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pamelag committed Jul 6, 2017
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2,222 changes: 2,222 additions & 0 deletions LDA.go

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105 changes: 105 additions & 0 deletions Requirements.txt
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cdef class RandomState:
"""
RandomState(seed=None)

Container for the Mersenne Twister pseudo-random number generator.

`RandomState` exposes a number of methods for generating random numbers
drawn from a variety of probability distributions. In addition to the
distribution-specific arguments, each method takes a keyword argument
`size` that defaults to ``None``. If `size` is ``None``, then a single
value is generated and returned. If `size` is an integer, then a 1-D
array filled with generated values is returned. If `size` is a tuple,
then an array with that shape is filled and returned.

*Compatibility Guarantee*
A fixed seed and a fixed series of calls to 'RandomState' methods using
the same parameters will always produce the same results up to roundoff
error except when the values were incorrect. Incorrect values will be
fixed and the NumPy version in which the fix was made will be noted in
the relevant docstring. Extension of existing parameter ranges and the
addition of new parameters is allowed as long the previous behavior
remains unchanged.

Parameters
----------
seed : {None, int, array_like}, optional
Random seed used to initialize the pseudo-random number generator. Can
be any integer between 0 and 2**32 - 1 inclusive, an array (or other
sequence) of such integers, or ``None`` (the default). If `seed` is
``None``, then `RandomState` will try to read data from
``/dev/urandom`` (or the Windows analogue) if available or seed from
the clock otherwise.

Notes
-----
The Python stdlib module "random" also contains a Mersenne Twister
pseudo-random number generator with a number of methods that are similar
to the ones available in `RandomState`. `RandomState`, besides being
NumPy-aware, has the advantage that it provides a much larger number
of probability distributions to choose from.

"""
cdef rk_state *internal_state
cdef object lock
cdef object state_address
poisson_lam_max = np.iinfo('l').max - np.sqrt(np.iinfo('l').max)*10


cdef rk_state *internal_state
cdef object lock
cdef object state_address
poisson_lam_max = np.iinfo('l').max - np.sqrt(np.iinfo('l').max)*10

def __init__(self, seed=None):
self.internal_state = <rk_state*>PyMem_Malloc(sizeof(rk_state))
self.state_address = PyCapsule_New(self.internal_state, NULL, NULL)
self.lock = Lock()
self.seed(seed)

def __dealloc__(self):
if self.internal_state != NULL:
PyMem_Free(self.internal_state)
self.internal_state = NULL


def seed(self, seed=None):
"""
seed(seed=None)

Seed the generator.

This method is called when `RandomState` is initialized. It can be
called again to re-seed the generator. For details, see `RandomState`.

Parameters
----------
seed : int or array_like, optional
Seed for `RandomState`.
Must be convertible to 32 bit unsigned integers.

