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# cython: language_level=3
cimport cython
from cpython.object cimport PyObject
cimport numpy as np
from cpython.pycapsule cimport PyCapsule_IsValid, PyCapsule_GetPointer
from numpy.random cimport bitgen_t
from scipy._lib.ccallback cimport ccallback_t
from scipy._lib.messagestream cimport MessageStream
from .unuran cimport *
import warnings
import threading
import functools
from collections import namedtuple
import numpy as np
import scipy.stats as stats
from scipy.stats._distn_infrastructure import argsreduce, rv_frozen
from scipy._lib._util import check_random_state
import warnings
np.import_array()
__all__ = ['UNURANError', 'TransformedDensityRejection', 'DiscreteAliasUrn',
'NumericalInversePolynomial']
cdef extern from "Python.h":
PyObject *PyErr_Occurred()
void PyErr_Fetch(PyObject **ptype, PyObject **pvalue, PyObject **ptraceback)
void PyErr_Restore(PyObject *type, PyObject *value, PyObject *traceback)
# Internal API for handling Python callbacks.
# TODO: Maybe, support ``LowLevelCallable``s in the future?
cdef extern from "unuran_callback.h":
int init_unuran_callback(ccallback_t *callback, fcn) except -1
int release_unuran_callback(ccallback_t *callback) except -1
double pdf_thunk(double x, const unur_distr *distr) nogil
double dpdf_thunk(double x, const unur_distr *distr) nogil
double logpdf_thunk(double x, const unur_distr *distr) nogil
double cont_cdf_thunk(double x, const unur_distr *distr) nogil
double pmf_thunk(int x, const unur_distr *distr) nogil
double discr_cdf_thunk(int x, const unur_distr *distr) nogil
void error_handler(const char *objid, const char *file,
int line, const char *errortype,
int unur_errno, const char *reason) nogil
# https://stackoverflow.com/questions/5697479/how-can-a-defined-c-value-be-exposed-to-python-in-a-cython-module
cdef extern from "unuran.h":
cdef double UNUR_INFINITY
class UNURANError(RuntimeError):
"""Raised when an error occurs in the UNU.RAN library."""
pass
ctypedef double (*URNG_FUNCT)(void *) noexcept nogil
cdef object get_numpy_rng(object seed = None):
"""
Create a NumPy Generator object from a given seed.
Parameters
----------
seed : object, optional
Seed for the generator. If None, no seed is set. The seed can be
an integer, Generator, or RandomState.
Returns
-------
numpy_rng : object
An instance of NumPy's Generator class.
"""
seed = check_random_state(seed)
if isinstance(seed, np.random.RandomState):
return np.random.default_rng(seed._bit_generator)
return seed
@cython.final
cdef class _URNG:
"""
Build a UNU.RAN's uniform random number generator from a NumPy random
number generator.
Parameters
----------
numpy_rng : object
An instance of NumPy's Generator or RandomState class. i.e. a NumPy
random number generator.
"""
cdef object numpy_rng
cdef double[::1] qrvs_array
cdef size_t i
def __init__(self, numpy_rng):
self.numpy_rng = numpy_rng
@cython.boundscheck(False)
@cython.wraparound(False)
cdef double _next_qdouble(self) noexcept nogil:
self.i += 1
return self.qrvs_array[self.i-1]
cdef unur_urng * get_urng(self) except *:
"""
Get a ``unur_urng`` object from given ``numpy_rng``.
Returns
-------
unuran_urng : unur_urng *
A UNU.RAN uniform random number generator.
"""
cdef unur_urng *unuran_urng
cdef:
bitgen_t *numpy_urng
const char *capsule_name = "BitGenerator"
capsule = self.numpy_rng.bit_generator.capsule
if not PyCapsule_IsValid(capsule, capsule_name):
raise ValueError("Invalid pointer to anon_func_state.")
numpy_urng = <bitgen_t *> PyCapsule_GetPointer(capsule, capsule_name)
unuran_urng = unur_urng_new(numpy_urng.next_double,
<void *>(numpy_urng.state))
return unuran_urng
cdef unur_urng *get_qurng(self, size, qmc_engine) except *:
cdef unur_urng *unuran_urng
self.i = 0
self.qrvs_array = np.ascontiguousarray(
qmc_engine.random(size).ravel().astype(np.float64)
)
unuran_urng = unur_urng_new(<URNG_FUNCT>self._next_qdouble,
<void *>self)
return unuran_urng
# Module level lock. This is used to provide thread-safe error reporting.
# UNU.RAN has a thread-unsafe global FILE streams where errors are logged.
# To make it thread-safe, one can acquire a lock before calling
# `unur_set_stream` and release once the stream is not needed anymore.
cdef object _lock = threading.RLock()
cdef:
unur_urng *default_urng
object default_numpy_rng
_URNG _urng_builder
cdef object _setup_unuran():
"""
Sets the default UNU.RAN uniform random number generator and error
handler.
"""
global default_urng
global default_numpy_rng
global _urng_builder
default_numpy_rng = get_numpy_rng()
cdef MessageStream _messages = MessageStream()
_lock.acquire()
try:
unur_set_stream(_messages.handle)
# try to set a default URNG.
try:
_urng_builder = _URNG(default_numpy_rng)
default_urng = _urng_builder.get_urng()
if default_urng == NULL:
raise UNURANError(_messages.get())
except Exception as e:
msg = "Failed to initialize the default URNG."
raise RuntimeError(msg) from e
finally:
_lock.release()
unur_set_default_urng(default_urng)
unur_set_error_handler(error_handler)
_setup_unuran()
cdef dict _unpack_dist(object dist, str dist_type, list meths = None,
list optional_meths = None):
"""
Get the required methods/attributes from a Python class or object.
Parameters
----------
dist : object
An instance of a Python class or an object with required methods.
dist_type : str
Type of the distribution. "cont" for continuous distribution
and "discr" for discrete distribution.
meths : list
A list of methods to get from `dist`.
optional_meths : list, optional
A list of optional methods to be returned if found. No error
is raised if some of the methods in this list are not found.
Returns
-------
callbacks : dict
A dictionary of callbacks (methods found).
Raises
------
ValueError
A ValueError is raised in case some methods in the `meths` list
are not found.
"""
cdef dict callbacks = {}
if isinstance(dist, rv_frozen):
if isinstance(dist.dist, stats.rv_continuous):
class wrap_dist:
def __init__(self, dist):
self.dist = dist
(self.args, self.loc,
self.scale) = dist.dist._parse_args(*dist.args,
**dist.kwds)
self.support = dist.support
def pdf(self, x):
# some distributions require array inputs.
x = np.asarray((x-self.loc)/self.scale)
return max(0, self.dist.dist._pdf(x, *self.args)/self.scale)
def logpdf(self, x):
# some distributions require array inputs.
x = np.asarray((x-self.loc)/self.scale)
if self.pdf(x) > 0:
return self.dist.dist._logpdf(x, *self.args) - np.log(self.scale)
return -np.inf
def cdf(self, x):
x = np.asarray((x-self.loc)/self.scale)
res = self.dist.dist._cdf(x, *self.args)
if res < 0:
return 0
elif res > 1:
return 1
return res
elif isinstance(dist.dist, stats.rv_discrete):
class wrap_dist:
def __init__(self, dist):
self.dist = dist
(self.args, self.loc,
_) = dist.dist._parse_args(*dist.args,
**dist.kwds)
self.support = dist.support
def pmf(self, x):
# some distributions require array inputs.
x = np.asarray(x-self.loc)
return max(0, self.dist.dist._pmf(x, *self.args))
def cdf(self, x):
x = np.asarray(x-self.loc)
res = self.dist.dist._cdf(x, *self.args)
if res < 0:
return 0
elif res > 1:
return 1
return res
dist = wrap_dist(dist)
if meths is not None:
for meth in meths:
if hasattr(dist, meth):
callbacks[meth] = getattr(dist, meth)
else:
msg = f"`{meth}` required but not found."
raise ValueError(msg)
if optional_meths is not None:
for meth in optional_meths:
if hasattr(dist, meth):
callbacks[meth] = getattr(dist, meth)
return callbacks
cdef void _pack_distr(unur_distr *distr, dict callbacks) except *:
"""
Set the methods of a continuous or discrete distribution object
using a dictionary of callbacks.
Parameters
----------
distr : unur_distr *
A continuous or discrete distribution object.
callbacks : dict
A dictionary of callbacks.
"""
if unur_distr_is_cont(distr):
if "pdf" in callbacks:
unur_distr_cont_set_pdf(distr, pdf_thunk)
if "dpdf" in callbacks:
unur_distr_cont_set_dpdf(distr, dpdf_thunk)
if "cdf" in callbacks:
unur_distr_cont_set_cdf(distr, cont_cdf_thunk)
if "logpdf" in callbacks:
unur_distr_cont_set_logpdf(distr, logpdf_thunk)
else:
if "pmf" in callbacks:
unur_distr_discr_set_pmf(distr, pmf_thunk)
if "cdf" in callbacks:
unur_distr_discr_set_cdf(distr, discr_cdf_thunk)
def _validate_domain(domain, dist):
if domain is None and hasattr(dist, 'support'):
# if the distribution has a support method, use it
# to get the domain.
domain = dist.support()
if domain is not None:
# UNU.RAN doesn't recognize nans in the probability vector
# and throws an "unknown error". Hence, check for nans ourselves
if np.isnan(domain).any():
raise ValueError("`domain` must contain only non-nan values.")
# Length of the domain must be exactly 2.
if len(domain) != 2:
raise ValueError("`domain` must be a length 2 tuple.")
# Throw an error here if it can't be converted into a tuple.
domain = tuple(domain)
return domain
cdef double[::1] _validate_pv(pv) except *:
cdef double[::1] pv_view = None
if pv is not None:
# Make sure the PV is a contiguous array of doubles.
pv = pv_view = np.ascontiguousarray(pv, dtype=np.float64)
# Empty arrays not allowed.
if pv.size == 0:
raise ValueError("probability vector must contain at least "
"one element.")
# NaNs and infs not recognized by UNU.RAN so throw an error here
# only.
if not np.isfinite(pv).all():
raise ValueError("probability vector must contain only "
"finite / non-nan values.")
# This special case is not handled by UNU.RAN and it just throws
# an "unknown error".
if (pv == 0).all():
raise ValueError("probability vector must contain at least "
"one non-zero value.")
# return a contiguous memory view of the PV
return pv_view
def _validate_qmc_input(qmc_engine, d):
# Input validation for `qmc_engine` and `d`
# Error messages for invalid `d` are raised by QMCEngine
# we could probably use a stats.qmc.check_qrandom_state
if isinstance(qmc_engine, stats.qmc.QMCEngine):
if d is not None and qmc_engine.d != d:
message = "`d` must be consistent with dimension of `qmc_engine`."
raise ValueError(message)
d = qmc_engine.d if d is None else d
elif qmc_engine is None:
d = 1 if d is None else d
qmc_engine = stats.qmc.Halton(d)
else:
message = ("`qmc_engine` must be an instance of "
"`scipy.stats.qmc.QMCEngine` or `None`.")
raise ValueError(message)
return qmc_engine, d
cdef class Method:
"""
A base class for all the wrapped generators.
There are 6 basic functions of this base class:
* It provides a `_set_rng` method to initialize and set a `unur_gen`
object. It should be called during the setup stage in the `__cinit__`
method. As it uses MessageStream, the call must be protected under
the module-level lock.
* `_check_errorcode` must be called after calling a UNU.RAN function
that returns a error code. It raises an error if an error has
occurred in UNU.RAN.
* It implements the `rvs` public method for sampling. No child class
should override this method.
* Provides a `set_random_state` method to change the seed.
* Implements the __dealloc__ method. The child class must not override
this method.
