From 9c07bd167ce25e6110b40797c8462dfcdc1e5c52 Mon Sep 17 00:00:00 2001 From: Alexander Grigorievskiy Date: Fri, 4 Sep 2015 19:44:19 +0300 Subject: [PATCH] UPD: Major update, changed interface of the module, Cython support added. Although cython gives almost no speed-up. --- GPy/kern/_src/sde_stationary.py | 2 +- GPy/models/state_space_cython.c | 26990 ++++++++++++++++++++++++++++ GPy/models/state_space_cython.pyx | 947 + GPy/models/state_space_main.py | 1640 +- GPy/models/state_space_new.py | 41 +- setup.py | 4 + 6 files changed, 28927 insertions(+), 697 deletions(-) create mode 100644 GPy/models/state_space_cython.c create mode 100644 GPy/models/state_space_cython.pyx diff --git a/GPy/kern/_src/sde_stationary.py b/GPy/kern/_src/sde_stationary.py index 76b5266a..9504c5c3 100644 --- a/GPy/kern/_src/sde_stationary.py +++ b/GPy/kern/_src/sde_stationary.py @@ -139,7 +139,7 @@ class sde_Exponential(Exponential): F = np.array(((-1.0/lengthscale,),)) L = np.array(((1.0,),)) Qc = np.array( ((2.0*variance/lengthscale,),) ) - H = np.array(((1,),)) + H = np.array(((1.0,),)) Pinf = np.array(((variance,),)) P0 = Pinf.copy() diff --git a/GPy/models/state_space_cython.c b/GPy/models/state_space_cython.c new file mode 100644 index 00000000..eb54c00c --- /dev/null +++ b/GPy/models/state_space_cython.c @@ -0,0 +1,26990 @@ +/* Generated by Cython 0.22 */ + +/* BEGIN: Cython Metadata +{ + "distutils": { + "depends": [] + } +} +END: Cython Metadata */ + +#define PY_SSIZE_T_CLEAN +#ifndef CYTHON_USE_PYLONG_INTERNALS +#ifdef PYLONG_BITS_IN_DIGIT +#define CYTHON_USE_PYLONG_INTERNALS 0 +#else +#include "pyconfig.h" +#ifdef PYLONG_BITS_IN_DIGIT +#define CYTHON_USE_PYLONG_INTERNALS 1 +#else +#define CYTHON_USE_PYLONG_INTERNALS 0 +#endif +#endif +#endif +#include "Python.h" +#ifndef Py_PYTHON_H + #error Python headers needed to compile C extensions, please install development version of Python. +#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) + #error Cython requires Python 2.6+ or Python 3.2+. +#else +#define CYTHON_ABI "0_22" +#include +#ifndef offsetof +#define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) +#endif +#if !defined(WIN32) && !defined(MS_WINDOWS) + #ifndef __stdcall + #define __stdcall + #endif + #ifndef __cdecl + #define __cdecl + #endif + #ifndef __fastcall + #define __fastcall + #endif +#endif +#ifndef DL_IMPORT + #define DL_IMPORT(t) t +#endif +#ifndef DL_EXPORT + #define DL_EXPORT(t) t +#endif +#ifndef PY_LONG_LONG + #define PY_LONG_LONG LONG_LONG +#endif +#ifndef Py_HUGE_VAL + #define Py_HUGE_VAL HUGE_VAL +#endif +#ifdef PYPY_VERSION +#define CYTHON_COMPILING_IN_PYPY 1 +#define CYTHON_COMPILING_IN_CPYTHON 0 +#else +#define CYTHON_COMPILING_IN_PYPY 0 +#define CYTHON_COMPILING_IN_CPYTHON 1 +#endif +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) +#define Py_OptimizeFlag 0 +#endif +#define __PYX_BUILD_PY_SSIZE_T "n" +#define CYTHON_FORMAT_SSIZE_T "z" +#if PY_MAJOR_VERSION < 3 + #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyClass_Type +#else + #define __Pyx_BUILTIN_MODULE_NAME "builtins" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyType_Type +#endif +#if PY_MAJOR_VERSION >= 3 + #define Py_TPFLAGS_CHECKTYPES 0 + #define Py_TPFLAGS_HAVE_INDEX 0 + #define Py_TPFLAGS_HAVE_NEWBUFFER 0 +#endif +#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE) + #define Py_TPFLAGS_HAVE_FINALIZE 0 +#endif +#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) + #define CYTHON_PEP393_ENABLED 1 + #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ + 0 : _PyUnicode_Ready((PyObject *)(op))) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) + #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) + #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) + #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) +#else + #define CYTHON_PEP393_ENABLED 0 + #define __Pyx_PyUnicode_READY(op) (0) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) + #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) + #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) + #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) +#endif +#if CYTHON_COMPILING_IN_PYPY + #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) + #define __Pyx_PyFrozenSet_Size(s) PyObject_Size(s) +#else + #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \ + PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) + #define __Pyx_PyFrozenSet_Size(s) PySet_Size(s) +#endif +#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) +#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b) +#else + #define __Pyx_PyString_Format(a, b) PyString_Format(a, b) +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBaseString_Type PyUnicode_Type + #define PyStringObject PyUnicodeObject + #define PyString_Type PyUnicode_Type + #define PyString_Check PyUnicode_Check + #define PyString_CheckExact PyUnicode_CheckExact +#endif +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) + #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) +#else + #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj)) + #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj)) +#endif +#ifndef PySet_CheckExact + #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) +#endif +#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) +#if PY_MAJOR_VERSION >= 3 + #define PyIntObject PyLongObject + #define PyInt_Type PyLong_Type + #define PyInt_Check(op) PyLong_Check(op) + #define PyInt_CheckExact(op) PyLong_CheckExact(op) + #define PyInt_FromString PyLong_FromString + #define PyInt_FromUnicode PyLong_FromUnicode + #define PyInt_FromLong PyLong_FromLong + #define PyInt_FromSize_t PyLong_FromSize_t + #define PyInt_FromSsize_t PyLong_FromSsize_t + #define PyInt_AsLong PyLong_AsLong + #define PyInt_AS_LONG PyLong_AS_LONG + #define PyInt_AsSsize_t PyLong_AsSsize_t + #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask + #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask + #define PyNumber_Int PyNumber_Long +#endif +#if PY_MAJOR_VERSION >= 3 + #define PyBoolObject PyLongObject +#endif +#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY + #ifndef PyUnicode_InternFromString + #define PyUnicode_InternFromString(s) PyUnicode_FromString(s) + #endif +#endif +#if PY_VERSION_HEX < 0x030200A4 + typedef long Py_hash_t; + #define __Pyx_PyInt_FromHash_t PyInt_FromLong + #define __Pyx_PyInt_AsHash_t PyInt_AsLong +#else + #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t + #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t +#endif +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) +#else + #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) +#endif +#ifndef CYTHON_INLINE + #if defined(__GNUC__) + #define CYTHON_INLINE __inline__ + #elif defined(_MSC_VER) + #define CYTHON_INLINE __inline + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_INLINE inline + #else + #define CYTHON_INLINE + #endif +#endif +#ifndef CYTHON_RESTRICT + #if defined(__GNUC__) + #define CYTHON_RESTRICT __restrict__ + #elif defined(_MSC_VER) && _MSC_VER >= 1400 + #define CYTHON_RESTRICT __restrict + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_RESTRICT restrict + #else + #define CYTHON_RESTRICT + #endif +#endif +#ifdef NAN +#define __PYX_NAN() ((float) NAN) +#else +static CYTHON_INLINE float __PYX_NAN() { + /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and + a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is + a quiet NaN. */ + float value; + memset(&value, 0xFF, sizeof(value)); + return value; +} +#endif +#define __Pyx_void_to_None(void_result) (void_result, Py_INCREF(Py_None), Py_None) +#ifdef __cplusplus +template +void __Pyx_call_destructor(T* x) { + x->~T(); +} +template +class __Pyx_FakeReference { + public: + __Pyx_FakeReference() : ptr(NULL) { } + __Pyx_FakeReference(T& ref) : ptr(&ref) { } + T *operator->() { return ptr; } + operator T&() { return *ptr; } + private: + T *ptr; +}; +#endif + + +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) +#else + #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) +#endif + +#ifndef __PYX_EXTERN_C + #ifdef __cplusplus + #define __PYX_EXTERN_C extern "C" + #else + #define __PYX_EXTERN_C extern + #endif +#endif + +#if defined(WIN32) || defined(MS_WINDOWS) +#define _USE_MATH_DEFINES +#endif +#include +#define __PYX_HAVE__state_space_cython +#define __PYX_HAVE_API__state_space_cython +#include "string.h" +#include "stdio.h" +#include "stdlib.h" +#include "numpy/arrayobject.h" +#include "numpy/ufuncobject.h" +#ifdef _OPENMP +#include +#endif /* _OPENMP */ + +#ifdef PYREX_WITHOUT_ASSERTIONS +#define CYTHON_WITHOUT_ASSERTIONS +#endif + +#ifndef CYTHON_UNUSED +# if defined(__GNUC__) +# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +#endif +typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; + const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; + +#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 +#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0 +#define __PYX_DEFAULT_STRING_ENCODING "" +#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString +#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \ + (sizeof(type) < sizeof(Py_ssize_t)) || \ + (sizeof(type) > sizeof(Py_ssize_t) && \ + likely(v < (type)PY_SSIZE_T_MAX || \ + v == (type)PY_SSIZE_T_MAX) && \ + (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \ + v == (type)PY_SSIZE_T_MIN))) || \ + (sizeof(type) == sizeof(Py_ssize_t) && \ + (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \ + v == (type)PY_SSIZE_T_MAX))) ) +static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); +static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); +#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) +#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) +#define __Pyx_PyBytes_FromString PyBytes_FromString +#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#else + #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize +#endif +#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) +#if PY_MAJOR_VERSION < 3 +static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) +{ + const Py_UNICODE *u_end = u; + while (*u_end++) ; + return (size_t)(u_end - u - 1); +} +#else +#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen +#endif +#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) +#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode +#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode +#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None) +#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); +#if CYTHON_COMPILING_IN_CPYTHON +#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) +#else +#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) +#endif +#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII +static int __Pyx_sys_getdefaultencoding_not_ascii; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + PyObject* ascii_chars_u = NULL; + PyObject* ascii_chars_b = NULL; + const char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + if (strcmp(default_encoding_c, "ascii") == 0) { + __Pyx_sys_getdefaultencoding_not_ascii = 0; + } else { + char ascii_chars[128]; + int c; + for (c = 0; c < 128; c++) { + ascii_chars[c] = c; + } + __Pyx_sys_getdefaultencoding_not_ascii = 1; + ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); + if (!ascii_chars_u) goto bad; + ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); + if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { + PyErr_Format( + PyExc_ValueError, + "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", + default_encoding_c); + goto bad; + } + Py_DECREF(ascii_chars_u); + Py_DECREF(ascii_chars_b); + } + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + Py_XDECREF(ascii_chars_u); + Py_XDECREF(ascii_chars_b); + return -1; +} +#endif +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3 +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL) +#else +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL) +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +static char* __PYX_DEFAULT_STRING_ENCODING; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c)); + if (!__PYX_DEFAULT_STRING_ENCODING) goto bad; + strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + return -1; +} +#endif +#endif + + +/* Test for GCC > 2.95 */ +#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))) + #define likely(x) __builtin_expect(!!(x), 1) + #define unlikely(x) __builtin_expect(!!(x), 0) +#else /* !