See Also
--------
RandomState

"""
cdef rk_error errcode
cdef ndarray obj "arrayObject_obj"
try:
if seed is None:
with self.lock:
errcode = rk_randomseed(self.internal_state)
else:
idx = operator.index(seed)
if idx > int(2**32 - 1) or idx < 0:
raise ValueError("Seed must be between 0 and 2**32 - 1")
with self.lock:
rk_seed(idx, self.internal_state)
except TypeError:
obj = np.asarray(seed).astype(np.int64, casting='safe')
if ((obj > int(2**32 - 1)) | (obj < 0)).any():
raise ValueError("Seed must be between 0 and 2**32 - 1")
obj = obj.astype(L', casting='unsafe')
with self.lock:
init_by_array(self.internal_state, <unsigned long *>PyArray_DATA(obj),
PyArray_DIM(obj, 0))
252 changes: 252 additions & 0 deletions const.c
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/* const.c
*
* Globally declared constants
*
*
*
* SYNOPSIS:
*
* extern double nameofconstant;
*
*
*
*
* DESCRIPTION:
*
* This file contains a number of mathematical constants and
* also some needed size parameters of the computer arithmetic.
* The values are supplied as arrays of hexadecimal integers
* for IEEE arithmetic; arrays of octal constants for DEC
* arithmetic; and in a normal decimal scientific notation for
* other machines. The particular notation used is determined
* by a symbol (DEC, IBMPC, or UNK) defined in the include file
* mconf.h.
*
* The default size parameters are as follows.
*
* For DEC and UNK modes:
* MACHEP = 1.38777878078144567553E-17 2**-56
* MAXLOG = 8.8029691931113054295988E1 log(2**127)
* MINLOG = -8.872283911167299960540E1 log(2**-128)
* MAXNUM = 1.701411834604692317316873e38 2**127
*
* For IEEE arithmetic (IBMPC):
* MACHEP = 1.11022302462515654042E-16 2**-53
* MAXLOG = 7.09782712893383996843E2 log(2**1024)
* MINLOG = -7.08396418532264106224E2 log(2**-1022)
* MAXNUM = 1.7976931348623158E308 2**1024
*
* The global symbols for mathematical constants are
* PI = 3.14159265358979323846 pi
* PIO2 = 1.57079632679489661923 pi/2
* PIO4 = 7.85398163397448309616E-1 pi/4
* SQRT2 = 1.41421356237309504880 sqrt(2)
* SQRTH = 7.07106781186547524401E-1 sqrt(2)/2
* LOG2E = 1.4426950408889634073599 1/log(2)
* SQ2OPI = 7.9788456080286535587989E-1 sqrt( 2/pi )
* LOGE2 = 6.93147180559945309417E-1 log(2)
* LOGSQ2 = 3.46573590279972654709E-1 log(2)/2
* THPIO4 = 2.35619449019234492885 3*pi/4
* TWOOPI = 6.36619772367581343075535E-1 2/pi
*
* These lists are subject to change.
*/

/* const.c */

/*
Cephes Math Library Release 2.3: March, 1995
Copyright 1984, 1995 by Stephen L. Moshier
*/

#include "mconf.h"

#ifdef UNK
#if 1
double MACHEP = 1.11022302462515654042E-16; /* 2**-53 */
#else
double MACHEP = 1.38777878078144567553E-17; /* 2**-56 */
#endif
double UFLOWTHRESH = 2.22507385850720138309E-308; /* 2**-1022 */
#ifdef DENORMAL
double MAXLOG = 7.09782712893383996732E2; /* log(MAXNUM) */
/* double MINLOG = -7.44440071921381262314E2; */ /* log(2**-1074) */
double MINLOG = -7.451332191019412076235E2; /* log(2**-1075) */
#else
double MAXLOG = 7.08396418532264106224E2; /* log 2**1022 */
double MINLOG = -7.08396418532264106224E2; /* log 2**-1022 */
#endif
double MAXNUM = 1.79769313486231570815E308; /* 2**1024*(1-MACHEP) */
double PI = 3.14159265358979323846; /* pi */
double PIO2 = 1.57079632679489661923; /* pi/2 */
double PIO4 = 7.85398163397448309616E-1; /* pi/4 */
double SQRT2 = 1.41421356237309504880; /* sqrt(2) */
double SQRTH = 7.07106781186547524401E-1; /* sqrt(2)/2 */
double LOG2E = 1.4426950408889634073599; /* 1/log(2) */
double SQ2OPI = 7.9788456080286535587989E-1; /* sqrt( 2/pi ) */
double LOGE2 = 6.93147180559945309417E-1; /* log(2) */
double LOGSQ2 = 3.46573590279972654709E-1; /* log(2)/2 */
double THPIO4 = 2.35619449019234492885; /* 3*pi/4 */
double TWOOPI = 6.36619772367581343075535E-1; /* 2/pi */
#ifdef INFINITIES
double INFINITY = 1.0/0.0; /* 99e999; */
#else
double INFINITY = 1.79769313486231570815E308; /* 2**1024*(1-MACHEP) */
#endif
#ifdef NANS
double NAN = 1.0/0.0 - 1.0/0.0;
#else
double NAN = 0.0;
#endif
#ifdef MINUSZERO
double NEGZERO = -0.0;
#else
double NEGZERO = 0.0;
#endif
#endif