* Implements __reduce__ method to allow pickling.
"""
cdef unur_distr *distr
cdef unur_par *par
cdef unur_gen *rng
cdef unur_urng *urng
cdef object numpy_rng
cdef _URNG _urng_builder
cdef object callbacks
cdef object _callback_wrapper
cdef MessageStream _messages
# save all the arguments to enable pickling
cdef object _kwargs
cdef inline void _check_errorcode(self, int errorcode) except *:
# check for non-zero errorcode
if errorcode != UNUR_SUCCESS:
msg = self._messages.get()
# the message must be non-empty whenever an error occurs in UNU.RAN.
# if the message is empty, means a warning was raised.
if msg:
raise UNURANError(msg)
cdef inline void _set_rng(self, object random_state) except *:
"""
Create a UNU.RAN random number generator.
Parameters
----------
random_state : object
Seed for the uniform random number generator. Can be a integer,
Generator, or RandomState.
"""
cdef ccallback_t callback
self.numpy_rng = get_numpy_rng(random_state)
self._urng_builder = _URNG(self.numpy_rng)
self.urng = self._urng_builder.get_urng()
if self.urng == NULL:
raise UNURANError(self._messages.get())
self._check_errorcode(unur_set_urng(self.par, self.urng))
has_callback_wrapper = (self._callback_wrapper is not None)
try:
if has_callback_wrapper:
init_unuran_callback(&callback, self._callback_wrapper)
self.rng = unur_init(self.par)
# set self.par = NULL because a call to `unur_init` destroys
# the parameter object. See "Creating a generator object" in
# http://statmath.wu.ac.at/software/unuran/doc/unuran.html#Concepts
self.par = NULL
if self.rng == NULL:
if PyErr_Occurred():
return
raise UNURANError(self._messages.get())
unur_distr_free(self.distr)
self.distr = NULL
finally:
if has_callback_wrapper:
release_unuran_callback(&callback)
@cython.boundscheck(False)
@cython.wraparound(False)
cdef inline void _rvs_cont(self, double[::1] out) except *:
"""
Sample random variates from a continuous distribution.
Parameters
----------
out : double[::1]
A memory view of size ``size`` to store the result.
"""
cdef:
ccallback_t callback
unur_gen *rng = self.rng
size_t i
size_t size = len(out)
PyObject *type
PyObject *value
PyObject *traceback
has_callback_wrapper = (self._callback_wrapper is not None)
error = 0
_lock.acquire()
try:
self._messages.clear()
unur_set_stream(self._messages.handle)
if has_callback_wrapper:
init_unuran_callback(&callback, self._callback_wrapper)
for i in range(size):
out[i] = unur_sample_cont(rng)
if PyErr_Occurred():
error = 1
return
msg = self._messages.get()
if msg:
raise UNURANError(msg)
finally:
if error:
PyErr_Fetch(&type, &value, &traceback)
_lock.release()
if error:
PyErr_Restore(type, value, traceback)
if has_callback_wrapper:
release_unuran_callback(&callback)
@cython.boundscheck(False)
@cython.wraparound(False)
cdef inline void _rvs_discr(self, int[::1] out) except *:
"""
Sample random variates from a discrete distribution.
Parameters
----------
out : int[::1]
A memory view of size ``size`` to store the result.
"""
cdef:
ccallback_t callback
unur_gen *rng = self.rng
size_t i
size_t size = len(out)
PyObject *type
PyObject *value
PyObject *traceback
has_callback_wrapper = (self._callback_wrapper is not None)
error = 0
_lock.acquire()
try:
self._messages.clear()
unur_set_stream(self._messages.handle)
if has_callback_wrapper:
init_unuran_callback(&callback, self._callback_wrapper)
for i in range(size):
out[i] = unur_sample_discr(rng)
if PyErr_Occurred():
error = 1
return
msg = self._messages.get()
if msg:
raise UNURANError(msg)
finally:
if error:
PyErr_Fetch(&type, &value, &traceback)
_lock.release()
if error:
PyErr_Restore(type, value, traceback)
if has_callback_wrapper:
release_unuran_callback(&callback)
def rvs(self, size=None, random_state=None):
"""
rvs(size=None, random_state=None)
Sample from the distribution.
Parameters
----------
size : int or tuple, optional
The shape of samples. Default is ``None`` in which case a scalar
sample is returned.
random_state : {None, int, `numpy.random.Generator`,
`numpy.random.RandomState`}, optional
A NumPy random number generator or seed for the underlying NumPy random
number generator used to generate the stream of uniform random numbers.
If `random_state` is None (or `np.random`), `random_state` provided during
initialization is used.
If `random_state` is an int, a new ``RandomState`` instance is used,
seeded with `random_state`.
If `random_state` is already a ``Generator`` or ``RandomState`` instance then
that instance is used.
Returns
-------
rvs : array_like
A NumPy array of random variates.
"""
cdef double[::1] out_cont
cdef int[::1] out_discr
N = 1 if size is None else np.prod(size)
prev_random_state = self.numpy_rng
if random_state is not None:
self.set_random_state(random_state)
if unur_distr_is_cont(unur_get_distr(self.rng)):
out_cont = np.empty(N, dtype=np.float64)
self._rvs_cont(out_cont)
if random_state is not None:
self.set_random_state(prev_random_state)
if size is None:
return out_cont[0]
return np.asarray(out_cont).reshape(size)
elif unur_distr_is_discr(unur_get_distr(self.rng)):
out_discr = np.empty(N, dtype=np.int32)
self._rvs_discr(out_discr)
if random_state is not None:
self.set_random_state(prev_random_state)
if size is None:
return out_discr[0]
return np.asarray(out_discr).reshape(size)
else:
raise NotImplementedError("only univariate continuous and "
"discrete distributions supported")
def set_random_state(self, random_state=None):
"""
set_random_state(random_state=None)
Set the underlying uniform random number generator.
Parameters
----------
random_state : {None, int, `numpy.random.Generator`,
`numpy.random.RandomState`}, optional
A NumPy random number generator or seed for the underlying NumPy random
number generator used to generate the stream of uniform random numbers.
If `random_state` is None (or `np.random`), the `numpy.random.RandomState`
singleton is used.
If `random_state` is an int, a new ``RandomState`` instance is used,
seeded with `random_state`.
If `random_state` is already a ``Generator`` or ``RandomState`` instance then
that instance is used.
"""
self.numpy_rng = get_numpy_rng(random_state)
_lock.acquire()
try:
self._messages.clear()
unur_set_stream(self._messages.handle)
unur_urng_free(self.urng)
self._urng_builder = _URNG(self.numpy_rng)
self.urng = self._urng_builder.get_urng()
if self.urng == NULL:
raise UNURANError(self._messages.get())
unur_chg_urng(self.rng, self.urng)
finally:
_lock.release()
@cython.final
def __dealloc__(self):
if self.distr != NULL:
unur_distr_free(self.distr)
self.distr = NULL
if self.par != NULL:
unur_par_free(self.par)
self.par = NULL
if self.rng != NULL:
unur_free(self.rng)
self.rng = NULL
if self.urng != NULL:
unur_urng_free(self.urng)
self.urng = NULL
# Pickling support
@cython.final
def __reduce__(self):
klass = functools.partial(self.__class__, **self._kwargs)
return (klass, ())
cdef class TransformedDensityRejection(Method):
r"""
TransformedDensityRejection(dist, *, mode=None, center=None, domain=None, c=-0.5, construction_points=30, use_dars=True, max_squeeze_hat_ratio=0.99, random_state=None)
Transformed Density Rejection (TDR) Method.
TDR is an acceptance/rejection method that uses the concavity of a
transformed density to construct hat function and squeezes automatically.
Most universal algorithms are very slow compared to algorithms that are
specialized to that distribution. Algorithms that are fast have a slow
setup and require large tables. The aim of this universal method is to
provide an algorithm that is not too slow and needs only a short setup.
This method can be applied to univariate and unimodal continuous
distributions with T-concave density function. See [1]_ and [2]_ for
more details.
Parameters
----------
dist : object
An instance of a class with ``pdf`` and ``dpdf`` methods.
* ``pdf``: PDF of the distribution. The signature of the PDF is
expected to be: ``def pdf(self, x: float) -> float``. i.e.
the PDF should accept a Python float and
return a Python float. It doesn't need to integrate to 1 i.e.
the PDF doesn't need to be normalized.
* ``dpdf``: Derivative of the PDF w.r.t x (i.e. the variate). Must
have the same signature as the PDF.
mode : float, optional
(Exact) Mode of the distribution. Default is ``None``.
center : float, optional
Approximate location of the mode or the mean of the distribution.
This location provides some information about the main part of the
PDF and is used to avoid numerical problems. Default is ``None``.
domain : list or tuple of length 2, optional
The support of the distribution.
Default is ``None``. When ``None``:
* If a ``support`` method is provided by the distribution object
`dist`, it is used to set the domain of the distribution.
* Otherwise the support is assumed to be :math:`(-\infty, \infty)`.
c : {-0.5, 0.}, optional
Set parameter ``c`` for the transformation function ``T``. The
default is -0.5. The transformation of the PDF must be concave in
order to construct the hat function. Such a PDF is called T-concave.
Currently the following transformations are supported:
.. math::
c = 0.: T(x) &= \log(x)\\
c = -0.5: T(x) &= \frac{1}{\sqrt{x}} \text{ (Default)}
construction_points : int or array_like, optional
If an integer, it defines the number of construction points. If it
is array-like, the elements of the array are used as construction
points. Default is 30.
use_dars : bool, optional
If True, "derandomized adaptive rejection sampling" (DARS) is used
in setup. See [1]_ for the details of the DARS algorithm. Default
is True.
max_squeeze_hat_ratio : float, optional
Set upper bound for the ratio (area below squeeze) / (area below hat).
It must be a number between 0 and 1. Default is 0.99.
random_state : {None, int, `numpy.random.Generator`,
`numpy.random.RandomState`}, optional
A NumPy random number generator or seed for the underlying NumPy random
number generator used to generate the stream of uniform random numbers.
If `random_state` is None (or `np.random`), the `numpy.random.RandomState`
singleton is used.
If `random_state` is an int, a new ``RandomState`` instance is used,
seeded with `random_state`.
If `random_state` is already a ``Generator`` or ``RandomState`` instance then
that instance is used.
References
----------
.. [1] UNU.RAN reference manual, Section 5.3.16,
"TDR - Transformed Density Rejection",
http://statmath.wu.ac.at/software/unuran/doc/unuran.html#TDR
.. [2] Hörmann, Wolfgang. "A rejection technique for sampling from
T-concave distributions." ACM Transactions on Mathematical
Software (TOMS) 21.2 (1995): 182-193
.. [3] W.R. Gilks and P. Wild (1992). Adaptive rejection sampling for
Gibbs sampling, Applied Statistics 41, pp. 337-348.
Examples
--------
>>> from scipy.stats.sampling import TransformedDensityRejection
>>> import numpy as np
Suppose we have a density:
.. math::
f(x) = \begin{cases}
1 - x^2, & -1 \leq x \leq 1 \\
0, & \text{otherwise}
\end{cases}
The derivative of this density function is:
.. math::
\frac{df(x)}{dx} = \begin{cases}
-2x, & -1 \leq x \leq 1 \\
0, & \text{otherwise}
\end{cases}
Notice that the PDF doesn't integrate to 1. As this is a rejection based
method, we need not have a normalized PDF. To initialize the generator,
we can use:
>>> urng = np.random.default_rng()
>>> class MyDist:
... def pdf(self, x):
... return 1-x*x
... def dpdf(self, x):
... return -2*x
...