__GNUC__ or GCC < 2.95 */ + #define likely(x) (x) + #define unlikely(x) (x) +#endif /* __GNUC__ */ + +static PyObject *__pyx_m; +static PyObject *__pyx_d; +static PyObject *__pyx_b; +static PyObject *__pyx_empty_tuple; +static PyObject *__pyx_empty_bytes; +static int __pyx_lineno; +static int __pyx_clineno = 0; +static const char * __pyx_cfilenm= __FILE__; +static const char *__pyx_filename; + +#if !defined(CYTHON_CCOMPLEX) + #if defined(__cplusplus) + #define CYTHON_CCOMPLEX 1 + #elif defined(_Complex_I) + #define CYTHON_CCOMPLEX 1 + #else + #define CYTHON_CCOMPLEX 0 + #endif +#endif +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #include + #else + #include + #endif +#endif +#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__) + #undef _Complex_I + #define _Complex_I 1.0fj +#endif + + +static const char *__pyx_f[] = { + "state_space_cython.pyx", + "__init__.pxd", + "type.pxd", +}; +#define IS_UNSIGNED(type) (((type) -1) > 0) +struct __Pyx_StructField_; +#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0) +typedef struct { + const char* name; + struct __Pyx_StructField_* fields; + size_t size; + size_t arraysize[8]; + int ndim; + char typegroup; + char is_unsigned; + int flags; +} __Pyx_TypeInfo; +typedef struct __Pyx_StructField_ { + __Pyx_TypeInfo* type; + const char* name; + size_t offset; +} __Pyx_StructField; +typedef struct { + __Pyx_StructField* field; + size_t parent_offset; +} __Pyx_BufFmt_StackElem; +typedef struct { + __Pyx_StructField root; + __Pyx_BufFmt_StackElem* head; + size_t fmt_offset; + size_t new_count, enc_count; + size_t struct_alignment; + int is_complex; + char enc_type; + char new_packmode; + char enc_packmode; + char is_valid_array; +} __Pyx_BufFmt_Context; + + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 + * # in Cython to enable them only on the right systems. + * + * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + */ +typedef npy_int8 __pyx_t_5numpy_int8_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":727 + * + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t + */ +typedef npy_int16 __pyx_t_5numpy_int16_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":728 + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< + * ctypedef npy_int64 int64_t + * #ctypedef npy_int96 int96_t + */ +typedef npy_int32 __pyx_t_5numpy_int32_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":729 + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< + * #ctypedef npy_int96 int96_t + * #ctypedef npy_int128 int128_t + */ +typedef npy_int64 __pyx_t_5numpy_int64_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 + * #ctypedef npy_int128 int128_t + * + * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + */ +typedef npy_uint8 __pyx_t_5numpy_uint8_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":734 + * + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t + */ +typedef npy_uint16 __pyx_t_5numpy_uint16_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":735 + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< + * ctypedef npy_uint64 uint64_t + * #ctypedef npy_uint96 uint96_t + */ +typedef npy_uint32 __pyx_t_5numpy_uint32_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":736 + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< + * #ctypedef npy_uint96 uint96_t + * #ctypedef npy_uint128 uint128_t + */ +typedef npy_uint64 __pyx_t_5numpy_uint64_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":740 + * #ctypedef npy_uint128 uint128_t + * + * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< + * ctypedef npy_float64 float64_t + * #ctypedef npy_float80 float80_t + */ +typedef npy_float32 __pyx_t_5numpy_float32_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":741 + * + * ctypedef npy_float32 float32_t + * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< + * #ctypedef npy_float80 float80_t + * #ctypedef npy_float128 float128_t + */ +typedef npy_float64 __pyx_t_5numpy_float64_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":750 + * # The int types are mapped a bit surprising -- + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t + */ +typedef npy_long __pyx_t_5numpy_int_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751 + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong longlong_t + * + */ +typedef npy_longlong __pyx_t_5numpy_long_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":752 + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_ulong uint_t + */ +typedef npy_longlong __pyx_t_5numpy_longlong_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":754 + * ctypedef npy_longlong longlong_t + * + * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t + */ +typedef npy_ulong __pyx_t_5numpy_uint_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755 + * + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulonglong_t + * + */ +typedef npy_ulonglong __pyx_t_5numpy_ulong_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":756 + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_intp intp_t + */ +typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 + * ctypedef npy_ulonglong ulonglong_t + * + * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< + * ctypedef npy_uintp uintp_t + * + */ +typedef npy_intp __pyx_t_5numpy_intp_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759 + * + * ctypedef npy_intp intp_t + * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< + * + * ctypedef npy_double float_t + */ +typedef npy_uintp __pyx_t_5numpy_uintp_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":761 + * ctypedef npy_uintp uintp_t + * + * ctypedef npy_double float_t # <<<<<<<<<<<<<< + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t + */ +typedef npy_double __pyx_t_5numpy_float_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762 + * + * ctypedef npy_double float_t + * ctypedef npy_double double_t # <<<<<<<<<<<<<< + * ctypedef npy_longdouble longdouble_t + * + */ +typedef npy_double __pyx_t_5numpy_double_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":763 + * ctypedef npy_double float_t + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cfloat cfloat_t + */ +typedef npy_longdouble __pyx_t_5numpy_longdouble_t; + +/* "state_space_cython.pyx":13 + * DTYPE_int = np.int64 + * + * ctypedef np.float64_t DTYPE_t # <<<<<<<<<<<<<< + * ctypedef np.int64_t DTYPE_int_t + * + */ +typedef __pyx_t_5numpy_float64_t __pyx_t_18state_space_cython_DTYPE_t; + +/* "state_space_cython.pyx":14 + * + * ctypedef np.float64_t DTYPE_t + * ctypedef np.int64_t DTYPE_int_t # <<<<<<<<<<<<<< + * + * # Template class for dynamic callables + */ +typedef __pyx_t_5numpy_int64_t __pyx_t_18state_space_cython_DTYPE_int_t; +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< float > __pyx_t_float_complex; + #else + typedef float _Complex __pyx_t_float_complex; + #endif +#else + typedef struct { float real, imag; } __pyx_t_float_complex; +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< double > __pyx_t_double_complex; + #else + typedef double _Complex __pyx_t_double_complex; + #endif +#else + typedef struct { double real, imag; } __pyx_t_double_complex; +#endif + + +/*--- Type declarations ---*/ +struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython; +struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython; +struct __pyx_obj_18state_space_cython_R_handling_Cython; +struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython; +struct __pyx_obj_18state_space_cython_Q_handling_Cython; +struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython; +struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":765 + * ctypedef npy_longdouble longdouble_t + * + * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< + * ctypedef npy_cdouble cdouble_t + * ctypedef npy_clongdouble clongdouble_t + */ +typedef npy_cfloat __pyx_t_5numpy_cfloat_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766 + * + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< + * ctypedef npy_clongdouble clongdouble_t + * + */ +typedef npy_cdouble __pyx_t_5numpy_cdouble_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":767 + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t + * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cdouble complex_t + */ +typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; + +/* "../../../../../../Work/anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":769 + * ctypedef npy_clongdouble clongdouble_t + * + * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< + * + * cdef inline object PyArray_MultiIterNew1(a): + */ +typedef npy_cdouble __pyx_t_5numpy_complex_t; +struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset; +struct __pyx_opt_args_18state_space_cython_28Measurement_Callables_Cython_reset; +struct __pyx_opt_args_18state_space_cython_28Std_Dynamic_Callables_Cython_reset; +struct __pyx_opt_args_18state_space_cython_22AQcompute_batch_Cython_reset; + +/* "state_space_cython.pyx":36 + * raise NotImplemented("(cython) dQk is not implemented!") + * + * cpdef reset(self, bint compute_derivatives = False): # <<<<<<<<<<<<<< + * raise NotImplemented("(cython) reset is not implemented!") + * + */ +struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset { + int __pyx_n; + int compute_derivatives; +}; + +/* "state_space_cython.pyx":59 + * raise NotImplemented("(cython) dQk is not implemented!") + * + * cpdef reset(self,compute_derivatives = False): # <<<<<<<<<<<<<< + * raise NotImplemented("(cython) reset is not implemented!") + * + */ +struct __pyx_opt_args_18state_space_cython_28Measurement_Callables_Cython_reset { + int __pyx_n; + PyObject *compute_derivatives; +}; + +/* "state_space_cython.pyx":361 + * + * + * cpdef reset(self, bint compute_derivatives=False): # <<<<<<<<<<<<<< + * """ + * For reusing this object e.g. in smoother computation. It makes sence + */ +struct __pyx_opt_args_18state_space_cython_28Std_Dynamic_Callables_Cython_reset { + int __pyx_n; + int compute_derivatives; +}; + +/* "state_space_cython.pyx":440 + * return np.dot(A, m) # default dynamic model + * + * cpdef reset(self, bint compute_derivatives=False): # <<<<<<<<<<<<<< + * """ + * For reusing this object e.g. in smoother computation. It makes sence + */ +struct __pyx_opt_args_18state_space_cython_22AQcompute_batch_Cython_reset { + int __pyx_n; + int compute_derivatives; +}; + +/* "state_space_cython.pyx":17 + * + * # Template class for dynamic callables + * cdef class Dynamic_Callables_Cython: # <<<<<<<<<<<<<< + * cpdef f_a(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] A): + * raise NotImplemented("(cython) f_a is not implemented!") + */ +struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython { + PyObject_HEAD + struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython *__pyx_vtab; +}; + + +/* "state_space_cython.pyx":40 + * + * # Template class for measurement callables + * cdef class Measurement_Callables_Cython: # <<<<<<<<<<<<<< + * cpdef f_h(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] Hk): + * raise NotImplemented("(cython) f_a is not implemented!") + */ +struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython { + PyObject_HEAD + struct __pyx_vtabstruct_18state_space_cython_Measurement_Callables_Cython *__pyx_vtab; +}; + + +/* "state_space_cython.pyx":62 + * raise NotImplemented("(cython) reset is not implemented!") + * + * cdef class R_handling_Cython(Measurement_Callables_Cython): # <<<<<<<<<<<<<< + * """ + * The calss handles noise matrix R. + */ +struct __pyx_obj_18state_space_cython_R_handling_Cython { + struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython __pyx_base; + PyArrayObject *R; + PyArrayObject *index; + int R_time_var_index; + PyArrayObject *dR; + int svd_each_time; + PyObject *R_square_root; +}; + + +/* "state_space_cython.pyx":161 + * + * + * cdef class Std_Measurement_Callables_Cython(R_handling_Cython): # <<<<<<<<<<<<<< + * + * cdef: + */ +struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython { + struct __pyx_obj_18state_space_cython_R_handling_Cython __pyx_base; + PyArrayObject *H; + int H_time_var_index; + PyArrayObject *dH; +}; + + +/* "state_space_cython.pyx":208 + * + * + * cdef class Q_handling_Cython(Dynamic_Callables_Cython): # <<<<<<<<<<<<<< + * + * cdef: + */ +struct __pyx_obj_18state_space_cython_Q_handling_Cython { + struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython __pyx_base; + PyArrayObject *Q; + PyArrayObject *index; + int Q_time_var_index; + PyArrayObject *dQ; + PyObject *Q_square_root; + int svd_each_time; +}; + + +/* "state_space_cython.pyx":314 + * return square_root + * + * cdef class Std_Dynamic_Callables_Cython(Q_handling_Cython): # <<<<<<<<<<<<<< + * cdef: + * np.ndarray A + */ +struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython { + struct __pyx_obj_18state_space_cython_Q_handling_Cython __pyx_base; + PyArrayObject *A; + int A_time_var_index; + PyArrayObject *dA; +}; + + +/* "state_space_cython.pyx":369 + * return self + * + * cdef class AQcompute_batch_Cython(Q_handling_Cython): # <<<<<<<<<<<<<< + * """ + * Class for calculating matrices A, Q, dA, dQ of the discrete Kalman Filter + */ +struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython { + struct __pyx_obj_18state_space_cython_Q_handling_Cython __pyx_base; + PyArrayObject *As; + PyArrayObject *Qs; + PyArrayObject *dAs; + PyArrayObject *dQs; + PyArrayObject *reconstruct_indices; + PyObject *Q_svd_dict; + int last_k; +}; + + + +/* "state_space_cython.pyx":17 + * + * # Template class for dynamic callables + * cdef class Dynamic_Callables_Cython: # <<<<<<<<<<<<<< + * cpdef f_a(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] A): + * raise NotImplemented("(cython) f_a is not implemented!") + */ + +struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython { + PyObject *(*f_a)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch); + PyObject *(*Ak)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch); + PyObject *(*Qk)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch); + PyObject *(*Q_srk)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch); + PyObject *(*dAk)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch); + PyObject *(*dQk)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch); + PyObject *(*reset)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset *__pyx_optional_args); +}; +static struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython *__pyx_vtabptr_18state_space_cython_Dynamic_Callables_Cython; + + +/* "state_space_cython.pyx":40 + * + * # Template class for measurement callables + * cdef class Measurement_Callables_Cython: # <<<<<<<<<<<<<< + * cpdef f_h(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] Hk): + * raise NotImplemented("(cython) f_a is not implemented!") + */ + +struct __pyx_vtabstruct_18state_space_cython_Measurement_Callables_Cython { + PyObject *(*f_h)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch); + PyObject *(*Hk)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch); + PyObject *(*Rk)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch); + PyObject *(*R_isrk)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch); + PyObject *(*dHk)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch); + PyObject *(*dRk)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch); + PyObject *(*reset)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_28Measurement_Callables_Cython_reset *__pyx_optional_args); +}; +static struct __pyx_vtabstruct_18state_space_cython_Measurement_Callables_Cython *__pyx_vtabptr_18state_space_cython_Measurement_Callables_Cython; + + +/* "state_space_cython.pyx":62 + * raise NotImplemented("(cython) reset is not implemented!") + * + * cdef class R_handling_Cython(Measurement_Callables_Cython): # <<<<<<<<<<<<<< + * """ + * The calss handles noise matrix R. + */ + +struct __pyx_vtabstruct_18state_space_cython_R_handling_Cython { + struct __pyx_vtabstruct_18state_space_cython_Measurement_Callables_Cython __pyx_base; +}; +static struct __pyx_vtabstruct_18state_space_cython_R_handling_Cython *__pyx_vtabptr_18state_space_cython_R_handling_Cython; + + +/* "state_space_cython.pyx":161 + * + * + * cdef class Std_Measurement_Callables_Cython(R_handling_Cython): # <<<<<<<<<<<<<< + * + * cdef: + */ + +struct __pyx_vtabstruct_18state_space_cython_Std_Measurement_Callables_Cython { + struct __pyx_vtabstruct_18state_space_cython_R_handling_Cython __pyx_base; +}; +static struct __pyx_vtabstruct_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_vtabptr_18state_space_cython_Std_Measurement_Callables_Cython; + + +/* "state_space_cython.pyx":208 + * + * + * cdef class Q_handling_Cython(Dynamic_Callables_Cython): # <<<<<<<<<<<<<< + * + * cdef: + */ + +struct __pyx_vtabstruct_18state_space_cython_Q_handling_Cython { + struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython __pyx_base; +}; +static struct __pyx_vtabstruct_18state_space_cython_Q_handling_Cython *__pyx_vtabptr_18state_space_cython_Q_handling_Cython; + + +/* "state_space_cython.pyx":314 + * return square_root + * + * cdef class Std_Dynamic_Callables_Cython(Q_handling_Cython): # <<<<<<<<<<<<<< + * cdef: + * np.ndarray A + */ + +struct __pyx_vtabstruct_18state_space_cython_Std_Dynamic_Callables_Cython { + struct __pyx_vtabstruct_18state_space_cython_Q_handling_Cython __pyx_base; +}; +static struct __pyx_vtabstruct_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_vtabptr_18state_space_cython_Std_Dynamic_Callables_Cython; + + +/* "state_space_cython.pyx":369 + * return self + * + * cdef class AQcompute_batch_Cython(Q_handling_Cython): # <<<<<<<<<<<<<< + * """ + * Class for calculating matrices A, Q, dA, dQ of the discrete Kalman Filter + */ + +struct __pyx_vtabstruct_18state_space_cython_AQcompute_batch_Cython { + struct __pyx_vtabstruct_18state_space_cython_Q_handling_Cython __pyx_base; +}; +static struct __pyx_vtabstruct_18state_space_cython_AQcompute_batch_Cython *__pyx_vtabptr_18state_space_cython_AQcompute_batch_Cython; + +/* --- Runtime support code (head) --- */ +#ifndef CYTHON_REFNANNY + #define CYTHON_REFNANNY 0 +#endif +#if CYTHON_REFNANNY + typedef struct { + void (*INCREF)(void*, PyObject*, int); + void (*DECREF)(void*, PyObject*, int); + void (*GOTREF)(void*, PyObject*, int); + void (*GIVEREF)(void*, PyObject*, int); + void* (*SetupContext)(const char*, int, const char*); + void (*FinishContext)(void**); + } __Pyx_RefNannyAPIStruct; + static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL; + static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); + #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL; +#ifdef WITH_THREAD + #define __Pyx_RefNannySetupContext(name, acquire_gil) \ + if (acquire_gil) { \ + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); \ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \ + PyGILState_Release(__pyx_gilstate_save); \ + } else { \ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); 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\ + r = v; __Pyx_XDECREF(tmp); \ + } while (0) +#define __Pyx_DECREF_SET(r, v) do { \ + PyObject *tmp = (PyObject *) r; \ + r = v; __Pyx_DECREF(tmp); \ + } while (0) +#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0) +#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0) + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_getattro)) + return tp->tp_getattro(obj, attr_name); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_getattr)) + return tp->tp_getattr(obj, PyString_AS_STRING(attr_name)); +#endif + return PyObject_GetAttr(obj, attr_name); +} +#else +#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n) +#endif + +static PyObject *__Pyx_GetBuiltinName(PyObject *name); + +static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, + __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); +static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); +#else +#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw) +#endif + +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); + +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); + +static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, + Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); + +static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); + +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ + const char* function_name); + +static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, + const char *name, int exact); + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); + +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); + +static void __Pyx_RaiseBufferFallbackError(void); + +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +static CYTHON_INLINE int __Pyx_IterFinish(void); + +static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); + +static CYTHON_INLINE int __Pyx_PyDict_Contains(PyObject* item, PyObject* dict, int eq) { + int result = PyDict_Contains(dict, item); + return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); +} + +#if PY_MAJOR_VERSION >= 3 +static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { + PyObject *value; + value = PyDict_GetItemWithError(d, key); + if (unlikely(!value)) { + if (!PyErr_Occurred()) { + PyObject* args = PyTuple_Pack(1, key); + if (likely(args)) + PyErr_SetObject(PyExc_KeyError, args); + Py_XDECREF(args); + } + return NULL; + } + Py_INCREF(value); + return value; +} +#else + #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +#define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o,n,NULL) +static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_setattro)) + return tp->tp_setattro(obj, attr_name, value); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_setattr)) + return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value); +#endif + return PyObject_SetAttr(obj, attr_name, value); +} +#else +#define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n) +#define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v) +#endif + +#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ + __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \ + __Pyx_GetItemInt_Generic(o, to_py_func(i)))) +#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ + __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ + (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ + __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ + (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, + int is_list, int wraparound, int boundscheck); + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); + +static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse); + +static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_dealloc); + +static int __Pyx_SetVtable(PyObject *dict, void *vtable); + +typedef struct { + int code_line; + PyCodeObject* code_object; +} __Pyx_CodeObjectCacheEntry; +struct __Pyx_CodeObjectCache { + int count; + int max_count; + __Pyx_CodeObjectCacheEntry* entries; +}; +static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); +static PyCodeObject *__pyx_find_code_object(int code_line); +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); + +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename); + +typedef struct { + Py_ssize_t shape, strides, suboffsets; +} __Pyx_Buf_DimInfo; +typedef struct { + size_t refcount; + Py_buffer pybuffer; +} __Pyx_Buffer; +typedef struct { + __Pyx_Buffer *rcbuffer; + char *data; + __Pyx_Buf_DimInfo diminfo[8]; +} __Pyx_LocalBuf_ND; + +#if PY_MAJOR_VERSION < 3 + static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); + static void __Pyx_ReleaseBuffer(Py_buffer *view); +#else + #define __Pyx_GetBuffer PyObject_GetBuffer + #define __Pyx_ReleaseBuffer PyBuffer_Release +#endif + + +static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0}; +static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; + +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); + +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value); + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #define __Pyx_CREAL(z) ((z).real()) + #define __Pyx_CIMAG(z) ((z).imag()) + #else + #define __Pyx_CREAL(z) (__real__(z)) + #define __Pyx_CIMAG(z) (__imag__(z)) + #endif +#else + #define __Pyx_CREAL(z) ((z).real) + #define __Pyx_CIMAG(z) ((z).imag) +#endif +#if (defined(_WIN32) || defined(__clang__)) && defined(__cplusplus) && CYTHON_CCOMPLEX + #define __Pyx_SET_CREAL(z,x) ((z).real(x)) + #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) +#else + #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) + #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) +#endif + +static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); + +#if CYTHON_CCOMPLEX + #define __Pyx_c_eqf(a, b) ((a)==(b)) + #define __Pyx_c_sumf(a, b) ((a)+(b)) + #define __Pyx_c_difff(a, b) ((a)-(b)) + #define __Pyx_c_prodf(a, b) ((a)*(b)) + #define __Pyx_c_quotf(a, b) ((a)/(b)) + #define __Pyx_c_negf(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zerof(z) ((z)==(float)0) + #define __Pyx_c_conjf(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_absf(z) (::std::abs(z)) + #define __Pyx_c_powf(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zerof(z) ((z)==0) + #define __Pyx_c_conjf(z) (conjf(z)) + #if 1 + #define __Pyx_c_absf(z) (cabsf(z)) + #define __Pyx_c_powf(a, b) (cpowf(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex); + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex); + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex); + #endif +#endif + +static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); + +#if CYTHON_CCOMPLEX + #define __Pyx_c_eq(a, b) ((a)==(b)) + #define __Pyx_c_sum(a, b) ((a)+(b)) + #define __Pyx_c_diff(a, b) ((a)-(b)) + #define __Pyx_c_prod(a, b) ((a)*(b)) + #define __Pyx_c_quot(a, b) ((a)/(b)) + #define __Pyx_c_neg(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zero(z) ((z)==(double)0) + #define __Pyx_c_conj(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_abs(z) (::std::abs(z)) + #define __Pyx_c_pow(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zero(z) ((z)==0) + #define __Pyx_c_conj(z) (conj(z)) + #if 1 + #define __Pyx_c_abs(z) (cabs(z)) + #define __Pyx_c_pow(a, b) (cpow(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex); + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex); + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex); + #endif +#endif + +static int __Pyx_check_binary_version(void); + +#if !defined(__Pyx_PyIdentifier_FromString) +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) +#else + #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) +#endif +#endif + +static PyObject *__Pyx_ImportModule(const char *name); + +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); + +static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_f_a(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m, CYTHON_UNUSED PyArrayObject *__pyx_v_A, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Ak(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m, CYTHON_UNUSED PyArrayObject *__pyx_v_P, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Qk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Q_srk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_dAk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_dQk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_reset(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset *__pyx_optional_args); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_f_h(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_Hk, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Hk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_P_pred, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Rk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_R_isrk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_dHk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_dRk(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_28Measurement_Callables_Cython_reset(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_28Measurement_Callables_Cython_reset *__pyx_optional_args); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_Rk(struct __pyx_obj_18state_space_cython_R_handling_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_dRk(struct __pyx_obj_18state_space_cython_R_handling_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk(struct __pyx_obj_18state_space_cython_R_handling_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython_f_h(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_H, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython_Hk(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_P_pred, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython_dHk(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_17Q_handling_Cython_Qk(struct __pyx_obj_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_17Q_handling_Cython_dQk(struct __pyx_obj_18state_space_cython_Q_handling_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_17Q_handling_Cython_Q_srk(struct __pyx_obj_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_f_a(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_Ak(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m_pred, CYTHON_UNUSED PyArrayObject *__pyx_v_P_pred, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_dAk(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_28Std_Dynamic_Callables_Cython_reset(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_28Std_Dynamic_Callables_Cython_reset *__pyx_optional_args); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_f_a(CYTHON_UNUSED struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, CYTHON_UNUSED int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_reset(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_22AQcompute_batch_Cython_reset *__pyx_optional_args); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Ak(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, CYTHON_UNUSED PyArrayObject *__pyx_v_m, CYTHON_UNUSED PyArrayObject *__pyx_v_P, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Qk(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_dAk(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_dQk(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ +static PyObject *__pyx_f_18state_space_cython_22AQcompute_batch_Cython_Q_srk(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, int __pyx_skip_dispatch); /* proto*/ + +/* Module declarations from 'cpython.buffer' */ + +/* Module declarations from 'cpython.ref' */ + +/* Module declarations from 'libc.string' */ + +/* Module declarations from 'libc.stdio' */ + +/* Module declarations from 'cpython.object' */ + +/* Module declarations from '__builtin__' */ + +/* Module declarations from 'cpython.type' */ +static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; + +/* Module declarations from 'libc.stdlib' */ + +/* Module declarations from 'numpy' */ + +/* Module declarations from 'numpy' */ +static PyTypeObject *__pyx_ptype_5numpy_dtype = 0; +static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0; +static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0; +static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; +static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; +static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ + +/* Module declarations from 'cython' */ + +/* Module declarations from 'state_space_cython' */ +static PyTypeObject *__pyx_ptype_18state_space_cython_Dynamic_Callables_Cython = 0; +static PyTypeObject *__pyx_ptype_18state_space_cython_Measurement_Callables_Cython = 0; +static PyTypeObject *__pyx_ptype_18state_space_cython_R_handling_Cython = 0; +static PyTypeObject *__pyx_ptype_18state_space_cython_Std_Measurement_Callables_Cython = 0; +static PyTypeObject *__pyx_ptype_18state_space_cython_Q_handling_Cython = 0; +static PyTypeObject *__pyx_ptype_18state_space_cython_Std_Dynamic_Callables_Cython = 0; +static PyTypeObject *__pyx_ptype_18state_space_cython_AQcompute_batch_Cython = 0; +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t = { "DTYPE_t", NULL, sizeof(__pyx_t_18state_space_cython_DTYPE_t), { 0 }, 0, 'R', 0, 0 }; +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_int_t = { "DTYPE_int_t", NULL, sizeof(__pyx_t_18state_space_cython_DTYPE_int_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_18state_space_cython_DTYPE_int_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_18state_space_cython_DTYPE_int_t), 0 }; +#define __Pyx_MODULE_NAME "state_space_cython" +int __pyx_module_is_main_state_space_cython = 0; + +/* Implementation of 'state_space_cython' */ +static PyObject *__pyx_builtin_NotImplemented; +static PyObject *__pyx_builtin_ValueError; +static PyObject *__pyx_builtin_super; +static PyObject *__pyx_builtin_range; +static PyObject *__pyx_builtin_RuntimeError; +static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_f_a(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_2Ak(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_P); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_4Qk(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_6Q_srk(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_8dAk(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_10dQk(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_24Dynamic_Callables_Cython_12reset(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_compute_derivatives); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_f_h(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_Hk); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_2Hk(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_P_pred); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_4Rk(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_6R_isrk(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_8dHk(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_10dRk(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_28Measurement_Callables_Cython_12reset(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_self, PyObject *__pyx_v_compute_derivatives); /* proto */ +static int __pyx_pf_18state_space_cython_17R_handling_Cython___init__(struct __pyx_obj_18state_space_cython_R_handling_Cython *__pyx_v_self, PyArrayObject *__pyx_v_R, PyArrayObject *__pyx_v_index, int __pyx_v_R_time_var_index, int __pyx_v_p_unique_R_number, PyArrayObject *__pyx_v_dR); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_17R_handling_Cython_2Rk(struct __pyx_obj_18state_space_cython_R_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_17R_handling_Cython_4dRk(struct __pyx_obj_18state_space_cython_R_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_17R_handling_Cython_6R_isrk(struct __pyx_obj_18state_space_cython_R_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static int __pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cython___init__(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, PyArrayObject *__pyx_v_H, int __pyx_v_H_time_var_index, PyArrayObject *__pyx_v_R, PyArrayObject *__pyx_v_index, int __pyx_v_R_time_var_index, int __pyx_v_unique_R_number, PyArrayObject *__pyx_v_dH, PyArrayObject *__pyx_v_dR); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cython_2f_h(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_H); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cython_4Hk(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_P_pred); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_32Std_Measurement_Callables_Cython_6dHk(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static int __pyx_pf_18state_space_cython_17Q_handling_Cython___init__(struct __pyx_obj_18state_space_cython_Q_handling_Cython *__pyx_v_self, PyArrayObject *__pyx_v_Q, PyArrayObject *__pyx_v_index, int __pyx_v_Q_time_var_index, int __pyx_v_p_unique_Q_number, PyArrayObject *__pyx_v_dQ); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_17Q_handling_Cython_2Qk(struct __pyx_obj_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_17Q_handling_Cython_4dQk(struct __pyx_obj_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_17Q_handling_Cython_6Q_srk(struct __pyx_obj_18state_space_cython_Q_handling_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static int __pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython___init__(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, PyArrayObject *__pyx_v_A, int __pyx_v_A_time_var_index, PyArrayObject *__pyx_v_Q, PyArrayObject *__pyx_v_index, int __pyx_v_Q_time_var_index, int __pyx_v_unique_Q_number, PyArrayObject *__pyx_v_dA, PyArrayObject *__pyx_v_dQ); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_2f_a(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_4Ak(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m_pred, PyArrayObject *__pyx_v_P_pred); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_6dAk(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_28Std_Dynamic_Callables_Cython_8reset(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *__pyx_v_self, int __pyx_v_compute_derivatives); /* proto */ +static int __pyx_pf_18state_space_cython_22AQcompute_batch_Cython___init__(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, PyArrayObject *__pyx_v_As, PyArrayObject *__pyx_v_Qs, PyArrayObject *__pyx_v_reconstruct_indices, PyArrayObject *__pyx_v_dAs, PyArrayObject *__pyx_v_dQs); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_2f_a(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_A); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_4reset(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_compute_derivatives); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_6Ak(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k, PyArrayObject *__pyx_v_m, PyArrayObject *__pyx_v_P); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_8Qk(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_10dAk(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_12dQk(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_22AQcompute_batch_Cython_14Q_srk(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *__pyx_v_self, int __pyx_v_k); /* proto */ +static PyObject *__pyx_pf_18state_space_cython__kalman_prediction_step_SVD_Cython(CYTHON_UNUSED PyObject *__pyx_self, long __pyx_v_k, PyArrayObject *__pyx_v_p_m, PyObject *__pyx_v_p_P, struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_p_dynamic_callables, int __pyx_v_calc_grad_log_likelihood, PyArrayObject *__pyx_v_p_dm, PyArrayObject *__pyx_v_p_dP); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_2_kalman_update_step_SVD_Cython(CYTHON_UNUSED PyObject *__pyx_self, long __pyx_v_k, PyArrayObject *__pyx_v_p_m, PyObject *__pyx_v_p_P, struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_p_measurement_callables, PyArrayObject *__pyx_v_measurement, int __pyx_v_calc_log_likelihood, int __pyx_v_calc_grad_log_likelihood, PyArrayObject *__pyx_v_p_dm, PyArrayObject *__pyx_v_p_dP); /* proto */ +static PyObject *__pyx_pf_18state_space_cython_4_cont_discr_kalman_filter_raw_Cython(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_state_dim, struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *__pyx_v_p_dynamic_callables, struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *__pyx_v_p_measurement_callables, CYTHON_UNUSED PyObject *__pyx_v_X, PyObject *__pyx_v_Y, PyArrayObject *__pyx_v_m_init, PyArrayObject *__pyx_v_P_init, CYTHON_UNUSED PyObject *__pyx_v_p_kalman_filter_type, int __pyx_v_calc_log_likelihood, int __pyx_v_calc_grad_log_likelihood, int __pyx_v_grad_params_no, PyArrayObject *__pyx_v_dm_init, PyArrayObject *__pyx_v_dP_init); /* proto */ +static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ +static PyObject *__pyx_tp_new_18state_space_cython_Dynamic_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_18state_space_cython_Measurement_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_18state_space_cython_R_handling_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_18state_space_cython_Std_Measurement_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_18state_space_cython_Q_handling_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_18state_space_cython_Std_Dynamic_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_18state_space_cython_AQcompute_batch_Cython(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static char __pyx_k_A[] = "A"; +static char __pyx_k_B[] = "B"; +static char __pyx_k_H[] = "H"; +static char __pyx_k_I[] = "I"; +static char __pyx_k_K[] = "K"; +static char __pyx_k_L[] = "L"; +static char __pyx_k_M[] = "M"; +static char __pyx_k_O[] = "O"; +static char __pyx_k_P[] = "P"; +static char __pyx_k_Q[] = "Q"; +static char __pyx_k_R[] = "R"; +static char __pyx_k_S[] = "S"; +static char __pyx_k_T[] = "T"; +static char __pyx_k_U[] = "U"; +static char __pyx_k_X[] = "X"; +static char __pyx_k_Y[] = "Y"; +static char __pyx_k_b[] = "b"; +static char __pyx_k_d[] = "d"; +static char __pyx_k_f[] = "f"; +static char __pyx_k_g[] = "g"; +static char __pyx_k_h[] = "h"; +static char __pyx_k_i[] = "i"; +static char __pyx_k_j[] = "j"; +static char __pyx_k_k[] = "k"; +static char __pyx_k_l[] = "l"; +static char __pyx_k_m[] = "m"; +static char __pyx_k_q[] = "q"; +static char __pyx_k_v[] = "v"; +static char __pyx_k_Ak[] = "Ak"; +static char __pyx_k_As[] = "As"; +static char __pyx_k_Hk[] = "Hk"; +static char __pyx_k_Qk[] = "Qk"; +static char __pyx_k_Qs[] = "Qs"; +static char __pyx_k_Rk[] = "Rk"; +static char __pyx_k_Vh[] = "Vh"; +static char __pyx_k_Zd[] = "Zd"; +static char __pyx_k_Zf[] = "Zf"; +static char __pyx_k_Zg[] = "Zg"; +static char __pyx_k_dA[] = "dA"; +static char __pyx_k_dH[] = "dH"; +static char __pyx_k_dK[] = "dK"; +static char __pyx_k_dQ[] = "dQ"; +static char __pyx_k_dR[] = "dR"; +static char __pyx_k_dS[] = "dS"; +static char __pyx_k_dv[] = "dv"; +static char __pyx_k_np[] = "np"; +static char __pyx_k_pi[] = "pi"; +static char __pyx_k_sp[] = "sp"; +static char __pyx_k_any[] = "any"; +static char __pyx_k_dAk[] = "dAk"; +static char __pyx_k_dAs[] = "dAs"; +static char __pyx_k_dHk[] = "dHk"; +static char __pyx_k_dQk[] = "dQk"; +static char __pyx_k_dQs[] = "dQs"; +static char __pyx_k_dRk[] = "dRk"; +static char __pyx_k_dot[] = "dot"; +static char __pyx_k_f_a[] = "f_a"; +static