#ifdef IBMPC
/* 2**-53 = 1.11022302462515654042E-16 */
unsigned short MACHEP[4] = {0x0000,0x0000,0x0000,0x3ca0};
unsigned short UFLOWTHRESH[4] = {0x0000,0x0000,0x0000,0x0010};
#ifdef DENORMAL
/* log(MAXNUM) = 7.09782712893383996732224E2 */
unsigned short MAXLOG[4] = {0x39ef,0xfefa,0x2e42,0x4086};
/* log(2**-1074) = - -7.44440071921381262314E2 */
/*unsigned short MINLOG[4] = {0x71c3,0x446d,0x4385,0xc087};*/
unsigned short MINLOG[4] = {0x3052,0xd52d,0x4910,0xc087};
#else
/* log(2**1022) = 7.08396418532264106224E2 */
unsigned short MAXLOG[4] = {0xbcd2,0xdd7a,0x232b,0x4086};
/* log(2**-1022) = - 7.08396418532264106224E2 */
unsigned short MINLOG[4] = {0xbcd2,0xdd7a,0x232b,0xc086};
#endif
/* 2**1024*(1-MACHEP) = 1.7976931348623158E308 */
unsigned short MAXNUM[4] = {0xffff,0xffff,0xffff,0x7fef};
unsigned short PI[4] = {0x2d18,0x5444,0x21fb,0x4009};
unsigned short PIO2[4] = {0x2d18,0x5444,0x21fb,0x3ff9};
unsigned short PIO4[4] = {0x2d18,0x5444,0x21fb,0x3fe9};
unsigned short SQRT2[4] = {0x3bcd,0x667f,0xa09e,0x3ff6};
unsigned short SQRTH[4] = {0x3bcd,0x667f,0xa09e,0x3fe6};
unsigned short LOG2E[4] = {0x82fe,0x652b,0x1547,0x3ff7};
unsigned short SQ2OPI[4] = {0x3651,0x33d4,0x8845,0x3fe9};
unsigned short LOGE2[4] = {0x39ef,0xfefa,0x2e42,0x3fe6};
unsigned short LOGSQ2[4] = {0x39ef,0xfefa,0x2e42,0x3fd6};
unsigned short THPIO4[4] = {0x21d2,0x7f33,0xd97c,0x4002};
unsigned short TWOOPI[4] = {0xc883,0x6dc9,0x5f30,0x3fe4};
#ifdef INFINITIES
unsigned short INFINITY[4] = {0x0000,0x0000,0x0000,0x7ff0};
#else
unsigned short INFINITY[4] = {0xffff,0xffff,0xffff,0x7fef};
#endif
#ifdef NANS
unsigned short NAN[4] = {0x0000,0x0000,0x0000,0x7ffc};
#else
unsigned short NAN[4] = {0x0000,0x0000,0x0000,0x0000};
#endif
#ifdef MINUSZERO
unsigned short NEGZERO[4] = {0x0000,0x0000,0x0000,0x8000};
#else
unsigned short NEGZERO[4] = {0x0000,0x0000,0x0000,0x0000};
#endif
#endif

#ifdef MIEEE
/* 2**-53 = 1.11022302462515654042E-16 */
unsigned short MACHEP[4] = {0x3ca0,0x0000,0x0000,0x0000};
unsigned short UFLOWTHRESH[4] = {0x0010,0x0000,0x0000,0x0000};
#ifdef DENORMAL
/* log(2**1024) = 7.09782712893383996843E2 */
unsigned short MAXLOG[4] = {0x4086,0x2e42,0xfefa,0x39ef};
/* log(2**-1074) = - -7.44440071921381262314E2 */
/* unsigned short MINLOG[4] = {0xc087,0x4385,0x446d,0x71c3}; */
unsigned short MINLOG[4] = {0xc087,0x4910,0xd52d,0x3052};
#else
/* log(2**1022) = 7.08396418532264106224E2 */
unsigned short MAXLOG[4] = {0x4086,0x232b,0xdd7a,0xbcd2};
/* log(2**-1022) = - 7.08396418532264106224E2 */
unsigned short MINLOG[4] = {0xc086,0x232b,0xdd7a,0xbcd2};
#endif
/* 2**1024*(1-MACHEP) = 1.7976931348623158E308 */
unsigned short MAXNUM[4] = {0x7fef,0xffff,0xffff,0xffff};
unsigned short PI[4] = {0x4009,0x21fb,0x5444,0x2d18};
unsigned short PIO2[4] = {0x3ff9,0x21fb,0x5444,0x2d18};
unsigned short PIO4[4] = {0x3fe9,0x21fb,0x5444,0x2d18};
unsigned short SQRT2[4] = {0x3ff6,0xa09e,0x667f,0x3bcd};
unsigned short SQRTH[4] = {0x3fe6,0xa09e,0x667f,0x3bcd};
unsigned short LOG2E[4] = {0x3ff7,0x1547,0x652b,0x82fe};
unsigned short SQ2OPI[4] = {0x3fe9,0x8845,0x33d4,0x3651};
unsigned short LOGE2[4] = {0x3fe6,0x2e42,0xfefa,0x39ef};
unsigned short LOGSQ2[4] = {0x3fd6,0x2e42,0xfefa,0x39ef};
unsigned short THPIO4[4] = {0x4002,0xd97c,0x7f33,0x21d2};
unsigned short TWOOPI[4] = {0x3fe4,0x5f30,0x6dc9,0xc883};
#ifdef INFINITIES
unsigned short INFINITY[4] = {0x7ff0,0x0000,0x0000,0x0000};
#else
unsigned short INFINITY[4] = {0x7fef,0xffff,0xffff,0xffff};
#endif
#ifdef NANS
unsigned short NAN[4] = {0x7ff8,0x0000,0x0000,0x0000};
#else
unsigned short NAN[4] = {0x0000,0x0000,0x0000,0x0000};
#endif
#ifdef MINUSZERO
unsigned short NEGZERO[4] = {0x8000,0x0000,0x0000,0x0000};
#else
unsigned short NEGZERO[4] = {0x0000,0x0000,0x0000,0x0000};
#endif
#endif