>>> dist = MyDist()
>>> rng = TransformedDensityRejection(dist, domain=(-1, 1),
... random_state=urng)
Domain can be very useful to truncate the distribution but to avoid passing
it every time to the constructor, a default domain can be set by providing a
`support` method in the distribution object (`dist`):
>>> class MyDist:
... def pdf(self, x):
... return 1-x*x
... def dpdf(self, x):
... return -2*x
... def support(self):
... return (-1, 1)
...
>>> dist = MyDist()
>>> rng = TransformedDensityRejection(dist, random_state=urng)
Now, we can use the `rvs` method to generate samples from the distribution:
>>> rvs = rng.rvs(1000)
We can check that the samples are from the given distribution by visualizing
its histogram:
>>> import matplotlib.pyplot as plt
>>> x = np.linspace(-1, 1, 1000)
>>> fx = 3/4 * dist.pdf(x) # 3/4 is the normalizing constant
>>> plt.plot(x, fx, 'r-', lw=2, label='true distribution')
>>> plt.hist(rvs, bins=20, density=True, alpha=0.8, label='random variates')
>>> plt.xlabel('x')
>>> plt.ylabel('PDF(x)')
>>> plt.title('Transformed Density Rejection Samples')
>>> plt.legend()
>>> plt.show()
"""
cdef double[::1] construction_points_array
def __cinit__(self,
dist,
*,
mode=None,
center=None,
domain=None,
c=-0.5,
construction_points=30,
use_dars=True,
max_squeeze_hat_ratio=0.99,
random_state=None):
(domain, c, construction_points) = self._validate_args(dist, domain, c, construction_points)
# save all the arguments for pickling support
self._kwargs = {
'dist': dist,
'mode': mode,
'center': center,
'domain': domain,
'c': c,
'construction_points': construction_points,
'use_dars': use_dars,
'max_squeeze_hat_ratio': max_squeeze_hat_ratio,
'random_state': random_state
}
self.callbacks = _unpack_dist(dist, "cont", meths=["pdf", "dpdf"])
def _callback_wrapper(x, name):
return self.callbacks[name](x)
self._callback_wrapper = _callback_wrapper
self._messages = MessageStream()
_lock.acquire()
try:
unur_set_stream(self._messages.handle)
self.distr = unur_distr_cont_new()
if self.distr == NULL:
raise UNURANError(self._messages.get())
_pack_distr(self.distr, self.callbacks)
if domain is not None:
self._check_errorcode(unur_distr_cont_set_domain(self.distr, domain[0],
domain[1]))
if mode is not None:
self._check_errorcode(unur_distr_cont_set_mode(self.distr, mode))
if center is not None:
self._check_errorcode(unur_distr_cont_set_center(self.distr, center))
self.par = unur_tdr_new(self.distr)
if self.par == NULL:
raise UNURANError(self._messages.get())
self._check_errorcode(unur_tdr_set_c(self.par, c))
if self.construction_points_array is None:
self._check_errorcode(unur_tdr_set_cpoints(self.par, construction_points, NULL))
else:
self._check_errorcode(unur_tdr_set_cpoints(self.par, len(self.construction_points_array),
&self.construction_points_array[0]))
# PS variant is the default in UNU.RAN
self._check_errorcode(unur_tdr_set_variant_ps(self.par))
self._check_errorcode(unur_tdr_set_usedars(self.par, use_dars))
self._check_errorcode(unur_tdr_set_max_sqhratio(self.par, max_squeeze_hat_ratio))
# the parameter max_intervals is not part of the SciPy API
# UNU.RAN default is 100, we use a higher value to avoid problems
# if max_squeeze_hat_ratio is increased
self._check_errorcode(unur_tdr_set_max_intervals(self.par, 10000))
self._set_rng(random_state)
finally:
_lock.release()
cdef object _validate_args(self, dist, domain, c, construction_points):
domain = _validate_domain(domain, dist)
if c not in {-0.5, 0.}:
raise ValueError("`c` must either be -0.5 or 0.")
if not np.isscalar(construction_points):
self.construction_points_array = np.ascontiguousarray(construction_points,
dtype=np.float64)
if len(self.construction_points_array) == 0:
raise ValueError("`construction_points` must either be a scalar or a "
"non-empty array.")
else:
self.construction_points_array = None
if (construction_points <= 0 or
construction_points != int(construction_points)):
raise ValueError("`construction_points` must be a positive integer.")
return domain, c, construction_points
@property
def squeeze_hat_ratio(self):
"""
Get the current ratio (area below squeeze) / (area below hat) for the
generator.
"""
return unur_tdr_get_sqhratio(self.rng)
@property
def hat_area(self):
"""Get the area below the hat for the generator."""
return unur_tdr_get_hatarea(self.rng)
@property
def squeeze_area(self):
"""Get the area below the squeeze for the generator."""
return unur_tdr_get_squeezearea(self.rng)
@cython.boundscheck(False)
@cython.wraparound(False)
cdef inline void _ppf_hat(self, const double *u, double *out, size_t N) except *:
cdef:
size_t i
for i in range(N):
out[i] = unur_tdr_eval_invcdfhat(self.rng, u[i], NULL, NULL, NULL)
def ppf_hat(self, u):
"""
ppf_hat(u)
Evaluate the inverse of the CDF of the hat distribution at `u`.
Parameters
----------
u : array_like
An array of percentiles
Returns
-------
ppf_hat : array_like
Array of quantiles corresponding to the given percentiles.
Examples
--------
>>> from scipy.stats.sampling import TransformedDensityRejection
>>> from scipy.stats import norm
>>> import numpy as np
>>> from math import exp
>>>
>>> class MyDist:
... def pdf(self, x):
... return exp(-0.5 * x**2)
... def dpdf(self, x):
... return -x * exp(-0.5 * x**2)
...
>>> dist = MyDist()
>>> rng = TransformedDensityRejection(dist)
>>>
>>> rng.ppf_hat(0.5)
-0.00018050266342393984
>>> norm.ppf(0.5)
0.0
>>> u = np.linspace(0, 1, num=1000)
>>> ppf_hat = rng.ppf_hat(u)
"""
u = np.asarray(u, dtype='d')
oshape = u.shape
u = u.ravel()
# UNU.RAN fills in ends of the support when u < 0 or u > 1 while
# SciPy fills in nans. Prefer SciPy behaviour.
cond0 = 0 <= u
cond1 = u <= 1
cond2 = cond0 & cond1
goodu = argsreduce(cond2, u)[0]
out = np.empty_like(u)
cdef double[::1] u_view = np.ascontiguousarray(goodu)
cdef double[::1] goodout = np.empty_like(u_view)
if cond2.any():
self._ppf_hat(&u_view[0], &goodout[0], len(goodu))
np.place(out, cond2, goodout)
np.place(out, ~cond2, np.nan)
return np.asarray(out).reshape(oshape)[()]
cdef class SimpleRatioUniforms(Method):
r"""
SimpleRatioUniforms(dist, *, mode=None, pdf_area=1, domain=None, cdf_at_mode=None, random_state=None)
Simple Ratio-of-Uniforms (SROU) Method.
SROU is based on the ratio-of-uniforms method that uses universal inequalities for
constructing a (universal) bounding rectangle. It works for T-concave distributions
with ``T(x) = -1/sqrt(x)``. The main advantage of the method is a fast setup. This
can be beneficial if one repeatedly needs to generate small to moderate samples of
a distribution with different shape parameters. In such a situation, the setup step of
`NumericalInverseHermite` or `NumericalInversePolynomial` will lead to poor performance.
Parameters
----------
dist : object
An instance of a class with ``pdf`` method.
* ``pdf``: PDF of the distribution. The signature of the PDF is
expected to be: ``def pdf(self, x: float) -> float``. i.e.
the PDF should accept a Python float and
return a Python float. It doesn't need to integrate to 1 i.e.
the PDF doesn't need to be normalized. If not normalized, `pdf_area`
should be set to the area under the PDF.
mode : float, optional
(Exact) Mode of the distribution. When the mode is ``None``, a slow
numerical routine is used to approximate it. Default is ``None``.
pdf_area : float, optional
Area under the PDF. Optionally, an upper bound to the area under
the PDF can be passed at the cost of increased rejection constant.
Default is 1.
domain : list or tuple of length 2, optional
The support of the distribution.
Default is ``None``. When ``None``:
* If a ``support`` method is provided by the distribution object
`dist`, it is used to set the domain of the distribution.
* Otherwise the support is assumed to be :math:`(-\infty, \infty)`.
cdf_at_mode : float, optional
CDF at the mode. It can be given to increase the performance of the
algorithm. The rejection constant is halfed when CDF at mode is given.
Default is ``None``.
random_state : {None, int, `numpy.random.Generator`,
`numpy.random.RandomState`}, optional
A NumPy random number generator or seed for the underlying NumPy random
number generator used to generate the stream of uniform random numbers.
If `random_state` is None (or `np.random`), the `numpy.random.RandomState`
singleton is used.
If `random_state` is an int, a new ``RandomState`` instance is used,
seeded with `random_state`.
If `random_state` is already a ``Generator`` or ``RandomState`` instance then
that instance is used.
References
----------
.. [1] UNU.RAN reference manual, Section 5.3.16,
"SROU - Simple Ratio-of-Uniforms method",
http://statmath.wu.ac.at/software/unuran/doc/unuran.html#SROU
.. [2] Leydold, Josef. "A simple universal generator for continuous and
discrete univariate T-concave distributions." ACM Transactions on
Mathematical Software (TOMS) 27.1 (2001): 66-82
.. [3] Leydold, Josef. "Short universal generators via generalized ratio-of-uniforms
method." Mathematics of Computation 72.243 (2003): 1453-1471
Examples
--------
>>> from scipy.stats.sampling import SimpleRatioUniforms
>>> import numpy as np
Suppose we have the normal distribution:
>>> class StdNorm:
... def pdf(self, x):
... return np.exp(-0.5 * x**2)
Notice that the PDF doesn't integrate to 1. We can either pass the exact
area under the PDF during initialization of the generator or an upper
bound to the exact area under the PDF. Also, it is recommended to pass
the mode of the distribution to speed up the setup:
>>> urng = np.random.default_rng()
>>> dist = StdNorm()
>>> rng = SimpleRatioUniforms(dist, mode=0,
... pdf_area=np.sqrt(2*np.pi),
... random_state=urng)
Now, we can use the `rvs` method to generate samples from the distribution:
>>> rvs = rng.rvs(10)
If the CDF at mode is available, it can be set to improve the performance of `rvs`:
>>> from scipy.stats import norm
>>> rng = SimpleRatioUniforms(dist, mode=0,
... pdf_area=np.sqrt(2*np.pi),
... cdf_at_mode=norm.cdf(0),
... random_state=urng)
>>> rvs = rng.rvs(1000)
We can check that the samples are from the given distribution by visualizing
its histogram:
>>> import matplotlib.pyplot as plt
>>> x = np.linspace(rvs.min()-0.1, rvs.max()+0.1, 1000)
>>> fx = 1/np.sqrt(2*np.pi) * dist.pdf(x)
>>> fig, ax = plt.subplots()
>>> ax.plot(x, fx, 'r-', lw=2, label='true distribution')
>>> ax.hist(rvs, bins=10, density=True, alpha=0.8, label='random variates')
>>> ax.set_xlabel('x')
>>> ax.set_ylabel('PDF(x)')
>>> ax.set_title('Simple Ratio-of-Uniforms Samples')
>>> ax.legend()
>>> plt.show()
"""
def __cinit__(self,
dist,
*,
mode=None,
pdf_area=1,
domain=None,
cdf_at_mode=None,
random_state=None):
(domain, pdf_area) = self._validate_args(dist, domain, pdf_area)
# save all the arguments for pickling support
self._kwargs = {
'dist': dist,
'mode': mode,
'pdf_area': pdf_area,
'domain': domain,
'cdf_at_mode': cdf_at_mode,
'random_state': random_state
}
self.callbacks = _unpack_dist(dist, "cont", meths=["pdf"])
def _callback_wrapper(x, name):
return self.callbacks[name](x)
self._callback_wrapper = _callback_wrapper
self._messages = MessageStream()
_lock.acquire()
try:
unur_set_stream(self._messages.handle)
self.distr = unur_distr_cont_new()
if self.distr == NULL:
raise UNURANError(self._messages.get())
_pack_distr(self.distr, self.callbacks)
if domain is not None:
self._check_errorcode(unur_distr_cont_set_domain(self.distr, domain[0],
domain[1]))
if mode is not None:
self._check_errorcode(unur_distr_cont_set_mode(self.distr, mode))
self._check_errorcode(unur_distr_cont_set_pdfarea(self.distr, pdf_area))
self.par = unur_srou_new(self.distr)
if self.par == NULL:
raise UNURANError(self._messages.get())
if cdf_at_mode is not None:
self._check_errorcode(unur_srou_set_cdfatmode(self.par, cdf_at_mode))
# Always use squeeze when CDF at mode is given to improve performance
self._check_errorcode(unur_srou_set_usesqueeze(self.par, True))
self._set_rng(random_state)
finally:
_lock.release()
cdef object _validate_args(self, dist, domain, pdf_area):
# validate args
domain = _validate_domain(domain, dist)
if pdf_area < 0:
raise ValueError("`pdf_area` must be > 0")
return domain, pdf_area
UError = namedtuple('UError', ['max_error', 'mean_absolute_error'])
cdef class NumericalInversePolynomial(Method):
"""
NumericalInversePolynomial(dist, *, mode=None, center=None, domain=None, order=5, u_resolution=1e-10, random_state=None)
Polynomial interpolation based INVersion of CDF (PINV).