char __pyx_k_f_h[] = "f_h"; +static char __pyx_k_log[] = "log"; +static char __pyx_k_p_P[] = "p_P"; +static char __pyx_k_p_m[] = "p_m"; +static char __pyx_k_res[] = "res"; +static char __pyx_k_ret[] = "ret"; +static char __pyx_k_sum[] = "sum"; +static char __pyx_k_svd[] = "svd"; +static char __pyx_k_Q_sr[] = "Q_sr"; +static char __pyx_k_axis[] = "axis"; +static char __pyx_k_diag[] = "diag"; +static char __pyx_k_init[] = "__init__"; +static char __pyx_k_main[] = "__main__"; +static char __pyx_k_p_dP[] = "p_dP"; +static char __pyx_k_p_dm[] = "p_dm"; +static char __pyx_k_sqrt[] = "sqrt"; +static char __pyx_k_test[] = "__test__"; +static char __pyx_k_tmp1[] = "tmp1"; +static char __pyx_k_tmp2[] = "tmp2"; +static char __pyx_k_tmp3[] = "tmp3"; +static char __pyx_k_tmp5[] = "tmp5"; +static char __pyx_k_DTYPE[] = "DTYPE"; +static char __pyx_k_P_upd[] = "P_upd"; +static char __pyx_k_Q_srk[] = "Q_srk"; +static char __pyx_k_R_isr[] = "R_isr"; +static char __pyx_k_S_new[] = "S_new"; +static char __pyx_k_S_old[] = "S_old"; +static char __pyx_k_S_svd[] = "S_svd"; +static char __pyx_k_S_upd[] = "S_upd"; +static char __pyx_k_U_upd[] = "U_upd"; +static char __pyx_k_V_new[] = "V_new"; +static char __pyx_k_V_old[] = "V_old"; +static char __pyx_k_dtype[] = "dtype"; +static char __pyx_k_empty[] = "empty"; +static char __pyx_k_index[] = "index"; +static char __pyx_k_int64[] = "int64"; +static char __pyx_k_isnan[] = "isnan"; +static char __pyx_k_m_upd[] = "m_upd"; +static char __pyx_k_numpy[] = "numpy"; +static char __pyx_k_param[] = "param"; +static char __pyx_k_range[] = "range"; +static char __pyx_k_reset[] = "reset"; +static char __pyx_k_scipy[] = "scipy"; +static char __pyx_k_shape[] = "shape"; +static char __pyx_k_super[] = "super"; +static char __pyx_k_zeros[] = "zeros"; +static char __pyx_k_P_init[] = "P_init"; +static char __pyx_k_P_pred[] = "P_pred"; +static char __pyx_k_R_isrk[] = "R_isrk"; +static char __pyx_k_S_pred[] = "S_pred"; +static char __pyx_k_V_pred[] = "V_pred"; +static char __pyx_k_dP_upd[] = "dP_upd"; +static char __pyx_k_dm_upd[] = "dm_upd"; +static char __pyx_k_import[] = "__import__"; +static char __pyx_k_linalg[] = "linalg"; +static char __pyx_k_m_init[] = "m_init"; +static char __pyx_k_m_pred[] = "m_pred"; +static char __pyx_k_nbytes[] = "nbytes"; +static char __pyx_k_unique[] = "unique"; +static char __pyx_k_vstack[] = "vstack"; +static char __pyx_k_dP_init[] = "dP_init"; +static char __pyx_k_dP_pred[] = "dP_pred"; +static char __pyx_k_dm_init[] = "dm_init"; +static char __pyx_k_dm_pred[] = "dm_pred"; +static char __pyx_k_float64[] = "float64"; +static char __pyx_k_regular[] = "regular"; +static char __pyx_k_Prev_cov[] = "Prev_cov"; +static char __pyx_k_steps_no[] = "steps_no"; +static char __pyx_k_DTYPE_int[] = "DTYPE_int"; +static char __pyx_k_prev_mean[] = "prev_mean"; +static char __pyx_k_state_dim[] = "state_dim"; +static char __pyx_k_ValueError[] = "ValueError"; +static char __pyx_k_compute_uv[] = "compute_uv"; +static char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; +static char __pyx_k_svd_1_matr[] = "svd_1_matr"; +static char __pyx_k_svd_2_matr[] = "svd_2_matr"; +static char __pyx_k_measurement[] = "measurement"; +static char __pyx_k_overwrite_a[] = "overwrite_a"; +static char __pyx_k_RuntimeError[] = "RuntimeError"; +static char __pyx_k_check_finite[] = "check_finite"; +static char __pyx_k_k_measurment[] = "k_measurment"; +static char __pyx_k_param_number[] = "param_number"; +static char __pyx_k_dA_all_params[] = "dA_all_params"; +static char __pyx_k_dH_all_params[] = "dH_all_params"; +static char __pyx_k_dQ_all_params[] = "dQ_all_params"; +static char __pyx_k_dR_all_params[] = "dR_all_params"; +static char __pyx_k_full_matrices[] = "full_matrices"; +static char __pyx_k_NotImplemented[] = "NotImplemented"; +static char __pyx_k_grad_params_no[] = "grad_params_no"; +static char __pyx_k_log_likelihood[] = "log_likelihood"; +static char __pyx_k_time_series_no[] = "time_series_no"; +static char __pyx_k_unique_Q_number[] = "unique_Q_number"; +static char __pyx_k_unique_R_number[] = "unique_R_number"; +static char __pyx_k_A_time_var_index[] = "A_time_var_index"; +static char __pyx_k_H_time_var_index[] = "H_time_var_index"; +static char __pyx_k_Q_time_var_index[] = "Q_time_var_index"; +static char __pyx_k_R_time_var_index[] = "R_time_var_index"; +static char __pyx_k_p_unique_Q_number[] = "p_unique_Q_number"; +static char __pyx_k_p_unique_R_number[] = "p_unique_R_number"; +static char __pyx_k_dP_pred_all_params[] = "dP_pred_all_params"; +static char __pyx_k_dm_pred_all_params[] = "dm_pred_all_params"; +static char __pyx_k_state_space_cython[] = "state_space_cython"; +static char __pyx_k_total_size_of_data[] = "total_size_of_data"; +static char __pyx_k_calc_log_likelihood[] = "calc_log_likelihood"; +static char __pyx_k_compute_derivatives[] = "compute_derivatives"; +static char __pyx_k_grad_log_likelihood[] = "grad_log_likelihood"; +static char __pyx_k_p_dynamic_callables[] = "p_dynamic_callables"; +static char __pyx_k_reconstruct_indices[] = "reconstruct_indices"; +static char __pyx_k_p_kalman_filter_type[] = "p_kalman_filter_type"; +static char __pyx_k_dA_derivative_is_None[] = "dA derivative is None"; +static char __pyx_k_dH_derivative_is_None[] = "dH derivative is None"; +static char __pyx_k_dQ_derivative_is_None[] = "dQ derivative is None"; +static char __pyx_k_dR_derivative_is_None[] = "dR derivative is None"; +static char __pyx_k_log_likelihood_update[] = "log_likelihood_update"; +static char __pyx_k_measurement_dim_gt_one[] = "measurement_dim_gt_one"; +static char __pyx_k_d_log_likelihood_update[] = "d_log_likelihood_update"; +static char __pyx_k_p_measurement_callables[] = "p_measurement_callables"; +static char __pyx_k_calc_grad_log_likelihood[] = "calc_grad_log_likelihood"; +static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; +static char __pyx_k_cython_Ak_is_not_implemented[] = "(cython) Ak is not implemented!"; +static char __pyx_k_cython_Hk_is_not_implemented[] = "(cython) Hk is not implemented!"; +static char __pyx_k_cython_Qk_is_not_implemented[] = "(cython) Qk is not implemented!"; +static char __pyx_k_cython_Rk_is_not_implemented[] = "(cython) Rk is not implemented!"; +static char __pyx_k_cython_dAk_is_not_implemented[] = "(cython) dAk is not implemented!"; +static char __pyx_k_cython_dQk_is_not_implemented[] = "(cython) dQk is not implemented!"; +static char __pyx_k_cython_f_a_is_not_implemented[] = "(cython) f_a is not implemented!"; +static char __pyx_k_kalman_update_step_SVD_Cython[] = "_kalman_update_step_SVD_Cython"; +static char __pyx_k_Contains_some_cython_code_for_s[] = "\nContains some cython code for state space modelling.\n"; +static char __pyx_k_Nan_values_in_likelihood_update[] = "Nan values in likelihood update!"; +static char __pyx_k_cont_discr_kalman_filter_raw_Cy[] = "_cont_discr_kalman_filter_raw_Cython"; +static char __pyx_k_cython_Q_srk_is_not_implemented[] = "(cython) Q_srk is not implemented!"; +static char __pyx_k_cython_reset_is_not_implemented[] = "(cython) reset is not implemented!"; +static char __pyx_k_kalman_prediction_step_SVD_Cyth[] = "_kalman_prediction_step_SVD_Cython"; +static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; +static char __pyx_k_users_agrigori_SpiderOak_sp_hiv[] = "/users/agrigori/SpiderOak/sp_hive/Programming/python/my_utils/state_space/state_space_cython.pyx"; +static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; +static char __pyx_k_Kalman_Filter_Update_SVD_S_is_ne[] = "Kalman Filter Update SVD: S is negative step %i"; +static char __pyx_k_Measurement_dimension_larger_the[] = "Measurement dimension larger then 1 is currently not supported"; +static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; +static char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; +static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; +static PyObject *__pyx_n_s_A; +static PyObject *__pyx_n_s_A_time_var_index; +static PyObject *__pyx_n_s_Ak; +static PyObject *__pyx_n_s_As; +static PyObject *__pyx_n_s_DTYPE; +static PyObject *__pyx_n_s_DTYPE_int; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2; +static PyObject *__pyx_n_s_H; +static PyObject *__pyx_n_s_H_time_var_index; +static PyObject *__pyx_n_s_Hk; +static PyObject *__pyx_n_s_K; +static PyObject *__pyx_kp_s_Kalman_Filter_Update_SVD_S_is_ne; +static PyObject *__pyx_n_s_M; +static PyObject *__pyx_kp_s_Measurement_dimension_larger_the; +static PyObject *__pyx_kp_s_Nan_values_in_likelihood_update; +static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; +static PyObject *__pyx_n_s_NotImplemented; +static PyObject *__pyx_n_s_P; +static PyObject *__pyx_n_s_P_init; +static PyObject *__pyx_n_s_P_pred; +static PyObject *__pyx_n_s_P_upd; +static PyObject *__pyx_n_s_Prev_cov; +static PyObject *__pyx_n_s_Q; +static PyObject *__pyx_n_s_Q_sr; +static PyObject *__pyx_n_s_Q_srk; +static PyObject *__pyx_n_s_Q_time_var_index; +static PyObject *__pyx_n_s_Qk; +static PyObject *__pyx_n_s_Qs; +static PyObject *__pyx_n_s_R; +static PyObject *__pyx_n_s_R_isr; +static PyObject *__pyx_n_s_R_isrk; +static PyObject *__pyx_n_s_R_time_var_index; +static PyObject *__pyx_n_s_Rk; +static PyObject *__pyx_n_s_RuntimeError; +static PyObject *__pyx_n_s_S; +static PyObject *__pyx_n_s_S_new; +static PyObject *__pyx_n_s_S_old; +static PyObject *__pyx_n_s_S_pred; +static PyObject *__pyx_n_s_S_svd; +static PyObject *__pyx_n_s_S_upd; +static PyObject *__pyx_n_s_T; +static PyObject *__pyx_n_s_U; +static PyObject *__pyx_n_s_U_upd; +static PyObject *__pyx_n_s_V_new; +static PyObject *__pyx_n_s_V_old; +static PyObject *__pyx_n_s_V_pred; +static PyObject *__pyx_n_s_ValueError; +static PyObject *__pyx_n_s_Vh; +static PyObject *__pyx_n_s_X; +static PyObject *__pyx_n_s_Y; +static PyObject *__pyx_n_s_any; +static PyObject *__pyx_n_s_axis; +static PyObject *__pyx_n_s_calc_grad_log_likelihood; +static PyObject *__pyx_n_s_calc_log_likelihood; +static PyObject *__pyx_n_s_check_finite; +static PyObject *__pyx_n_s_compute_derivatives; +static PyObject *__pyx_n_s_compute_uv; +static PyObject *__pyx_n_s_cont_discr_kalman_filter_raw_Cy; +static PyObject *__pyx_kp_s_cython_Ak_is_not_implemented; +static PyObject *__pyx_kp_s_cython_Hk_is_not_implemented; +static PyObject *__pyx_kp_s_cython_Q_srk_is_not_implemented; +static PyObject *__pyx_kp_s_cython_Qk_is_not_implemented; +static PyObject *__pyx_kp_s_cython_Rk_is_not_implemented; +static PyObject *__pyx_kp_s_cython_dAk_is_not_implemented; +static PyObject *__pyx_kp_s_cython_dQk_is_not_implemented; +static PyObject *__pyx_kp_s_cython_f_a_is_not_implemented; +static PyObject *__pyx_kp_s_cython_reset_is_not_implemented; +static PyObject *__pyx_n_s_dA; +static PyObject *__pyx_n_s_dA_all_params; +static PyObject *__pyx_kp_s_dA_derivative_is_None; +static PyObject *__pyx_n_s_dAk; +static PyObject *__pyx_n_s_dAs; +static PyObject *__pyx_n_s_dH; +static PyObject *__pyx_n_s_dH_all_params; +static PyObject *__pyx_kp_s_dH_derivative_is_None; +static PyObject *__pyx_n_s_dHk; +static PyObject *__pyx_n_s_dK; +static PyObject *__pyx_n_s_dP_init; +static PyObject *__pyx_n_s_dP_pred; +static PyObject *__pyx_n_s_dP_pred_all_params; +static PyObject *__pyx_n_s_dP_upd; +static PyObject *__pyx_n_s_dQ; +static PyObject *__pyx_n_s_dQ_all_params; +static PyObject *__pyx_kp_s_dQ_derivative_is_None; 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+static PyObject *__pyx_n_s_isnan; +static PyObject *__pyx_n_s_j; +static PyObject *__pyx_n_s_k; +static PyObject *__pyx_n_s_k_measurment; +static PyObject *__pyx_n_s_kalman_prediction_step_SVD_Cyth; +static PyObject *__pyx_n_s_kalman_update_step_SVD_Cython; +static PyObject *__pyx_n_s_linalg; +static PyObject *__pyx_n_s_log; +static PyObject *__pyx_n_s_log_likelihood; +static PyObject *__pyx_n_s_log_likelihood_update; +static PyObject *__pyx_n_s_m; +static PyObject *__pyx_n_s_m_init; +static PyObject *__pyx_n_s_m_pred; +static PyObject *__pyx_n_s_m_upd; +static PyObject *__pyx_n_s_main; +static PyObject *__pyx_n_s_measurement; +static PyObject *__pyx_n_s_measurement_dim_gt_one; +static PyObject *__pyx_n_s_nbytes; +static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; +static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; +static PyObject *__pyx_n_s_np; +static PyObject *__pyx_n_s_numpy; +static PyObject *__pyx_n_s_overwrite_a; +static PyObject *__pyx_n_s_p_P; +static PyObject *__pyx_n_s_p_dP; 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__pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyTuple_GET_ITEM(__pyx_v_p_P, 2); + __Pyx_INCREF(__pyx_t_1); + { + __Pyx_BufFmt_StackElem __pyx_stack[1]; + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_V_pred.rcbuffer->pybuffer, (PyObject*)((PyArrayObject *)__pyx_t_1), &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + __pyx_v_V_pred = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_V_pred.rcbuffer->pybuffer.buf = NULL; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } else {__pyx_pybuffernd_V_pred.diminfo[0].strides = __pyx_pybuffernd_V_pred.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_V_pred.diminfo[0].shape = __pyx_pybuffernd_V_pred.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_V_pred.diminfo[1].strides = __pyx_pybuffernd_V_pred.