
|
||
|
if not isinstance(original, np.ndarray) and hasattr(original, '__array__'):
|
||
|
return False
|
||
|
return arr.base is None
|
||
|
|
||
|
|
||
|
def _fix_shape(x, shape, axes):
|
||
|
"""Internal auxiliary function for _raw_fft, _raw_fftnd."""
|
||
|
must_copy = False
|
||
|
|
||
|
# Build an nd slice with the dimensions to be read from x
|
||
|
index = [slice(None)]*x.ndim
|
||
|
for n, ax in zip(shape, axes):
|
||
|
if x.shape[ax] >= n:
|
||
|
index[ax] = slice(0, n)
|
||
|
else:
|
||
|
index[ax] = slice(0, x.shape[ax])
|
||
|
must_copy = True
|
||
|
|
||
|
index = tuple(index)
|
||
|
|
||
|
if not must_copy:
|
||
|
return x[index], False
|
||
|
|
||
|
s = list(x.shape)
|
||
|
for n, axis in zip(shape, axes):
|
||
|
s[axis] = n
|
||
|
|
||
|
z = np.zeros(s, x.dtype)
|
||
|
z[index] = x[index]
|
||
|
return z, True
|
||
|
|
||
|
|
||
|
def _fix_shape_1d(x, n, axis):
|
||
|
if n < 1:
|
||
|
raise ValueError(
|
||
|
"invalid number of data points ({0}) specified".format(n))
|
||
|
|
||
|
return _fix_shape(x, (n,), (axis,))
|
||
|
|
||
|
|
||
|
def _normalization(norm, forward):
|
||
|
"""Returns the pypocketfft normalization mode from the norm argument"""
|
||
|
|
||
|
if norm is None:
|
||
|
return 0 if forward else 2
|
||
|
|
||
|
if norm == 'ortho':
|
||
|
return 1
|
||
|
|
||
|
raise ValueError(
|
||
|
"Invalid norm value {}, should be None or \"ortho\".".format(norm))
|
||
|
|
||
|
|
||
|
def _workers(workers):
|
||
|
if workers is None:
|
||
|
return getattr(_config, 'default_workers', 1)
|
||
|
|
||
|
if workers < 0:
|
||
|
if workers >= -_cpu_count:
|
||
|
workers += 1 + _cpu_count
|
||
|
else:
|
||
|
raise ValueError("workers value out of range; got {}, must not be"
|
||
|
" less than {}".format(workers, -_cpu_count))
|
||
|
elif workers == 0:
|
||
|
raise ValueError("workers must not be zero")
|
||
|
|
||
|
return workers
|
||
|
|
||
|
|
||
|
@contextlib.contextmanager
|
||
|
def set_workers(workers):
|
||
|
"""Context manager for the default number of workers used in `scipy.fft`
|
||
|
|
||
|
Parameters
|
||
|
----------
|
||
|
workers : int
|
||
|
The default number of workers to use
|
||
|
|
||
|
Examples
|
||
|
--------
|
||
|
>>> from scipy import fft, signal
|
||
|
>>> x = np.random.randn(128, 64)
|
||
|
>>> with fft.set_workers(4):
|
||
|
... y = signal.fftconvolve(x, x)
|
||
|
|
||
|
"""
|
||
|
old_workers = get_workers()
|
||
|
_config.default_workers = _workers(operator.index(workers))
|
||
|
try:
|
||
|
yield
|
||
|
finally:
|
||
|
_config.default_workers = old_workers
|
||
|
|
||
|
|
||
|
def get_workers():
|
||
|
"""Returns the default number of workers within the current context
|
||
|
|
||
|
Examples
|
||
|
--------
|
||
|
>>> from scipy import fft
|
||
|
>>> fft.get_workers()
|
||
|
1
|
||
|
>>> with fft.set_workers(4):
|
||
|
... fft.get_workers()
|
||
|
4
|
||
|
"""
|
||
|
return getattr(_config, 'default_workers', 1)
|