PINV is a variant of numerical inversion, where the inverse CDF is approximated
using Newton's interpolating formula. The interval ``[0,1]`` is split into several
subintervals. In each of these, the inverse CDF is constructed at nodes ``(CDF(x),x)``
for some points ``x`` in this subinterval. If the PDF is given, then the CDF is
computed numerically from the given PDF using adaptive Gauss-Lobatto integration with
5 points. Subintervals are split until the requested accuracy goal is reached.
The method is not exact, as it only produces random variates of the approximated
distribution. Nevertheless, the maximal tolerated approximation error can be set to
be the resolution (but, of course, is bounded by the machine precision). We use the
u-error ``|U - CDF(X)|`` to measure the error where ``X`` is the approximate
percentile corresponding to the quantile ``U`` i.e. ``X = approx_ppf(U)``. We call
the maximal tolerated u-error the u-resolution of the algorithm.
Both the order of the interpolating polynomial and the u-resolution can be selected.
Note that very small values of the u-resolution are possible but increase the cost
for the setup step.
The interpolating polynomials have to be computed in a setup step. However, it only
works for distributions with bounded domain; for distributions with unbounded domain
the tails are cut off such that the probability for the tail regions is small compared
to the given u-resolution.
The construction of the interpolation polynomial only works when the PDF is unimodal
or when the PDF does not vanish between two modes.
There are some restrictions for the given distribution:
* The support of the distribution (i.e., the region where the PDF is strictly
positive) must be connected. In practice this means, that the region where PDF
is "not too small" must be connected. Unimodal densities satisfy this condition.
If this condition is violated then the domain of the distribution might be
truncated.
* When the PDF is integrated numerically, then the given PDF must be continuous
and should be smooth.
* The PDF must be bounded.
* The algorithm has problems when the distribution has heavy tails (as then the
inverse CDF becomes very steep at 0 or 1) and the requested u-resolution is
very small. E.g., the Cauchy distribution is likely to show this problem when
the requested u-resolution is less then 1.e-12.
Parameters
----------
dist : object
An instance of a class with a ``pdf`` or ``logpdf`` method,
optionally a ``cdf`` method.
* ``pdf``: PDF of the distribution. The signature of the PDF is expected to be:
``def pdf(self, x: float) -> float``, i.e., the PDF should accept a Python
float and return a Python float. It doesn't need to integrate to 1,
i.e., the PDF doesn't need to be normalized. This method is optional,
but either ``pdf`` or ``logpdf`` need to be specified. If both are given,
``logpdf`` is used.
* ``logpdf``: The log of the PDF of the distribution. The signature is
the same as for ``pdf``. Similarly, log of the normalization constant
of the PDF can be ignored. This method is optional, but either ``pdf`` or
``logpdf`` need to be specified. If both are given, ``logpdf`` is used.
* ``cdf``: CDF of the distribution. This method is optional. If provided, it
enables the calculation of "u-error". See `u_error`. Must have the same
signature as the PDF.
mode : float, optional
(Exact) Mode of the distribution. Default is ``None``.
center : float, optional
Approximate location of the mode or the mean of the distribution. This location
provides some information about the main part of the PDF and is used to avoid
numerical problems. Default is ``None``.
domain : list or tuple of length 2, optional
The support of the distribution.
Default is ``None``. When ``None``:
* If a ``support`` method is provided by the distribution object
`dist`, it is used to set the domain of the distribution.
* Otherwise the support is assumed to be :math:`(-\infty, \infty)`.
order : int, optional
Order of the interpolating polynomial. Valid orders are between 3 and 17.
Higher orders result in fewer intervals for the approximations. Default
is 5.
u_resolution : float, optional
Set maximal tolerated u-error. Values of u_resolution must at least 1.e-15 and
1.e-5 at most. Notice that the resolution of most uniform random number sources
is 2-32= 2.3e-10. Thus a value of 1.e-10 leads to an inversion algorithm that
could be called exact. For most simulations slightly bigger values for the
maximal error are enough as well. Default is 1e-10.
random_state : {None, int, `numpy.random.Generator`,
`numpy.random.RandomState`}, optional
A NumPy random number generator or seed for the underlying NumPy random
number generator used to generate the stream of uniform random numbers.
If `random_state` is None (or `np.random`), the `numpy.random.RandomState`
singleton is used.
If `random_state` is an int, a new ``RandomState`` instance is used,
seeded with `random_state`.
If `random_state` is already a ``Generator`` or ``RandomState`` instance then
that instance is used.
References
----------
.. [1] Derflinger, Gerhard, Wolfgang Hörmann, and Josef Leydold. "Random variate
generation by numerical inversion when only the density is known." ACM
Transactions on Modeling and Computer Simulation (TOMACS) 20.4 (2010): 1-25.
.. [2] UNU.RAN reference manual, Section 5.3.12,
"PINV - Polynomial interpolation based INVersion of CDF",
https://statmath.wu.ac.at/software/unuran/doc/unuran.html#PINV
Examples
--------
>>> from scipy.stats.sampling import NumericalInversePolynomial
>>> from scipy.stats import norm
>>> import numpy as np
To create a generator to sample from the standard normal distribution, do:
>>> class StandardNormal:
... def pdf(self, x):
... return np.exp(-0.5 * x*x)
...
>>> dist = StandardNormal()
>>> urng = np.random.default_rng()
>>> rng = NumericalInversePolynomial(dist, random_state=urng)
Once a generator is created, samples can be drawn from the distribution by calling
the `rvs` method:
>>> rng.rvs()
-1.5244996276336318
To check that the random variates closely follow the given distribution, we can
look at it's histogram:
>>> import matplotlib.pyplot as plt
>>> rvs = rng.rvs(10000)
>>> x = np.linspace(rvs.min()-0.1, rvs.max()+0.1, 1000)
>>> fx = norm.pdf(x)
>>> plt.plot(x, fx, 'r-', lw=2, label='true distribution')
>>> plt.hist(rvs, bins=20, density=True, alpha=0.8, label='random variates')
>>> plt.xlabel('x')
>>> plt.ylabel('PDF(x)')
>>> plt.title('Numerical Inverse Polynomial Samples')
>>> plt.legend()
>>> plt.show()
It is possible to estimate the u-error of the approximated PPF if the exact
CDF is available during setup. To do so, pass a `dist` object with exact CDF of
the distribution during initialization:
>>> from scipy.special import ndtr
>>> class StandardNormal:
... def pdf(self, x):
... return np.exp(-0.5 * x*x)
... def cdf(self, x):
... return ndtr(x)
...
>>> dist = StandardNormal()
>>> urng = np.random.default_rng()
>>> rng = NumericalInversePolynomial(dist, random_state=urng)
Now, the u-error can be estimated by calling the `u_error` method. It runs a
Monte-Carlo simulation to estimate the u-error. By default, 100000 samples are
used. To change this, you can pass the number of samples as an argument:
>>> rng.u_error(sample_size=1000000) # uses one million samples
UError(max_error=8.785994154436594e-11, mean_absolute_error=2.930890027826552e-11)
This returns a namedtuple which contains the maximum u-error and the mean
absolute u-error.
The u-error can be reduced by decreasing the u-resolution (maximum allowed u-error):
>>> urng = np.random.default_rng()
>>> rng = NumericalInversePolynomial(dist, u_resolution=1.e-12, random_state=urng)
>>> rng.u_error(sample_size=1000000)
UError(max_error=9.07496300328603e-13, mean_absolute_error=3.5255644517257716e-13)
Note that this comes at the cost of increased setup time.
The approximated PPF can be evaluated by calling the `ppf` method:
>>> rng.ppf(0.975)
1.9599639857012559
>>> norm.ppf(0.975)
1.959963984540054
Since the PPF of the normal distribution is available as a special function, we
can also check the x-error, i.e. the difference between the approximated PPF and
exact PPF::
>>> import matplotlib.pyplot as plt
>>> u = np.linspace(0.01, 0.99, 1000)
>>> approxppf = rng.ppf(u)
>>> exactppf = norm.ppf(u)
>>> error = np.abs(exactppf - approxppf)
>>> plt.plot(u, error)
>>> plt.xlabel('u')
>>> plt.ylabel('error')
>>> plt.title('Error between exact and approximated PPF (x-error)')
>>> plt.show()
"""
def __cinit__(self,
dist,
*,
mode=None,
center=None,
domain=None,
order=5,
u_resolution=1e-10,
random_state=None):
(domain, order, u_resolution) = self._validate_args(
dist, domain, order, u_resolution
)
# save all the arguments for pickling support
self._kwargs = {
'dist': dist,
'center': center,
'domain': domain,
'order': order,
'u_resolution': u_resolution,
'random_state': random_state
}
# either logpdf or pdf are required: use meths = None and check separately
self.callbacks = _unpack_dist(dist, "cont", meths=None, optional_meths=["cdf", "pdf", "logpdf"])
if not ("pdf" in self.callbacks or "logpdf" in self.callbacks):
msg = ("Either of the methods `pdf` or `logpdf` must be specified "
"for the distribution object `dist`.")
raise ValueError(msg)
def _callback_wrapper(x, name):
return self.callbacks[name](x)
self._callback_wrapper = _callback_wrapper
self._messages = MessageStream()
_lock.acquire()
try:
unur_set_stream(self._messages.handle)
self.distr = unur_distr_cont_new()
if self.distr == NULL:
raise UNURANError(self._messages.get())
_pack_distr(self.distr, self.callbacks)
if domain is not None:
self._check_errorcode(unur_distr_cont_set_domain(self.distr, domain[0],
domain[1]))
if mode is not None:
self._check_errorcode(unur_distr_cont_set_mode(self.distr, mode))
if center is not None:
self._check_errorcode(unur_distr_cont_set_center(self.distr, center))
self.par = unur_pinv_new(self.distr)
if self.par == NULL:
raise UNURANError(self._messages.get())
self._check_errorcode(unur_pinv_set_order(self.par, order))
self._check_errorcode(unur_pinv_set_u_resolution(self.par, u_resolution))
# max_intervals is not part of the API. set it to the maximum
# allowed value in UNU.RAN which is 1_000_000
self._check_errorcode(unur_pinv_set_max_intervals(self.par, 1000000))
# always keep CDF in SciPy while UNU.RAN default is False
self._check_errorcode(unur_pinv_set_keepcdf(self.par, 1))
self._set_rng(random_state)
finally:
_lock.release()
cdef object _validate_args(self, dist, domain, order, u_resolution):
domain = _validate_domain(domain, dist)
# UNU.RAN raises warning and sets a default value. Prefer an error instead.
if not (3 <= order <= 17 and int(order) == order):
raise ValueError("`order` must be an integer in the range [3, 17].")