#ifdef DEC
/* 2**-56 = 1.38777878078144567553E-17 */
unsigned short MACHEP[4] = {0022200,0000000,0000000,0000000};
unsigned short UFLOWTHRESH[4] = {0x0080,0x0000,0x0000,0x0000};
/* log 2**127 = 88.029691931113054295988 */
unsigned short MAXLOG[4] = {041660,007463,0143742,025733,};
/* log 2**-128 = -88.72283911167299960540 */
unsigned short MINLOG[4] = {0141661,071027,0173721,0147572,};
/* 2**127 = 1.701411834604692317316873e38 */
unsigned short MAXNUM[4] = {077777,0177777,0177777,0177777,};
unsigned short PI[4] = {040511,007732,0121041,064302,};
unsigned short PIO2[4] = {040311,007732,0121041,064302,};
unsigned short PIO4[4] = {040111,007732,0121041,064302,};
unsigned short SQRT2[4] = {040265,002363,031771,0157145,};
unsigned short SQRTH[4] = {040065,002363,031771,0157144,};
unsigned short LOG2E[4] = {040270,0125073,024534,013761,};
unsigned short SQ2OPI[4] = {040114,041051,0117241,0131204,};
unsigned short LOGE2[4] = {040061,071027,0173721,0147572,};
unsigned short LOGSQ2[4] = {037661,071027,0173721,0147572,};
unsigned short THPIO4[4] = {040426,0145743,0174631,007222,};
unsigned short TWOOPI[4] = {040042,0174603,067116,042025,};
/* Approximate infinity by MAXNUM. */
unsigned short INFINITY[4] = {077777,0177777,0177777,0177777,};
unsigned short NAN[4] = {0000000,0000000,0000000,0000000};
#ifdef MINUSZERO
unsigned short NEGZERO[4] = {0000000,0000000,0000000,0100000};
#else
unsigned short NEGZERO[4] = {0000000,0000000,0000000,0000000};
#endif
#endif

#ifndef UNK
extern unsigned short MACHEP[];
extern unsigned short UFLOWTHRESH[];
extern unsigned short MAXLOG[];
extern unsigned short UNDLOG[];
extern unsigned short MINLOG[];
extern unsigned short MAXNUM[];
extern unsigned short PI[];
extern unsigned short PIO2[];
extern unsigned short PIO4[];
extern unsigned short SQRT2[];
extern unsigned short SQRTH[];
extern unsigned short LOG2E[];
extern unsigned short SQ2OPI[];
extern unsigned short LOGE2[];
extern unsigned short LOGSQ2[];
extern unsigned short THPIO4[];
extern unsigned short TWOOPI[];
extern unsigned short INFINITY[];
extern unsigned short NAN[];
extern unsigned short NEGZERO[];
#endif
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