# UNU.RAN seg faults when u_resolution is not finite. And throws a warning if
# it is not in the range [1.e-15, 1.e-5]. Prefer an error instead.
if not (1e-15 <= u_resolution <= 1e-5):
raise ValueError("`u_resolution` must be between 1e-15 and 1e-5.")
return (domain, order, u_resolution)
@property
def intervals(self):
"""Get the number of intervals used in the computation."""
return unur_pinv_get_n_intervals(self.rng)
@cython.boundscheck(False)
@cython.wraparound(False)
cdef inline void _cdf(self, const double *x, double *out, size_t N) except *:
cdef:
size_t i
ccallback_t callback
PyObject *type
PyObject *value
PyObject *traceback
error = 0
_lock.acquire()
try:
self._messages.clear()
unur_set_stream(self._messages.handle)
init_unuran_callback(&callback, self._callback_wrapper)
for i in range(N):
out[i] = unur_pinv_eval_approxcdf(self.rng, x[i])
if PyErr_Occurred():
error = 1
return
if out[i] == UNUR_INFINITY or out[i] == -UNUR_INFINITY:
raise UNURANError(self._messages.get())
finally:
if error:
PyErr_Fetch(&type, &value, &traceback)
_lock.release()
if error:
PyErr_Restore(type, value, traceback)
release_unuran_callback(&callback)
def cdf(self, x):
"""
cdf(x)
Approximated cumulative distribution function of the given distribution.
Parameters
----------
x : array_like
Quantiles, with the last axis of `x` denoting the components.
Returns
-------
cdf : array_like
Approximated cumulative distribution function evaluated at `x`.
"""
x = np.asarray(x, dtype='d')
oshape = x.shape
x = x.ravel()
cdef double[::1] x_view = np.ascontiguousarray(x)
cdef double[::1] out = np.empty_like(x)
if x.size == 0:
return np.asarray(out).reshape(oshape)
self._cdf(&x_view[0], &out[0], len(x_view))
return np.asarray(out).reshape(oshape)[()]
@cython.boundscheck(False)
@cython.wraparound(False)
cdef inline void _ppf(self, const double *u, double *out, size_t N) noexcept:
cdef:
size_t i
for i in range(N):
out[i] = unur_pinv_eval_approxinvcdf(self.rng, u[i])
def ppf(self, u):
"""
ppf(u)
Approximated PPF of the given distribution.
Parameters
----------
u : array_like
Quantiles.
Returns
-------
ppf : array_like
Percentiles corresponding to given quantiles `u`.
"""
u = np.asarray(u, dtype='d')
oshape = u.shape
u = u.ravel()
# UNU.RAN fills in ends of the support when u < 0 or u > 1 while
# SciPy fills in nans. Prefer SciPy behaviour.
cond0 = 0 <= u
cond1 = u <= 1
cond2 = cond0 & cond1
goodu = argsreduce(cond2, u)[0]
out = np.empty_like(u)
cdef double[::1] u_view = np.ascontiguousarray(goodu)
cdef double[::1] goodout = np.empty_like(u_view)
if cond2.any():
self._ppf(&u_view[0], &goodout[0], len(goodu))
np.place(out, cond2, goodout)
np.place(out, ~cond2, np.nan)
return np.asarray(out).reshape(oshape)[()]
def u_error(self, sample_size=100000):
"""
u_error(sample_size=100000)
Estimate the u-error of the approximation using Monte Carlo simulation.
This is only available if the generator was initialized with a `dist`
object containing the implementation of the exact CDF under `cdf` method.
Parameters
----------
sample_size : int, optional
Number of samples to use for the estimation. It must be greater than
or equal to 1000.
Returns
-------
max_error : float
Maximum u-error.
mean_absolute_error : float
Mean absolute u-error.
"""
# UNU.RAN doesn't return a proper error code for this condition.
if sample_size < 1000:
raise ValueError("`sample_size` must be greater than or equal to 1000.")
if 'cdf' not in self.callbacks:
raise ValueError("Exact CDF required but not found. Reinitialize the generator "
" with a `dist` object that contains a `cdf` method to enable "
" the estimation of u-error.")
cdef double max_error, mae
cdef ccallback_t callback
_lock.acquire()
try:
self._messages.clear()
unur_set_stream(self._messages.handle)
init_unuran_callback(&callback, self._callback_wrapper)
self._check_errorcode(unur_pinv_estimate_error(self.rng, sample_size,
&max_error, &mae))
finally:
_lock.release()
release_unuran_callback(&callback)
return UError(max_error, mae)
def qrvs(self, size=None, d=None, qmc_engine=None):
"""
qrvs(size=None, d=None, qmc_engine=None)
Quasi-random variates of the given RV.
The `qmc_engine` is used to draw uniform quasi-random variates, and
these are converted to quasi-random variates of the given RV using
inverse transform sampling.
Parameters
----------
size : int, tuple of ints, or None; optional
Defines shape of random variates array. Default is ``None``.
d : int or None, optional
Defines dimension of uniform quasi-random variates to be
transformed. Default is ``None``.
qmc_engine : scipy.stats.qmc.QMCEngine(d=1), optional
Defines the object to use for drawing
quasi-random variates. Default is ``None``, which uses
`scipy.stats.qmc.Halton(1)`.
Returns
-------
rvs : ndarray or scalar
Quasi-random variates. See Notes for shape information.
Notes
-----
The shape of the output array depends on `size`, `d`, and `qmc_engine`.
The intent is for the interface to be natural, but the detailed rules
to achieve this are complicated.
- If `qmc_engine` is ``None``, a `scipy.stats.qmc.Halton` instance is
created with dimension `d`. If `d` is not provided, ``d=1``.
- If `qmc_engine` is not ``None`` and `d` is ``None``, `d` is
determined from the dimension of the `qmc_engine`.
- If `qmc_engine` is not ``None`` and `d` is not ``None`` but the
dimensions are inconsistent, a ``ValueError`` is raised.
- After `d` is determined according to the rules above, the output
shape is ``tuple_shape + d_shape``, where:
- ``tuple_shape = tuple()`` if `size` is ``None``,
- ``tuple_shape = (size,)`` if `size` is an ``int``,
- ``tuple_shape = size`` if `size` is a sequence,
- ``d_shape = tuple()`` if `d` is ``None`` or `d` is 1, and
- ``d_shape = (d,)`` if `d` is greater than 1.
The elements of the returned array are part of a low-discrepancy
sequence. If `d` is 1, this means that none of the samples are truly
independent. If `d` > 1, each slice ``rvs[..., i]`` will be of a
quasi-independent sequence; see `scipy.stats.qmc.QMCEngine` for
details. Note that when `d` > 1, the samples returned are still those
of the provided univariate distribution, not a multivariate
generalization of that distribution.
"""
qmc_engine, d = _validate_qmc_input(qmc_engine, d)
# `rvs` is flexible about whether `size` is an int or tuple, so this
# should be, too.
try:
if size is None:
tuple_size = (1, )
else:
tuple_size = tuple(size)
except TypeError:
tuple_size = (size,)
cdef unur_urng *unuran_urng
cdef double[::1] qrvs_view
N = 1 if size is None else np.prod(size)
N = N*d
qrvs_view = np.empty(N, dtype=np.float64)
_lock.acquire()
try:
# the call below must be under a lock
unuran_urng = self._urng_builder.get_qurng(size=N, qmc_engine=qmc_engine)
unur_chg_urng(self.rng, unuran_urng)
self._rvs_cont(qrvs_view)
self.set_random_state(self.numpy_rng)
qrvs = np.asarray(qrvs_view).reshape(tuple_size + (d,))
finally:
_lock.release()
# Output reshaping for user convenience
if size is None:
return qrvs.squeeze()[()]
else:
if d == 1:
return qrvs.reshape(tuple_size)
else:
return qrvs.reshape(tuple_size + (d,))
cdef class NumericalInverseHermite(Method):
"""
NumericalInverseHermite(dist, *, domain=None, order=3, u_resolution=1e-12, construction_points=None, random_state=None)
Hermite interpolation based INVersion of CDF (HINV).
HINV is a variant of numerical inversion, where the inverse CDF is approximated using
Hermite interpolation, i.e., the interval [0,1] is split into several intervals and
in each interval the inverse CDF is approximated by polynomials constructed by means
of values of the CDF and PDF at interval boundaries. This makes it possible to improve
the accuracy by splitting a particular interval without recomputations in unaffected
intervals. Three types of splines are implemented: linear, cubic, and quintic
interpolation. For linear interpolation only the CDF is required. Cubic interpolation
also requires PDF and quintic interpolation PDF and its derivative.
These splines have to be computed in a setup step. However, it only works for
distributions with bounded domain; for distributions with unbounded domain the tails
are chopped off such that the probability for the tail regions is small compared to
the given u-resolution.
The method is not exact, as it only produces random variates of the approximated
distribution. Nevertheless, the maximal numerical error in "u-direction" (i.e.
``|U - CDF(X)|`` where ``X`` is the approximate percentile corresponding to the
quantile ``U`` i.e. ``X = approx_ppf(U)``) can be set to the
required resolution (within machine precision). Notice that very small values of
the u-resolution are possible but may increase the cost for the setup step.
Parameters
----------
dist : object
An instance of a class with a ``cdf`` and optionally a ``pdf`` and ``dpdf`` method.
* ``cdf``: CDF of the distribution. The signature of the CDF is expected to be:
``def cdf(self, x: float) -> float``. i.e. the CDF should accept a Python
float and return a Python float.
* ``pdf``: PDF of the distribution. This method is optional when ``order=1``.
Must have the same signature as the PDF.
* ``dpdf``: Derivative of the PDF w.r.t the variate (i.e. ``x``). This method is
optional with ``order=1`` or ``order=3``. Must have the same signature as the CDF.
domain : list or tuple of length 2, optional
The support of the distribution.
Default is ``None``. When ``None``:
* If a ``support`` method is provided by the distribution object
`dist`, it is used to set the domain of the distribution.
* Otherwise the support is assumed to be :math:`(-\infty, \infty)`.
order : int, default: ``3``
Set order of Hermite interpolation. Valid orders are 1, 3, and 5.
Valid orders are 1, 3, and 5. Notice that order greater than 1 requires the density
of the distribution, and order greater than 3 even requires the derivative of the
density. Using order 1 results for most distributions in a huge number of intervals
and is therefore not recommended. If the maximal error in u-direction is very small
(say smaller than 1.e-10), order 5 is recommended as it leads to considerably fewer
design points, as long there are no poles or heavy tails.
u_resolution : float, default: ``1e-12``
Set maximal tolerated u-error. Notice that the resolution of most uniform random
number sources is 2-32= 2.3e-10. Thus a value of 1.e-10 leads to an inversion
algorithm that could be called exact. For most simulations slightly bigger values
for the maximal error are enough as well. Default is 1e-12.
construction_points : array_like, optional
Set starting construction points (nodes) for Hermite interpolation. As the possible
maximal error is only estimated in the setup it may be necessary to set some
special design points for computing the Hermite interpolation to guarantee that the
maximal u-error can not be bigger than desired. Such points are points where the
density is not differentiable or has a local extremum.
random_state : {None, int, `numpy.random.Generator`,
`numpy.random.RandomState`}, optional
A NumPy random number generator or seed for the underlying NumPy random
number generator used to generate the stream of uniform random numbers.
If `random_state` is None (or `np.random`), the `numpy.random.RandomState`
singleton is used.
If `random_state` is an int, a new ``RandomState`` instance is used,
seeded with `random_state`.
If `random_state` is already a ``Generator`` or ``RandomState`` instance then
that instance is used.
Notes
-----
`NumericalInverseHermite` approximates the inverse of a continuous
statistical distribution's CDF with a Hermite spline. Order of the
hermite spline can be specified by passing the `order` parameter.
As described in [1]_, it begins by evaluating the distribution's PDF and
CDF at a mesh of quantiles ``x`` within the distribution's support.
It uses the results to fit a Hermite spline ``H`` such that
``H(p) == x``, where ``p`` is the array of percentiles corresponding
with the quantiles ``x``. Therefore, the spline approximates the inverse
of the distribution's CDF to machine precision at the percentiles ``p``,
but typically, the spline will not be as accurate at the midpoints between
the percentile points::
p_mid = (p[:-1] + p[1:])/2
so the mesh of quantiles is refined as needed to reduce the maximum
"u-error"::
u_error = np.max(np.abs(dist.cdf(H(p_mid)) - p_mid))
below the specified tolerance `u_resolution`. Refinement stops when the required
tolerance is achieved or when the number of mesh intervals after the next
refinement could exceed the maximum allowed number of intervals, which is
100000.
References
----------
.. [1] Hörmann, Wolfgang, and Josef Leydold. "Continuous random variate
generation by fast numerical inversion." ACM Transactions on
Modeling and Computer Simulation (TOMACS) 13.4 (2003): 347-362.
.. [2] UNU.RAN reference manual, Section 5.3.5,
"HINV - Hermite interpolation based INVersion of CDF",
https://statmath.wu.ac.at/software/unuran/doc/unuran.html#HINV
Examples
--------
>>> from scipy.stats.sampling import NumericalInverseHermite
>>> from scipy.stats import norm, genexpon
>>> from scipy.special import ndtr
>>> import numpy as np
To create a generator to sample from the standard normal distribution, do:
>>> class StandardNormal:
... def pdf(self, x):
... return 1/np.sqrt(2*np.pi) * np.exp(-x**2 / 2)
... def cdf(self, x):
... return ndtr(x)
...
>>> dist = StandardNormal()
>>> urng = np.random.default_rng()
>>> rng = NumericalInverseHermite(dist, random_state=urng)
The `NumericalInverseHermite` has a method that approximates the PPF of the
distribution.
>>> rng = NumericalInverseHermite(dist)
>>> p = np.linspace(0.01, 0.99, 99) # percentiles from 1% to 99%
>>> np.allclose(rng.ppf(p), norm.ppf(p))
True
Depending on the implementation of the distribution's random sampling
method, the random variates generated may be nearly identical, given
the same random state.
>>> dist = genexpon(9, 16, 3)
>>> rng = NumericalInverseHermite(dist)
>>> # `seed` ensures identical random streams are used by each `rvs` method
>>> seed = 500072020
>>> rvs1 = dist.rvs(size=100, random_state=np.random.default_rng(seed))
>>> rvs2 = rng.rvs(size=100, random_state=np.random.default_rng(seed))
>>> np.allclose(rvs1, rvs2)
True
To check that the random variates closely follow the given distribution, we can
look at its histogram:
>>> import matplotlib.pyplot as plt
>>> dist = StandardNormal()
>>> rng = NumericalInverseHermite(dist)
>>> rvs = rng.rvs(10000)
>>> x = np.linspace(rvs.min()-0.1, rvs.max()+0.1, 1000)
>>> fx = norm.pdf(x)
>>> plt.plot(x, fx, 'r-', lw=2, label='true distribution')
>>> plt.hist(rvs, bins=20, density=True, alpha=0.8, label='random variates')
>>> plt.xlabel('x')
>>> plt.ylabel('PDF(x)')
>>> plt.title('Numerical Inverse Hermite Samples')
>>> plt.legend()
>>> plt.show()
Given the derivative of the PDF w.r.t the variate (i.e. ``x``), we can use
quintic Hermite interpolation to approximate the PPF by passing the `order`
parameter:
>>> class StandardNormal:
... def pdf(self, x):
... return 1/np.sqrt(2*np.pi) * np.exp(-x**2 / 2)
... def dpdf(self, x):
... return -1/np.sqrt(2*np.pi) * x * np.exp(-x**2 / 2)
... def cdf(self, x):
... return ndtr(x)
...
>>> dist = StandardNormal()
>>> urng = np.random.default_rng()
>>> rng = NumericalInverseHermite(dist, order=5, random_state=urng)
Higher orders result in a fewer number of intervals:
>>> rng3 = NumericalInverseHermite(dist, order=3)
>>> rng5 = NumericalInverseHermite(dist, order=5)
>>> rng3.intervals, rng5.intervals
(3000, 522)
The u-error can be estimated by calling the `u_error` method. It runs a small
Monte-Carlo simulation to estimate the u-error. By default, 100,000 samples are
used. This can be changed by passing the `sample_size` argument:
>>> rng1 = NumericalInverseHermite(dist, u_resolution=1e-10)
>>> rng1.u_error(sample_size=1000000) # uses one million samples
UError(max_error=9.53167544892608e-11, mean_absolute_error=2.2450136432146864e-11)
This returns a namedtuple which contains the maximum u-error and the mean
absolute u-error.
The u-error can be reduced by decreasing the u-resolution (maximum allowed u-error):
>>> rng2 = NumericalInverseHermite(dist, u_resolution=1e-13)
>>> rng2.u_error(sample_size=1000000)
UError(max_error=9.32027892364129e-14, mean_absolute_error=1.5194172675685075e-14)
Note that this comes at the cost of increased setup time and number of intervals.
>>> rng1.intervals
1022
>>> rng2.intervals
5687
>>> from timeit import timeit
>>> f = lambda: NumericalInverseHermite(dist, u_resolution=1e-10)
>>> timeit(f, number=1)
0.017409582000254886 # may vary
>>> f = lambda: NumericalInverseHermite(dist, u_resolution=1e-13)
>>> timeit(f, number=1)
0.08671202100003939 # may vary
Since the PPF of the normal distribution is available as a special function, we
can also check the x-error, i.e. the difference between the approximated PPF and
exact PPF::
>>> import matplotlib.pyplot as plt
>>> u = np.linspace(0.01, 0.99, 1000)
>>> approxppf = rng.ppf(u)
>>> exactppf = norm.ppf(u)
>>> error = np.abs(exactppf - approxppf)
>>> plt.plot(u, error)
>>> plt.xlabel('u')
>>> plt.ylabel('error')
>>> plt.title('Error between exact and approximated PPF (x-error)')
>>> plt.show()
"""
cdef double[::1] construction_points_array
def __cinit__(self,
dist,
*,
domain=None,
order=3,
u_resolution=1e-12,
construction_points=None,
random_state=None):
domain, order, u_resolution = self._validate_args(dist, domain, order,
u_resolution, construction_points)
# save all the arguments for pickling support
self._kwargs = {
'dist': dist,
'domain': domain,
'order': order,
'u_resolution': u_resolution,
'construction_points': construction_points,
'random_state': random_state
}
self.callbacks = _unpack_dist(dist, "cont", meths=["cdf"], optional_meths=["pdf", "dpdf"])
def _callback_wrapper(x, name):
return self.callbacks[name](x)
self._callback_wrapper = _callback_wrapper
self._messages = MessageStream()
_lock.acquire()
try:
unur_set_stream(self._messages.handle)
self.distr = unur_distr_cont_new()
if self.distr == NULL:
raise UNURANError(self._messages.get())
_pack_distr(self.distr, self.callbacks)
if domain is not None:
self._check_errorcode(unur_distr_cont_set_domain(self.distr, domain[0],
domain[1]))
self.par = unur_hinv_new(self.distr)
if self.par == NULL:
raise UNURANError(self._messages.get())
self._check_errorcode(unur_hinv_set_order(self.par, order))
self._check_errorcode(unur_hinv_set_u_resolution(self.par, u_resolution))
self._check_errorcode(unur_hinv_set_cpoints(self.par, &self.construction_points_array[0],
len(self.construction_points_array)))
self._set_rng(random_state)
finally:
_lock.release()
def _validate_args(self, dist, domain, order, u_resolution, construction_points):
domain = _validate_domain(domain, dist)
# UNU.RAN raises warning and sets a default value. Prefer an error instead.
if order not in {1, 3, 5}:
raise ValueError("`order` must be either 1, 3, or 5.")
u_resolution = float(u_resolution)
self.construction_points_array = np.ascontiguousarray(construction_points,
dtype=np.float64)
if len(self.construction_points_array) == 0:
raise ValueError("`construction_points` must be a non-empty array.")
return (domain, order, u_resolution)
@cython.boundscheck(False)
@cython.wraparound(False)
cdef inline void _ppf(self, const double *u, double *out, size_t N) noexcept:
cdef:
size_t i
for i in range(N):
out[i] = unur_hinv_eval_approxinvcdf(self.rng, u[i])
def ppf(self, u):
"""
ppf(u)
Approximated PPF of the given distribution.
Parameters
----------
u : array_like
Quantiles.
Returns
-------
ppf : array_like
Percentiles corresponding to given quantiles `u`.
"""
u = np.asarray(u, dtype='d')
oshape = u.shape
u = u.ravel()
# UNU.RAN fills in ends of the support when u < 0 or u > 1 while
# SciPy fills in nans. Prefer SciPy behaviour.
cond0 = 0 <= u
cond1 = u <= 1
cond2 = cond0 & cond1
goodu = argsreduce(cond2, u)[0]
out = np.empty_like(u)
cdef double[::1] u_view = np.ascontiguousarray(goodu)
cdef double[::1] goodout = np.empty_like(u_view)
if cond2.any():
self._ppf(&u_view[0], &goodout[0], len(goodu))
np.place(out, cond2, goodout)
np.place(out, ~cond2, np.nan)
return np.asarray(out).reshape(oshape)[()]
def u_error(self, sample_size=100000):
"""
u_error(sample_size=100000)
Estimate the u-error of the approximation using Monte Carlo simulation.
This is only available if the generator was initialized with a `dist`
object containing the implementation of the exact CDF under `cdf` method.
Parameters
----------
sample_size : int, optional
Number of samples to use for the estimation. It must be greater than
or equal to 1000.
Returns
-------
max_error : float
Maximum u-error.
mean_absolute_error : float
Mean absolute u-error.
"""
# UNU.RAN doesn't return a proper error code for this condition.
if sample_size < 1000:
raise ValueError("`sample_size` must be greater than or equal to 1000.")
cdef double max_error, mae
cdef ccallback_t callback
_lock.acquire()
try:
self._messages.clear()
unur_set_stream(self._messages.handle)
init_unuran_callback(&callback, self._callback_wrapper)
self._check_errorcode(unur_hinv_estimate_error(self.rng, sample_size,
&max_error, &mae))
finally:
_lock.release()
release_unuran_callback(&callback)
return UError(max_error, mae)
def qrvs(self, size=None, d=None, qmc_engine=None):
"""
qrvs(size=None, d=None, qmc_engine=None)
Quasi-random variates of the given RV.
The `qmc_engine` is used to draw uniform quasi-random variates, and
these are converted to quasi-random variates of the given RV using
inverse transform sampling.
Parameters
----------
size : int, tuple of ints, or None; optional
Defines shape of random variates array. Default is ``None``.
d : int or None, optional
Defines dimension of uniform quasi-random variates to be
transformed. Default is ``None``.
qmc_engine : scipy.stats.qmc.QMCEngine(d=1), optional
Defines the object to use for drawing
quasi-random variates. Default is ``None``, which uses
`scipy.stats.qmc.Halton(1)`.
Returns
-------
rvs : ndarray or scalar
Quasi-random variates. See Notes for shape information.
Notes
-----
The shape of the output array depends on `size`, `d`, and `qmc_engine`.
The intent is for the interface to be natural, but the detailed rules
to achieve this are complicated.
- If `qmc_engine` is ``None``, a `scipy.stats.qmc.Halton` instance is
created with dimension `d`. If `d` is not provided, ``d=1``.
- If `qmc_engine` is not ``None`` and `d` is ``None``, `d` is
determined from the dimension of the `qmc_engine`.
- If `qmc_engine` is not ``None`` and `d` is not ``None`` but the
dimensions are inconsistent, a ``ValueError`` is raised.
- After `d` is determined according to the rules above, the output
shape is ``tuple_shape + d_shape``, where:
- ``tuple_shape = tuple()`` if `size` is ``None``,
- ``tuple_shape = (size,)`` if `size` is an ``int``,
- ``tuple_shape = size`` if `size` is a sequence,
- ``d_shape = tuple()`` if `d` is ``None`` or `d` is 1, and
- ``d_shape = (d,)`` if `d` is greater than 1.
The elements of the returned array are part of a low-discrepancy
sequence. If `d` is 1, this means that none of the samples are truly
independent. If `d` > 1, each slice ``rvs[..., i]`` will be of a
quasi-independent sequence; see `scipy.stats.qmc.QMCEngine` for
details. Note that when `d` > 1, the samples returned are still those
of the provided univariate distribution, not a multivariate
generalization of that distribution.
"""
qmc_engine, d = _validate_qmc_input(qmc_engine, d)
# `rvs` is flexible about whether `size` is an int or tuple, so this
# should be, too.
try:
if size is None:
tuple_size = (1, )
else:
tuple_size = tuple(size)
except TypeError:
tuple_size = (size,)
cdef unur_urng *unuran_urng
cdef double[::1] qrvs_view
N = 1 if size is None else np.prod(size)
N = N*d
qrvs_view = np.empty(N, dtype=np.float64)
_lock.acquire()
try:
# the call below must be under a lock
unuran_urng = self._urng_builder.get_qurng(size=N, qmc_engine=qmc_engine)
unur_chg_urng(self.rng, unuran_urng)
self._rvs_cont(qrvs_view)
self.set_random_state(self.numpy_rng)
qrvs = np.asarray(qrvs_view).reshape(tuple_size + (d,))
finally:
_lock.release()
# Output reshaping for user convenience
if size is None:
return qrvs.squeeze()[()]
else:
if d == 1:
return qrvs.reshape(tuple_size)
else:
return qrvs.reshape(tuple_size + (d,))
@property
def intervals(self):
"""
Get number of nodes (design points) used for Hermite interpolation in the
generator object. The number of intervals is the number of nodes minus 1.
"""
return unur_hinv_get_n_intervals(self.rng)
@property
def midpoint_error(self):
return self.u_error()[0]
cdef class DiscreteAliasUrn(Method):
r"""
DiscreteAliasUrn(dist, *, domain=None, urn_factor=1, random_state=None)
Discrete Alias-Urn Method.
This method is used to sample from univariate discrete distributions with
a finite domain. It uses the probability vector of size :math:`N` or a
probability mass function with a finite support to generate random
numbers from the distribution.
Parameters
----------
dist : array_like or object, optional
Probability vector (PV) of the distribution. If PV isn't available,
an instance of a class with a ``pmf`` method is expected. The signature
of the PMF is expected to be: ``def pmf(self, k: int) -> float``. i.e. it
should accept a Python integer and return a Python float.
domain : int, optional
Support of the PMF. If a probability vector (``pv``) is not available, a
finite domain must be given. i.e. the PMF must have a finite support.
Default is ``None``. When ``None``:
* If a ``support`` method is provided by the distribution object
`dist`, it is used to set the domain of the distribution.
* Otherwise, the support is assumed to be ``(0, len(pv))``. When this
parameter is passed in combination with a probability vector, ``domain[0]``
is used to relocate the distribution from ``(0, len(pv))`` to
``(domain[0], domain[0]+len(pv))`` and ``domain[1]`` is ignored. See Notes
and tutorial for a more detailed explanation.
urn_factor : float, optional
Size of the urn table *relative* to the size of the probability
vector. It must not be less than 1. Larger tables result in faster
generation times but require a more expensive setup. Default is 1.
random_state : {None, int, `numpy.random.Generator`,
`numpy.random.RandomState`}, optional
A NumPy random number generator or seed for the underlying NumPy random
number generator used to generate the stream of uniform random numbers.
If `random_state` is None (or `np.random`), the `numpy.random.RandomState`
singleton is used.
If `random_state` is an int, a new ``RandomState`` instance is used,
seeded with `random_state`.
If `random_state` is already a ``Generator`` or ``RandomState`` instance then
that instance is used.
Notes
-----
This method works when either a finite probability vector is available or
the PMF of the distribution is available. In case a PMF is only available,
the *finite* support (domain) of the PMF must also be given. It is
recommended to first obtain the probability vector by evaluating the PMF
at each point in the support and then using it instead.
If a probability vector is given, it must be a 1-dimensional array of
non-negative floats without any ``inf`` or ``nan`` values. Also, there
must be at least one non-zero entry otherwise an exception is raised.
By default, the probability vector is indexed starting at 0. However, this
can be changed by passing a ``domain`` parameter. When ``domain`` is given
in combination with the PV, it has the effect of relocating the
distribution from ``(0, len(pv))`` to ``(domain[0]``, ``domain[0] + len(pv))``.
``domain[1]`` is ignored in this case.
The parameter ``urn_factor`` can be increased for faster generation at the
cost of increased setup time. This method uses a table for random
variate generation. ``urn_factor`` controls the size of this table
relative to the size of the probability vector (or width of the support,
in case a PV is not available). As this table is computed during setup
time, increasing this parameter linearly increases the time required to
setup. It is recommended to keep this parameter under 2.
References
----------
.. [1] UNU.RAN reference manual, Section 5.8.2,
"DAU - (Discrete) Alias-Urn method",
http://statmath.wu.ac.at/software/unuran/doc/unuran.html#DAU
.. [2] A.J. Walker (1977). An efficient method for generating discrete
random variables with general distributions, ACM Trans. Math.
Software 3, pp. 253-256.
Examples
--------
>>> from scipy.stats.sampling import DiscreteAliasUrn
>>> import numpy as np
To create a random number generator using a probability vector, use:
>>> pv = [0.1, 0.3, 0.6]
>>> urng = np.random.default_rng()
>>> rng = DiscreteAliasUrn(pv, random_state=urng)
The RNG has been setup. Now, we can now use the `rvs` method to
generate samples from the distribution:
>>> rvs = rng.rvs(size=1000)
To verify that the random variates follow the given distribution, we can
use the chi-squared test (as a measure of goodness-of-fit):
>>> from scipy.stats import chisquare
>>> _, freqs = np.unique(rvs, return_counts=True)
>>> freqs = freqs / np.sum(freqs)
>>> freqs
array([0.092, 0.292, 0.616])
>>> chisquare(freqs, pv).pvalue
0.9993602047563164
As the p-value is very high, we fail to reject the null hypothesis that
the observed frequencies are the same as the expected frequencies. Hence,
we can safely assume that the variates have been generated from the given
distribution. Note that this just gives the correctness of the algorithm
and not the quality of the samples.
If a PV is not available, an instance of a class with a PMF method and a
finite domain can also be passed.
>>> urng = np.random.default_rng()
>>> class Binomial:
... def __init__(self, n, p):
... self.n = n
... self.p = p
... def pmf(self, x):
... # note that the pmf doesn't need to be normalized.
... return self.p**x * (1-self.p)**(self.n-x)
... def support(self):
... return (0, self.n)
...
>>> n, p = 10, 0.2
>>> dist = Binomial(n, p)
>>> rng = DiscreteAliasUrn(dist, random_state=urng)
Now, we can sample from the distribution using the `rvs` method
and also measure the goodness-of-fit of the samples:
>>> rvs = rng.rvs(1000)
>>> _, freqs = np.unique(rvs, return_counts=True)
>>> freqs = freqs / np.sum(freqs)
>>> obs_freqs = np.zeros(11) # some frequencies may be zero.
>>> obs_freqs[:freqs.size] = freqs
>>> pv = [dist.pmf(i) for i in range(0, 11)]
>>> pv = np.asarray(pv) / np.sum(pv)
>>> chisquare(obs_freqs, pv).pvalue
0.9999999999999999
To check that the samples have been drawn from the correct distribution,
we can visualize the histogram of the samples:
>>> import matplotlib.pyplot as plt
>>> rvs = rng.rvs(1000)
>>> fig = plt.figure()
>>> ax = fig.add_subplot(111)
>>> x = np.arange(0, n+1)
>>> fx = dist.pmf(x)
>>> fx = fx / fx.sum()
>>> ax.plot(x, fx, 'bo', label='true distribution')
>>> ax.vlines(x, 0, fx, lw=2)
>>> ax.hist(rvs, bins=np.r_[x, n+1]-0.5, density=True, alpha=0.5,
... color='r', label='samples')
>>> ax.set_xlabel('x')
>>> ax.set_ylabel('PMF(x)')
>>> ax.set_title('Discrete Alias Urn Samples')
>>> plt.legend()
>>> plt.show()
To set the ``urn_factor``, use:
>>> rng = DiscreteAliasUrn(pv, urn_factor=2, random_state=urng)
This uses a table twice the size of the probability vector to generate
random variates from the distribution.
"""
cdef double[::1] pv_view
def __cinit__(self,
dist,
*,
domain=None,
urn_factor=1,
random_state=None):
cdef double[::1] pv_view
(pv_view, domain) = self._validate_args(dist, domain)
# increment ref count of pv_view to make sure it doesn't get garbage collected.
self.pv_view = pv_view
# save all the arguments for pickling support
self._kwargs = {'dist': dist, 'domain': domain, 'urn_factor': urn_factor, 'random_state': random_state}
self._messages = MessageStream()
_lock.acquire()
try:
unur_set_stream(self._messages.handle)
self.distr = unur_distr_discr_new()
if self.distr == NULL:
raise UNURANError(self._messages.get())
n_pv = len(pv_view)
self._check_errorcode(unur_distr_discr_set_pv(self.distr, &pv_view[0], n_pv))
if domain is not None:
self._check_errorcode(unur_distr_discr_set_domain(self.distr, domain[0],
domain[1]))
self.par = unur_dau_new(self.distr)
if self.par == NULL:
raise UNURANError(self._messages.get())
self._check_errorcode(unur_dau_set_urnfactor(self.par, urn_factor))
self._set_rng(random_state)
finally:
_lock.release()
cdef object _validate_args(self, dist, domain):
cdef double[::1] pv_view
domain = _validate_domain(domain, dist)
if domain is not None:
if not np.isfinite(domain).all():
raise ValueError("`domain` must be finite.")
else:
if hasattr(dist, 'pmf'):
raise ValueError("`domain` must be provided when the "
"probability vector is not available.")
if hasattr(dist, 'pmf'):
# we assume the PMF accepts and return floats. So, we need
# to vectorize it to call with an array of points in the domain.
pmf = np.vectorize(dist.pmf)
k = np.arange(domain[0], domain[1]+1)
pv = pmf(k)
try:
pv_view = _validate_pv(pv)
except ValueError as err:
msg = "PMF returned invalid values: " + err.args[0]
raise ValueError(msg) from None
else:
pv_view = _validate_pv(dist)
return pv_view, domain
cdef class DiscreteGuideTable(Method):
r"""
DiscreteGuideTable(dist, *, domain=None, guide_factor=1, random_state=None)
Discrete Guide Table method.
The Discrete Guide Table method samples from arbitrary, but finite,
probability vectors. It uses the probability vector of size :math:`N` or a
probability mass function with a finite support to generate random
numbers from the distribution. Discrete Guide Table has a very slow set up
(linear with the vector length) but provides very fast sampling.
Parameters
----------
dist : array_like or object, optional
Probability vector (PV) of the distribution. If PV isn't available,
an instance of a class with a ``pmf`` method is expected. The signature
of the PMF is expected to be: ``def pmf(self, k: int) -> float``. i.e. it
should accept a Python integer and return a Python float.
domain : int, optional
Support of the PMF. If a probability vector (``pv``) is not available, a
finite domain must be given. i.e. the PMF must have a finite support.
Default is ``None``. When ``None``:
* If a ``support`` method is provided by the distribution object
`dist`, it is used to set the domain of the distribution.
* Otherwise, the support is assumed to be ``(0, len(pv))``. When this
parameter is passed in combination with a probability vector, ``domain[0]``
is used to relocate the distribution from ``(0, len(pv))`` to
``(domain[0], domain[0]+len(pv))`` and ``domain[1]`` is ignored. See Notes
and tutorial for a more detailed explanation.
guide_factor: int, optional
Size of the guide table relative to length of PV. Larger guide tables
result in faster generation time but require a more expensive setup.
Sizes larger than 3 are not recommended. If the relative size is set to
0, sequential search is used. Default is 1.
random_state : {None, int, `numpy.random.Generator`,
`numpy.random.RandomState`}, optional
A NumPy random number generator or seed for the underlying NumPy random
number generator used to generate the stream of uniform random numbers.
If `random_state` is None (or `np.random`), the `numpy.random.RandomState`
singleton is used.
If `random_state` is an int, a new ``RandomState`` instance is used,
seeded with `random_state`.
If `random_state` is already a ``Generator`` or ``RandomState`` instance then
that instance is used.
Notes
-----
This method works when either a finite probability vector is available or
the PMF of the distribution is available. In case a PMF is only available,
the *finite* support (domain) of the PMF must also be given. It is
recommended to first obtain the probability vector by evaluating the PMF
at each point in the support and then using it instead.
DGT samples from arbitrary but finite probability vectors. Random numbers
are generated by the inversion method, i.e.
1. Generate a random number U ~ U(0,1).
2. Find smallest integer I such that F(I) = P(X<=I) >= U.
Step (2) is the crucial step. Using sequential search requires O(E(X))
comparisons, where E(X) is the expectation of the distribution. Indexed
search, however, uses a guide table to jump to some I' <= I near I to find
X in constant time. Indeed the expected number of comparisons is reduced to
2, when the guide table has the same size as the probability vector
(this is the default). For larger guide tables this number becomes smaller
(but is always larger than 1), for smaller tables it becomes larger. For the
limit case of table size 1 the algorithm simply does sequential search.
On the other hand the setup time for guide table is O(N), where N denotes
the length of the probability vector (for size 1 no preprocessing is
required). Moreover, for very large guide tables memory effects might even
reduce the speed of the algorithm. So we do not recommend to use guide
tables that are more than three times larger than the given probability
vector. If only a few random numbers have to be generated, (much) smaller
table sizes are better. The size of the guide table relative to the length
of the given probability vector can be set by the ``guide_factor`` parameter.
If a probability vector is given, it must be a 1-dimensional array of
non-negative floats without any ``inf`` or ``nan`` values. Also, there
must be at least one non-zero entry otherwise an exception is raised.
By default, the probability vector is indexed starting at 0. However, this
can be changed by passing a ``domain`` parameter. When ``domain`` is given
in combination with the PV, it has the effect of relocating the
distribution from ``(0, len(pv))`` to ``(domain[0], domain[0] + len(pv))``.
``domain[1]`` is ignored in this case.
References
----------
.. [1] UNU.RAN reference manual, Section 5.8.4,
"DGT - (Discrete) Guide Table method (indexed search)"
https://statmath.wu.ac.at/unuran/doc/unuran.html#DGT
.. [2] H.C. Chen and Y. Asau (1974). On generating random variates from an
empirical distribution, AIIE Trans. 6, pp. 163-166.
Examples
--------
>>> from scipy.stats.sampling import DiscreteGuideTable
>>> import numpy as np
To create a random number generator using a probability vector, use:
>>> pv = [0.1, 0.3, 0.6]
>>> urng = np.random.default_rng()
>>> rng = DiscreteGuideTable(pv, random_state=urng)
The RNG has been setup. Now, we can now use the `rvs` method to
generate samples from the distribution:
>>> rvs = rng.rvs(size=1000)
To verify that the random variates follow the given distribution, we can
use the chi-squared test (as a measure of goodness-of-fit):
>>> from scipy.stats import chisquare
>>> _, freqs = np.unique(rvs, return_counts=True)
>>> freqs = freqs / np.sum(freqs)
>>> freqs
array([0.092, 0.355, 0.553])
>>> chisquare(freqs, pv).pvalue
0.9987382966178464
As the p-value is very high, we fail to reject the null hypothesis that
the observed frequencies are the same as the expected frequencies. Hence,
we can safely assume that the variates have been generated from the given
distribution. Note that this just gives the correctness of the algorithm
and not the quality of the samples.
If a PV is not available, an instance of a class with a PMF method and a
finite domain can also be passed.
>>> urng = np.random.default_rng()
>>> from scipy.stats import binom
>>> n, p = 10, 0.2
>>> dist = binom(n, p)
>>> rng = DiscreteGuideTable(dist, random_state=urng)
Now, we can sample from the distribution using the `rvs` method
and also measure the goodness-of-fit of the samples:
>>> rvs = rng.rvs(1000)
>>> _, freqs = np.unique(rvs, return_counts=True)
>>> freqs = freqs / np.sum(freqs)
>>> obs_freqs = np.zeros(11) # some frequencies may be zero.
>>> obs_freqs[:freqs.size] = freqs
>>> pv = [dist.pmf(i) for i in range(0, 11)]
>>> pv = np.asarray(pv) / np.sum(pv)
>>> chisquare(obs_freqs, pv).pvalue
0.9999999999999989
To check that the samples have been drawn from the correct distribution,
we can visualize the histogram of the samples:
>>> import matplotlib.pyplot as plt
>>> rvs = rng.rvs(1000)
>>> fig = plt.figure()
>>> ax = fig.add_subplot(111)
>>> x = np.arange(0, n+1)
>>> fx = dist.pmf(x)
>>> fx = fx / fx.sum()
>>> ax.plot(x, fx, 'bo', label='true distribution')
>>> ax.vlines(x, 0, fx, lw=2)
>>> ax.hist(rvs, bins=np.r_[x, n+1]-0.5, density=True, alpha=0.5,
... color='r', label='samples')
>>> ax.set_xlabel('x')
>>> ax.set_ylabel('PMF(x)')
>>> ax.set_title('Discrete Guide Table Samples')
>>> plt.legend()
>>> plt.show()
To set the size of the guide table use the `guide_factor` keyword argument.
This sets the size of the guide table relative to the probability vector
>>> rng = DiscreteGuideTable(pv, guide_factor=1, random_state=urng)
To calculate the PPF of a binomial distribution with :math:`n=4` and
:math:`p=0.1`: we can set up a guide table as follows:
>>> n, p = 4, 0.1
>>> dist = binom(n, p)
>>> rng = DiscreteGuideTable(dist, random_state=42)
>>> rng.ppf(0.5)
0.0
"""
cdef double[::1] pv_view
cdef object domain
def __cinit__(self,
dist,
*,
domain=None,
guide_factor=1,
random_state=None):
cdef double[::1] pv_view
(pv_view, domain) = self._validate_args(dist, domain, guide_factor)
self.domain = domain
# increment ref count of pv_view to make sure it doesn't get garbage collected.
self.pv_view = pv_view
# save all the arguments for pickling support
self._kwargs = {
'dist': dist,
'domain': domain,
'guide_factor': guide_factor,
'random_state': random_state
}
self._messages = MessageStream()
_lock.acquire()
try:
unur_set_stream(self._messages.handle)
self.distr = unur_distr_discr_new()
if self.distr == NULL:
raise UNURANError(self._messages.get())
n_pv = len(pv_view)
self._check_errorcode(unur_distr_discr_set_pv(self.distr, &pv_view[0], n_pv))
if domain is not None:
self._check_errorcode(unur_distr_discr_set_domain(self.distr, domain[0], domain[1]))
self.par = unur_dgt_new(self.distr)
if self.par == NULL:
raise UNURANError(self._messages.get())
self._check_errorcode(unur_dgt_set_guidefactor(self.par, guide_factor))
self._set_rng(random_state)
finally:
_lock.release()
cdef object _validate_args(self, dist, domain, guide_factor):
cdef double[::1] pv_view
domain = _validate_domain(domain, dist)
if domain is not None:
if not np.isfinite(domain).all():
raise ValueError("`domain` must be finite.")
else:
if hasattr(dist, 'pmf'):
raise ValueError("`domain` must be provided when the "
"probability vector is not available.")
if guide_factor > 3:
msg = "guide_factor sizes larger than 3 are not recommended."
warnings.warn(msg, RuntimeWarning)
if guide_factor == 0:
msg = ("If the relative size (guide_factor) is set to 0, "
"sequential search is used. However, this is not "
"recommended, except in exceptional cases, since the "
"discrete sequential search method has almost no setup and "
"is thus faster.")
warnings.warn(msg, RuntimeWarning)
if hasattr(dist, 'pmf'):
# we assume the PMF accepts and return floats. So, we need
# to vectorize it to call with an array of points in the domain.
pmf = np.vectorize(dist.pmf)
k = np.arange(domain[0], domain[1]+1)
pv = pmf(k)
try:
pv_view = _validate_pv(pv)
except ValueError as err:
msg = "PMF returned invalid values: " + err.args[0]
raise ValueError(msg) from None
else:
pv_view = _validate_pv(dist)
return pv_view, domain
@cython.boundscheck(False)
@cython.wraparound(False)
cdef inline void _ppf(self, const double *u, double *out, size_t N) noexcept:
cdef:
size_t i
for i in range(N):
out[i] = unur_dgt_eval_invcdf(self.rng, u[i])
def ppf(self, u):
"""
ppf(u)
PPF of the given distribution.
Parameters
----------
u : array_like
Quantiles.
Returns
-------
ppf : array_like
Percentiles corresponding to given quantiles `u`.
"""
u = np.asarray(u, dtype='d')
oshape = u.shape
u = u.ravel()
# UNU.RAN fills in ends of the support when u < 0 or u > 1 while
# SciPy fills in nans. Prefer SciPy behaviour.
cond0 = 0 <= u
cond1 = u <= 1
cond2 = cond0 & cond1
goodu = argsreduce(cond2, u)[0]
out = np.empty_like(u)
cdef double[::1] u_view = np.ascontiguousarray(goodu)
cdef double[::1] goodout = np.empty_like(u_view)
if cond2.any():
self._ppf(&u_view[0], &goodout[0], len(goodu))
np.place(out, cond2, goodout)
np.place(out, ~cond2, np.nan)
# UNU.RAN sets boundary at u = 0 to domain[0]
# SciPy fills it with domain[0] - 1. Prefer SciPy behaviour
if self.domain is not None:
np.place(out, u == 0, self.domain[0] - 1)
else:
# domain starts at 0. So, fill in -1.
np.place(out, u == 0, -1)
return np.asarray(out).reshape(oshape)[()]
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