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_V_pred.diminfo[1].shape = __pyx_pybuffernd_V_pred.rcbuffer->pybuffer.shape[1]; 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__pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = ((PyArrayObject *)__pyx_t_1); + { + __Pyx_BufFmt_StackElem __pyx_stack[1]; + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_H.rcbuffer->pybuffer, (PyObject*)__pyx_t_2, &__Pyx_TypeInfo_nn___pyx_t_18state_space_cython_DTYPE_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) { + __pyx_v_H = ((PyArrayObject *)Py_None); __Pyx_INCREF(Py_None); __pyx_pybuffernd_H.rcbuffer->pybuffer.buf = NULL; + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } else {__pyx_pybuffernd_H.diminfo[0].strides = __pyx_pybuffernd_H.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_H.diminfo[0].shape = __pyx_pybuffernd_H.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_H.diminfo[1].strides = __pyx_pybuffernd_H.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_H.diminfo[1].shape = __pyx_pybuffernd_H.rcbuffer->pybuffer.shape[1]; + } + } + __pyx_t_2 = 0; + __pyx_v_H = ((PyArrayObject *)__pyx_t_1); 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} else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_18state_space_cython_R_handling_Cython); + tmp = ((PyObject*)p->R); + p->R = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->index); + p->index = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->dR); + p->dR = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->R_square_root); + p->R_square_root = ((PyObject*)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyMethodDef __pyx_methods_18state_space_cython_R_handling_Cython[] = { + {"Rk", (PyCFunction)__pyx_pw_18state_space_cython_17R_handling_Cython_3Rk, METH_O, 0}, + {"dRk", (PyCFunction)__pyx_pw_18state_space_cython_17R_handling_Cython_5dRk, METH_O, 0}, + {"R_isrk", (PyCFunction)__pyx_pw_18state_space_cython_17R_handling_Cython_7R_isrk, METH_O, __pyx_doc_18state_space_cython_17R_handling_Cython_6R_isrk}, + {0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type_18state_space_cython_R_handling_Cython = { + PyVarObject_HEAD_INIT(0, 0) + "state_space_cython.R_handling_Cython", /*tp_name*/ + sizeof(struct __pyx_obj_18state_space_cython_R_handling_Cython), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_18state_space_cython_R_handling_Cython, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #else + 0, /*reserved*/ + #endif + 0, /*tp_repr*/ + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + "\n The calss handles noise matrix R.\n ", /*tp_doc*/ + __pyx_tp_traverse_18state_space_cython_R_handling_Cython, /*tp_traverse*/ + __pyx_tp_clear_18state_space_cython_R_handling_Cython, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_18state_space_cython_R_handling_Cython, /*tp_methods*/ + 0, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_pw_18state_space_cython_17R_handling_Cython_1__init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_18state_space_cython_R_handling_Cython, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; 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+ #if PY_VERSION_HEX >= 0x030400a1 + if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + PyObject_GC_UnTrack(o); + Py_CLEAR(p->H); + Py_CLEAR(p->dH); + PyObject_GC_Track(o); + __pyx_tp_dealloc_18state_space_cython_R_handling_Cython(o); +} + +static int __pyx_tp_traverse_18state_space_cython_Std_Measurement_Callables_Cython(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *p = (struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *)o; + e = __pyx_tp_traverse_18state_space_cython_R_handling_Cython(o, v, a); if (e) return e; + if (p->H) { + e = (*v)(((PyObject*)p->H), a); if (e) return e; + } + if (p->dH) { + e = (*v)(((PyObject*)p->dH), a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_18state_space_cython_Std_Measurement_Callables_Cython(PyObject *o) { + PyObject* tmp; + struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *p = (struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython *)o; + __pyx_tp_clear_18state_space_cython_R_handling_Cython(o); + tmp = ((PyObject*)p->H); + p->H = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->dH); + p->dH = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyMethodDef __pyx_methods_18state_space_cython_Std_Measurement_Callables_Cython[] = { + {"f_h", (PyCFunction)__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_3f_h, METH_VARARGS|METH_KEYWORDS, __pyx_doc_18state_space_cython_32Std_Measurement_Callables_Cython_2f_h}, + {"Hk", (PyCFunction)__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_5Hk, METH_VARARGS|METH_KEYWORDS, __pyx_doc_18state_space_cython_32Std_Measurement_Callables_Cython_4Hk}, + {"dHk", (PyCFunction)__pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_7dHk, METH_O, 0}, + {0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type_18state_space_cython_Std_Measurement_Callables_Cython = { + PyVarObject_HEAD_INIT(0, 0) + "state_space_cython.Std_Measurement_Callables_Cython", /*tp_name*/ + sizeof(struct __pyx_obj_18state_space_cython_Std_Measurement_Callables_Cython), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_18state_space_cython_Std_Measurement_Callables_Cython, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #else + 0, /*reserved*/ + #endif + 0, /*tp_repr*/ + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + 0, /*tp_doc*/ + __pyx_tp_traverse_18state_space_cython_Std_Measurement_Callables_Cython, /*tp_traverse*/ + __pyx_tp_clear_18state_space_cython_Std_Measurement_Callables_Cython, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_18state_space_cython_Std_Measurement_Callables_Cython, /*tp_methods*/ + 0, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_pw_18state_space_cython_32Std_Measurement_Callables_Cython_1__init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_18state_space_cython_Std_Measurement_Callables_Cython, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; +static struct __pyx_vtabstruct_18state_space_cython_Q_handling_Cython __pyx_vtable_18state_space_cython_Q_handling_Cython; + +static PyObject *__pyx_tp_new_18state_space_cython_Q_handling_Cython(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_18state_space_cython_Q_handling_Cython *p; + PyObject *o = __pyx_tp_new_18state_space_cython_Dynamic_Callables_Cython(t, a, k); + if (unlikely(!o)) return 0; + p = ((struct __pyx_obj_18state_space_cython_Q_handling_Cython *)o); + p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython*)__pyx_vtabptr_18state_space_cython_Q_handling_Cython; + p->Q = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + p->index = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + p->dQ = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + p->Q_square_root = ((PyObject*)Py_None); Py_INCREF(Py_None); + return o; +} + +static void __pyx_tp_dealloc_18state_space_cython_Q_handling_Cython(PyObject *o) { + struct __pyx_obj_18state_space_cython_Q_handling_Cython *p = (struct __pyx_obj_18state_space_cython_Q_handling_Cython *)o; + #if PY_VERSION_HEX >= 0x030400a1 + if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + PyObject_GC_UnTrack(o); + Py_CLEAR(p->Q); + Py_CLEAR(p->index); + Py_CLEAR(p->dQ); + Py_CLEAR(p->Q_square_root); + #if CYTHON_COMPILING_IN_CPYTHON + if (PyType_IS_GC(Py_TYPE(o)->tp_base)) + #endif + PyObject_GC_Track(o); + __pyx_tp_dealloc_18state_space_cython_Dynamic_Callables_Cython(o); +} + +static int __pyx_tp_traverse_18state_space_cython_Q_handling_Cython(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_obj_18state_space_cython_Q_handling_Cython *p = (struct __pyx_obj_18state_space_cython_Q_handling_Cython *)o; + e = ((likely(__pyx_ptype_18state_space_cython_Dynamic_Callables_Cython)) ? ((__pyx_ptype_18state_space_cython_Dynamic_Callables_Cython->tp_traverse) ? __pyx_ptype_18state_space_cython_Dynamic_Callables_Cython->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_18state_space_cython_Q_handling_Cython)); if (e) return e; + if (p->Q) { + e = (*v)(((PyObject*)p->Q), a); if (e) return e; + } + if (p->index) { + e = (*v)(((PyObject*)p->index), a); if (e) return e; + } + if (p->dQ) { + e = (*v)(((PyObject*)p->dQ), a); if (e) return e; + } + if (p->Q_square_root) { + e = (*v)(p->Q_square_root, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_18state_space_cython_Q_handling_Cython(PyObject *o) { + PyObject* tmp; + struct __pyx_obj_18state_space_cython_Q_handling_Cython *p = (struct __pyx_obj_18state_space_cython_Q_handling_Cython *)o; + if (likely(__pyx_ptype_18state_space_cython_Dynamic_Callables_Cython)) { if (__pyx_ptype_18state_space_cython_Dynamic_Callables_Cython->tp_clear) __pyx_ptype_18state_space_cython_Dynamic_Callables_Cython->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_18state_space_cython_Q_handling_Cython); + tmp = ((PyObject*)p->Q); + p->Q = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->index); + p->index = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->dQ); + p->dQ = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->Q_square_root); + p->Q_square_root = ((PyObject*)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyMethodDef __pyx_methods_18state_space_cython_Q_handling_Cython[] = { + {"Qk", (PyCFunction)__pyx_pw_18state_space_cython_17Q_handling_Cython_3Qk, METH_O, __pyx_doc_18state_space_cython_17Q_handling_Cython_2Qk}, + {"dQk", (PyCFunction)__pyx_pw_18state_space_cython_17Q_handling_Cython_5dQk, METH_O, 0}, + {"Q_srk", (PyCFunction)__pyx_pw_18state_space_cython_17Q_handling_Cython_7Q_srk, METH_O, __pyx_doc_18state_space_cython_17Q_handling_Cython_6Q_srk}, + {0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type_18state_space_cython_Q_handling_Cython = { + PyVarObject_HEAD_INIT(0, 0) + "state_space_cython.Q_handling_Cython", /*tp_name*/ + sizeof(struct __pyx_obj_18state_space_cython_Q_handling_Cython), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_18state_space_cython_Q_handling_Cython, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #else + 0, /*reserved*/ + #endif + 0, /*tp_repr*/ + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + 0, /*tp_doc*/ + __pyx_tp_traverse_18state_space_cython_Q_handling_Cython, /*tp_traverse*/ + __pyx_tp_clear_18state_space_cython_Q_handling_Cython, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_18state_space_cython_Q_handling_Cython, /*tp_methods*/ + 0, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_pw_18state_space_cython_17Q_handling_Cython_1__init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_18state_space_cython_Q_handling_Cython, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; +static struct __pyx_vtabstruct_18state_space_cython_Std_Dynamic_Callables_Cython __pyx_vtable_18state_space_cython_Std_Dynamic_Callables_Cython; + +static PyObject *__pyx_tp_new_18state_space_cython_Std_Dynamic_Callables_Cython(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *p; + PyObject *o = __pyx_tp_new_18state_space_cython_Q_handling_Cython(t, a, k); + if (unlikely(!o)) return 0; + p = ((struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *)o); + p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython*)__pyx_vtabptr_18state_space_cython_Std_Dynamic_Callables_Cython; + p->A = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + p->dA = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + return o; +} + +static void __pyx_tp_dealloc_18state_space_cython_Std_Dynamic_Callables_Cython(PyObject *o) { + struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *p = (struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *)o; + #if PY_VERSION_HEX >= 0x030400a1 + if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + PyObject_GC_UnTrack(o); + Py_CLEAR(p->A); + Py_CLEAR(p->dA); + PyObject_GC_Track(o); + __pyx_tp_dealloc_18state_space_cython_Q_handling_Cython(o); +} + +static int __pyx_tp_traverse_18state_space_cython_Std_Dynamic_Callables_Cython(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *p = (struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *)o; + e = __pyx_tp_traverse_18state_space_cython_Q_handling_Cython(o, v, a); if (e) return e; + if (p->A) { + e = (*v)(((PyObject*)p->A), a); if (e) return e; + } + if (p->dA) { + e = (*v)(((PyObject*)p->dA), a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_18state_space_cython_Std_Dynamic_Callables_Cython(PyObject *o) { + PyObject* tmp; + struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *p = (struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython *)o; + __pyx_tp_clear_18state_space_cython_Q_handling_Cython(o); + tmp = ((PyObject*)p->A); + p->A = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->dA); + p->dA = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyMethodDef __pyx_methods_18state_space_cython_Std_Dynamic_Callables_Cython[] = { + {"f_a", (PyCFunction)__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_3f_a, METH_VARARGS|METH_KEYWORDS, __pyx_doc_18state_space_cython_28Std_Dynamic_Callables_Cython_2f_a}, + {"Ak", (PyCFunction)__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_5Ak, METH_VARARGS|METH_KEYWORDS, __pyx_doc_18state_space_cython_28Std_Dynamic_Callables_Cython_4Ak}, + {"dAk", (PyCFunction)__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_7dAk, METH_O, 0}, + {"reset", (PyCFunction)__pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_9reset, METH_VARARGS|METH_KEYWORDS, __pyx_doc_18state_space_cython_28Std_Dynamic_Callables_Cython_8reset}, + {0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type_18state_space_cython_Std_Dynamic_Callables_Cython = { + PyVarObject_HEAD_INIT(0, 0) + "state_space_cython.Std_Dynamic_Callables_Cython", /*tp_name*/ + sizeof(struct __pyx_obj_18state_space_cython_Std_Dynamic_Callables_Cython), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_18state_space_cython_Std_Dynamic_Callables_Cython, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #else + 0, /*reserved*/ + #endif + 0, /*tp_repr*/ + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + 0, /*tp_doc*/ + __pyx_tp_traverse_18state_space_cython_Std_Dynamic_Callables_Cython, /*tp_traverse*/ + __pyx_tp_clear_18state_space_cython_Std_Dynamic_Callables_Cython, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_18state_space_cython_Std_Dynamic_Callables_Cython, /*tp_methods*/ + 0, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_pw_18state_space_cython_28Std_Dynamic_Callables_Cython_1__init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_18state_space_cython_Std_Dynamic_Callables_Cython, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + 0, /*tp_version_tag*/ + #if PY_VERSION_HEX >= 0x030400a1 + 0, /*tp_finalize*/ + #endif +}; +static struct __pyx_vtabstruct_18state_space_cython_AQcompute_batch_Cython __pyx_vtable_18state_space_cython_AQcompute_batch_Cython; + +static PyObject *__pyx_tp_new_18state_space_cython_AQcompute_batch_Cython(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *p; + PyObject *o = __pyx_tp_new_18state_space_cython_Q_handling_Cython(t, a, k); + if (unlikely(!o)) return 0; + p = ((struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *)o); + p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_18state_space_cython_Dynamic_Callables_Cython*)__pyx_vtabptr_18state_space_cython_AQcompute_batch_Cython; + p->As = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + p->Qs = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + p->dAs = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + p->dQs = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + p->reconstruct_indices = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + p->Q_svd_dict = ((PyObject*)Py_None); Py_INCREF(Py_None); + return o; +} + +static void __pyx_tp_dealloc_18state_space_cython_AQcompute_batch_Cython(PyObject *o) { + struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *p = (struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *)o; + #if PY_VERSION_HEX >= 0x030400a1 + if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + PyObject_GC_UnTrack(o); + Py_CLEAR(p->As); + Py_CLEAR(p->Qs); + Py_CLEAR(p->dAs); + Py_CLEAR(p->dQs); + Py_CLEAR(p->reconstruct_indices); + Py_CLEAR(p->Q_svd_dict); + PyObject_GC_Track(o); + __pyx_tp_dealloc_18state_space_cython_Q_handling_Cython(o); +} + +static int __pyx_tp_traverse_18state_space_cython_AQcompute_batch_Cython(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *p = (struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *)o; + e = __pyx_tp_traverse_18state_space_cython_Q_handling_Cython(o, v, a); if (e) return e; + if (p->As) { + e = (*v)(((PyObject*)p->As), a); if (e) return e; + } + if (p->Qs) { + e = (*v)(((PyObject*)p->Qs), a); if (e) return e; + } + if (p->dAs) { + e = (*v)(((PyObject*)p->dAs), a); if (e) return e; + } + if (p->dQs) { + e = (*v)(((PyObject*)p->dQs), a); if (e) return e; + } + if (p->reconstruct_indices) { + e = (*v)(((PyObject*)p->reconstruct_indices), a); if (e) return e; + } + if (p->Q_svd_dict) { + e = (*v)(p->Q_svd_dict, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_18state_space_cython_AQcompute_batch_Cython(PyObject *o) { + PyObject* tmp; + struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *p = (struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython *)o; + __pyx_tp_clear_18state_space_cython_Q_handling_Cython(o); + tmp = ((PyObject*)p->As); + p->As = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->Qs); + p->Qs = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->dAs); + p->dAs = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->dQs); + p->dQs = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->reconstruct_indices); + p->reconstruct_indices = ((PyArrayObject *)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->Q_svd_dict); + p->Q_svd_dict = ((PyObject*)Py_None); Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyMethodDef __pyx_methods_18state_space_cython_AQcompute_batch_Cython[] = { + {"f_a", (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_3f_a, METH_VARARGS|METH_KEYWORDS, __pyx_doc_18state_space_cython_22AQcompute_batch_Cython_2f_a}, + {"reset", (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_5reset, METH_VARARGS|METH_KEYWORDS, __pyx_doc_18state_space_cython_22AQcompute_batch_Cython_4reset}, + {"Ak", (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_7Ak, METH_VARARGS|METH_KEYWORDS, 0}, + {"Qk", (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_9Qk, METH_O, 0}, + {"dAk", (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_11dAk, METH_O, 0}, + {"dQk", (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_13dQk, METH_O, 0}, + {"Q_srk", (PyCFunction)__pyx_pw_18state_space_cython_22AQcompute_batch_Cython_15Q_srk, METH_O, __pyx_doc_18state_space_cython_22AQcompute_batch_Cython_14Q_srk}, + {0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type_18state_space_cython_AQcompute_batch_Cython = { + PyVarObject_HEAD_INIT(0, 0) + "state_space_cython.AQcompute_batch_Cython", /*tp_name*/ + sizeof(struct __pyx_obj_18state_space_cython_AQcompute_batch_Cython), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_18state_space_cython_AQcompute_batch_Cython, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #else + 0, /*reserved*/ + #endif + 0, /*tp_repr*/ + 0, /*tp_as_number*/ + 0, /*tp_as_sequence*/ + 0, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + 0, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + "\n Class for calculating matrices A, Q, dA, dQ of the discrete Kalman Filter\n from the matrices F, L, Qc, P_ing, dF, dQc, dP_inf of the continuos state\n equation. dt - time steps. \n \n It has the same interface as AQcompute_once.\n \n It computes matrices for all time steps. 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__Pyx_GIVEREF(__pyx_slice__16); + + /* "state_space_cython.pyx":120 + * cpdef dRk(self,int k): + * if self.dR is None: + * raise ValueError("dR derivative is None") # <<<<<<<<<<<<<< + * + * return self.dR # the same dirivative on each iteration + */ + __pyx_tuple__17 = PyTuple_Pack(1, __pyx_kp_s_dR_derivative_is_None); if (unlikely(!__pyx_tuple__17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 120; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__17); + __Pyx_GIVEREF(__pyx_tuple__17); + + /* "state_space_cython.pyx":129 + * """ + * cdef int ind = self.index[self.R_time_var_index, k] + * cdef np.ndarray[DTYPE_t, ndim=2] R = self.R[:,:, ind ] # <<<<<<<<<<<<<< + * + * cdef np.ndarray[DTYPE_t, ndim=2] inv_square_root + */ + __pyx_slice__18 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_slice__18); + __Pyx_GIVEREF(__pyx_slice__18); + __pyx_slice__19 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_slice__19); + __Pyx_GIVEREF(__pyx_slice__19); + + /* "state_space_cython.pyx":198 + * """ + * + * return self.H[:,:, self.index[self.H_time_var_index, k]] # <<<<<<<<<<<<<< + * + * cpdef dHk(self,int k): + */ + __pyx_slice__20 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_slice__20); + __Pyx_GIVEREF(__pyx_slice__20); + __pyx_slice__21 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_slice__21); + __Pyx_GIVEREF(__pyx_slice__21); + + /* "state_space_cython.pyx":202 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 265; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_slice__24); + __Pyx_GIVEREF(__pyx_slice__24); + + /* "state_space_cython.pyx":269 + * cpdef dQk(self, int k): + * if self.dQ is None: + * raise ValueError("dQ derivative is None") # <<<<<<<<<<<<<< + * + * return self.dQ # the same dirivative on each iteration + */ + __pyx_tuple__25 = PyTuple_Pack(1, __pyx_kp_s_dQ_derivative_is_None); if (unlikely(!__pyx_tuple__25)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 269; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__25); + __Pyx_GIVEREF(__pyx_tuple__25); + + /* "state_space_cython.pyx":281 + * """ + * cdef int ind = self.index[self.Q_time_var_index, k] + * cdef np.ndarray[DTYPE_t, ndim=2] Q = self.Q[:,:, ind] # <<<<<<<<<<<<<< + * + * + */ + __pyx_slice__26 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__26)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 281; __pyx_clineno = 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__Pyx_GIVEREF(__pyx_slice__29); + + /* "state_space_cython.pyx":356 + * cpdef dAk(self, int k): + * if self.dA is None: + * raise ValueError("dA derivative is None") # <<<<<<<<<<<<<< + * + * return self.dA # the same dirivative on each iteration + */ + __pyx_tuple__30 = PyTuple_Pack(1, __pyx_kp_s_dA_derivative_is_None); if (unlikely(!__pyx_tuple__30)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__30); + __Pyx_GIVEREF(__pyx_tuple__30); + + /* "state_space_cython.pyx":450 + * cpdef Ak(self,int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] P): + * self.last_k = k + * return self.As[:,:, self.reconstruct_indices[k]] # <<<<<<<<<<<<<< + * + * cpdef Qk(self,int k): + */ + __pyx_slice__31 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_slice__31); + __Pyx_GIVEREF(__pyx_slice__31); + __pyx_slice__32 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__32)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_slice__32); + __Pyx_GIVEREF(__pyx_slice__32); + + /* "state_space_cython.pyx":454 + * cpdef Qk(self,int k): + * self.last_k = k + * return self.Qs[:,:, self.reconstruct_indices[k]] # <<<<<<<<<<<<<< + * + * cpdef dAk(self, int k): + */ + __pyx_slice__33 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_slice__33); + __Pyx_GIVEREF(__pyx_slice__33); + __pyx_slice__34 = PySlice_New(Py_None, Py_None, Py_None); if (unlikely(!__pyx_slice__34)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_slice__34); + __Pyx_GIVEREF(__pyx_slice__34); + + /* 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__pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + return 0; + __pyx_L1_error:; + return -1; +} + +#if PY_MAJOR_VERSION < 3 +PyMODINIT_FUNC initstate_space_cython(void); /*proto*/ +PyMODINIT_FUNC initstate_space_cython(void) +#else +PyMODINIT_FUNC PyInit_state_space_cython(void); /*proto*/ +PyMODINIT_FUNC PyInit_state_space_cython(void) +#endif +{ + PyObject *__pyx_t_1 = NULL; + PyObject *__pyx_t_2 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannyDeclarations + #if CYTHON_REFNANNY + __Pyx_RefNanny = __Pyx_RefNannyImportAPI("refnanny"); + if (!__Pyx_RefNanny) { + PyErr_Clear(); + __Pyx_RefNanny = __Pyx_RefNannyImportAPI("Cython.Runtime.refnanny"); + if (!__Pyx_RefNanny) + Py_FatalError("failed to import 'refnanny' module"); + } + #endif + __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_state_space_cython(void)", 0); + if ( __Pyx_check_binary_version() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #ifdef __Pyx_CyFunction_USED + if (__Pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + #ifdef __Pyx_FusedFunction_USED + if (__pyx_FusedFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + #ifdef __Pyx_Generator_USED + if (__pyx_Generator_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + /*--- Library function declarations ---*/ + /*--- Threads initialization code ---*/ + #if defined(__PYX_FORCE_INIT_THREADS) && __PYX_FORCE_INIT_THREADS + #ifdef WITH_THREAD /* Python build with threading support? */ + PyEval_InitThreads(); + #endif + #endif + /*--- Module creation code ---*/ + #if PY_MAJOR_VERSION < 3 + __pyx_m = Py_InitModule4("state_space_cython", __pyx_methods, __pyx_k_Contains_some_cython_code_for_s, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m); + #else + __pyx_m = PyModule_Create(&__pyx_moduledef); + #endif + if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + Py_INCREF(__pyx_d); + __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #if CYTHON_COMPILING_IN_PYPY + Py_INCREF(__pyx_b); + #endif + if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + /*--- Initialize various global constants etc. ---*/ + if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) + if (__Pyx_init_sys_getdefaultencoding_params() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif + if (__pyx_module_is_main_state_space_cython) { + if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + } + #if PY_MAJOR_VERSION >= 3 + { + PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!PyDict_GetItemString(modules, "state_space_cython")) { + if (unlikely(PyDict_SetItemString(modules, "state_space_cython", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + } + #endif + /*--- Builtin init code ---*/ + if (unlikely(__Pyx_InitCachedBuiltins() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*--- Constants init code ---*/ + if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*--- Global init code ---*/ + /*--- Variable export code ---*/ + /*--- Function export code ---*/ + /*--- Type init code ---*/ + __pyx_vtabptr_18state_space_cython_Dynamic_Callables_Cython = &__pyx_vtable_18state_space_cython_Dynamic_Callables_Cython; + __pyx_vtable_18state_space_cython_Dynamic_Callables_Cython.f_a = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_f_a; + __pyx_vtable_18state_space_cython_Dynamic_Callables_Cython.Ak = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Ak; + __pyx_vtable_18state_space_cython_Dynamic_Callables_Cython.Qk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Qk; + __pyx_vtable_18state_space_cython_Dynamic_Callables_Cython.Q_srk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_Q_srk; + __pyx_vtable_18state_space_cython_Dynamic_Callables_Cython.dAk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_dAk; + __pyx_vtable_18state_space_cython_Dynamic_Callables_Cython.dQk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_dQk; + __pyx_vtable_18state_space_cython_Dynamic_Callables_Cython.reset = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_24Dynamic_Callables_Cython_reset *__pyx_optional_args))__pyx_f_18state_space_cython_24Dynamic_Callables_Cython_reset; + if (PyType_Ready(&__pyx_type_18state_space_cython_Dynamic_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_type_18state_space_cython_Dynamic_Callables_Cython.tp_print = 0; + if (__Pyx_SetVtable(__pyx_type_18state_space_cython_Dynamic_Callables_Cython.tp_dict, __pyx_vtabptr_18state_space_cython_Dynamic_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttrString(__pyx_m, "Dynamic_Callables_Cython", (PyObject *)&__pyx_type_18state_space_cython_Dynamic_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_18state_space_cython_Dynamic_Callables_Cython = &__pyx_type_18state_space_cython_Dynamic_Callables_Cython; + __pyx_vtabptr_18state_space_cython_Measurement_Callables_Cython = &__pyx_vtable_18state_space_cython_Measurement_Callables_Cython; + __pyx_vtable_18state_space_cython_Measurement_Callables_Cython.f_h = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_28Measurement_Callables_Cython_f_h; + __pyx_vtable_18state_space_cython_Measurement_Callables_Cython.Hk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Hk; + __pyx_vtable_18state_space_cython_Measurement_Callables_Cython.Rk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_28Measurement_Callables_Cython_Rk; + __pyx_vtable_18state_space_cython_Measurement_Callables_Cython.R_isrk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_28Measurement_Callables_Cython_R_isrk; + __pyx_vtable_18state_space_cython_Measurement_Callables_Cython.dHk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_28Measurement_Callables_Cython_dHk; + __pyx_vtable_18state_space_cython_Measurement_Callables_Cython.dRk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_28Measurement_Callables_Cython_dRk; + __pyx_vtable_18state_space_cython_Measurement_Callables_Cython.reset = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int __pyx_skip_dispatch, struct __pyx_opt_args_18state_space_cython_28Measurement_Callables_Cython_reset *__pyx_optional_args))__pyx_f_18state_space_cython_28Measurement_Callables_Cython_reset; + if (PyType_Ready(&__pyx_type_18state_space_cython_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_type_18state_space_cython_Measurement_Callables_Cython.tp_print = 0; + if (__Pyx_SetVtable(__pyx_type_18state_space_cython_Measurement_Callables_Cython.tp_dict, __pyx_vtabptr_18state_space_cython_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttrString(__pyx_m, "Measurement_Callables_Cython", (PyObject *)&__pyx_type_18state_space_cython_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 40; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_18state_space_cython_Measurement_Callables_Cython = &__pyx_type_18state_space_cython_Measurement_Callables_Cython; + __pyx_vtabptr_18state_space_cython_R_handling_Cython = &__pyx_vtable_18state_space_cython_R_handling_Cython; + __pyx_vtable_18state_space_cython_R_handling_Cython.__pyx_base = *__pyx_vtabptr_18state_space_cython_Measurement_Callables_Cython; + __pyx_vtable_18state_space_cython_R_handling_Cython.__pyx_base.Rk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_17R_handling_Cython_Rk; + __pyx_vtable_18state_space_cython_R_handling_Cython.__pyx_base.R_isrk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_17R_handling_Cython_R_isrk; + __pyx_vtable_18state_space_cython_R_handling_Cython.__pyx_base.dRk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_17R_handling_Cython_dRk; + __pyx_type_18state_space_cython_R_handling_Cython.tp_base = __pyx_ptype_18state_space_cython_Measurement_Callables_Cython; + if (PyType_Ready(&__pyx_type_18state_space_cython_R_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_type_18state_space_cython_R_handling_Cython.tp_print = 0; + #if CYTHON_COMPILING_IN_CPYTHON + { + PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_18state_space_cython_R_handling_Cython, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { + __pyx_wrapperbase_18state_space_cython_17R_handling_Cython___init__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_18state_space_cython_17R_handling_Cython___init__.doc = __pyx_doc_18state_space_cython_17R_handling_Cython___init__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_18state_space_cython_17R_handling_Cython___init__; + } + } + #endif + if (__Pyx_SetVtable(__pyx_type_18state_space_cython_R_handling_Cython.tp_dict, __pyx_vtabptr_18state_space_cython_R_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttrString(__pyx_m, "R_handling_Cython", (PyObject *)&__pyx_type_18state_space_cython_R_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_18state_space_cython_R_handling_Cython = &__pyx_type_18state_space_cython_R_handling_Cython; + __pyx_vtabptr_18state_space_cython_Std_Measurement_Callables_Cython = &__pyx_vtable_18state_space_cython_Std_Measurement_Callables_Cython; + __pyx_vtable_18state_space_cython_Std_Measurement_Callables_Cython.__pyx_base = *__pyx_vtabptr_18state_space_cython_R_handling_Cython; + __pyx_vtable_18state_space_cython_Std_Measurement_Callables_Cython.__pyx_base.__pyx_base.f_h = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython_f_h; + __pyx_vtable_18state_space_cython_Std_Measurement_Callables_Cython.__pyx_base.__pyx_base.Hk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, PyArrayObject *, PyArrayObject *, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython_Hk; + __pyx_vtable_18state_space_cython_Std_Measurement_Callables_Cython.__pyx_base.__pyx_base.dHk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Measurement_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_32Std_Measurement_Callables_Cython_dHk; + __pyx_type_18state_space_cython_Std_Measurement_Callables_Cython.tp_base = __pyx_ptype_18state_space_cython_R_handling_Cython; + if (PyType_Ready(&__pyx_type_18state_space_cython_Std_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 161; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_type_18state_space_cython_Std_Measurement_Callables_Cython.tp_print = 0; + if (__Pyx_SetVtable(__pyx_type_18state_space_cython_Std_Measurement_Callables_Cython.tp_dict, __pyx_vtabptr_18state_space_cython_Std_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 161; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttrString(__pyx_m, "Std_Measurement_Callables_Cython", (PyObject *)&__pyx_type_18state_space_cython_Std_Measurement_Callables_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 161; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_18state_space_cython_Std_Measurement_Callables_Cython = &__pyx_type_18state_space_cython_Std_Measurement_Callables_Cython; + __pyx_vtabptr_18state_space_cython_Q_handling_Cython = &__pyx_vtable_18state_space_cython_Q_handling_Cython; + __pyx_vtable_18state_space_cython_Q_handling_Cython.__pyx_base = *__pyx_vtabptr_18state_space_cython_Dynamic_Callables_Cython; + __pyx_vtable_18state_space_cython_Q_handling_Cython.__pyx_base.Qk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_17Q_handling_Cython_Qk; + __pyx_vtable_18state_space_cython_Q_handling_Cython.__pyx_base.Q_srk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_17Q_handling_Cython_Q_srk; + __pyx_vtable_18state_space_cython_Q_handling_Cython.__pyx_base.dQk = (PyObject *(*)(struct __pyx_obj_18state_space_cython_Dynamic_Callables_Cython *, int, int __pyx_skip_dispatch))__pyx_f_18state_space_cython_17Q_handling_Cython_dQk; + __pyx_type_18state_space_cython_Q_handling_Cython.tp_base = __pyx_ptype_18state_space_cython_Dynamic_Callables_Cython; + if (PyType_Ready(&__pyx_type_18state_space_cython_Q_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_type_18state_space_cython_Q_handling_Cython.tp_print = 0; + #if CYTHON_COMPILING_IN_CPYTHON + { + PyObject *wrapper = PyObject_GetAttrString((PyObject *)&__pyx_type_18state_space_cython_Q_handling_Cython, "__init__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) { + __pyx_wrapperbase_18state_space_cython_17Q_handling_Cython___init__ = *((PyWrapperDescrObject *)wrapper)->d_base; + __pyx_wrapperbase_18state_space_cython_17Q_handling_Cython___init__.doc = __pyx_doc_18state_space_cython_17Q_handling_Cython___init__; + ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_18state_space_cython_17Q_handling_Cython___init__; + } + } + #endif + if (__Pyx_SetVtable(__pyx_type_18state_space_cython_Q_handling_Cython.tp_dict, __pyx_vtabptr_18state_space_cython_Q_handling_Cython) < 0) {__pyx_filename = __pyx_f[0]; 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+ type = type->fields->type; + } +} +static int __Pyx_BufFmt_ParseNumber(const char** ts) { + int count; + const char* t = *ts; + if (*t < '0' || *t > '9') { + return -1; + } else { + count = *t++ - '0'; + while (*t >= '0' && *t < '9') { + count *= 10; + count += *t++ - '0'; + } + } + *ts = t; + return count; +} +static int __Pyx_BufFmt_ExpectNumber(const char **ts) { + int number = __Pyx_BufFmt_ParseNumber(ts); + if (number == -1) + PyErr_Format(PyExc_ValueError,\ + "Does not understand character buffer dtype format string ('%c')", **ts); + return number; +} +static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { + PyErr_Format(PyExc_ValueError, + "Unexpected format string character: '%c'", ch); +} +static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { + switch (ch) { + case 'c': return "'char'"; + case 'b': return "'signed char'"; + case 'B': return "'unsigned char'"; + case 'h': return "'short'"; + case 'H': return "'unsigned short'"; + case 'i': return "'int'"; + case 'I': return "'unsigned int'"; + case 'l': return "'long'"; + case 'L': return "'unsigned long'"; + case 'q': return "'long long'"; + case 'Q': return "'unsigned long long'"; + case 'f': return (is_complex ? "'complex float'" : "'float'"); + case 'd': return (is_complex ? "'complex double'" : "'double'"); + case 'g': return (is_complex ? "'complex long double'" : "'long double'"); + case 'T': return "a struct"; + case 'O': return "Python object"; + case 'P': return "a pointer"; + case 's': case 'p': return "a string"; + case 0: return "end"; + default: return "unparseable format string"; + } +} +static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return 2; + case 'i': case 'I': case 'l': case 'L': return 4; + case 'q': case 'Q': return 8; + case 'f': return (is_complex ? 8 : 4); + case 'd': return (is_complex ? 16 : 8); + case 'g': { + PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); + return 0; + } + case 'O': case 'P': return sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { + switch (ch) { + case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(short); + case 'i': case 'I': return sizeof(int); + case 'l': case 'L': return sizeof(long); + #ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(PY_LONG_LONG); + #endif + case 'f': return sizeof(float) * (is_complex ? 2 : 1); + case 'd': return sizeof(double) * (is_complex ? 2 : 1); + case 'g': return sizeof(long double) * (is_complex ? 2 : 1); + case 'O': case 'P': return sizeof(void*); + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +typedef struct { char c; short x; } __Pyx_st_short; +typedef struct { char c; int x; } __Pyx_st_int; +typedef struct { char c; long x; } __Pyx_st_long; +typedef struct { char c; float x; } __Pyx_st_float; +typedef struct { char c; double x; } __Pyx_st_double; +typedef struct { char c; long double x; } __Pyx_st_longdouble; +typedef struct { char c; void *x; } __Pyx_st_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_st_float) - sizeof(float); + case 'd': return sizeof(__Pyx_st_double) - sizeof(double); + case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +/* These are for computing the padding at the end of the struct to align + on the first member of the struct. This will probably the same as above, + but we don't have any guarantees. + */ +typedef struct { short x; char c; } __Pyx_pad_short; +typedef struct { int x; char c; } __Pyx_pad_int; +typedef struct { long x; char c; } __Pyx_pad_long; +typedef struct { float x; char c; } __Pyx_pad_float; +typedef struct { double x; char c; } __Pyx_pad_double; +typedef struct { long double x; char c; } __Pyx_pad_longdouble; +typedef struct { void *x; char c; } __Pyx_pad_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); + case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); + case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { + switch (ch) { + case 'c': + return 'H'; + case 'b': case 'h': case 'i': + case 'l': case 'q': case 's': case 'p': + return 'I'; + case 'B': case 'H': case 'I': case 'L': case 'Q': + return 'U'; + case 'f': case 'd': case 'g': + return (is_complex ? 'C' : 'R'); + case 'O': + return 'O'; + case 'P': + return 'P'; + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { + if (ctx->head == NULL || ctx->head->field == &ctx->root) { + const char* expected; + const char* quote; + if (ctx->head == NULL) { + expected = "end"; + quote = ""; + } else { + expected = ctx->head->field->type->name; + quote = "'"; + } + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected %s%s%s but got %s", + quote, expected, quote, + __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); + } else { + __Pyx_StructField* field = ctx->head->field; + __Pyx_StructField* parent = (ctx->head - 1)->field; + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", + field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), + parent->type->name, field->name); + } +} +static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { + char group; + size_t size, offset, arraysize = 1; + if (ctx->enc_type == 0) return 0; + if (ctx->head->field->type->arraysize[0]) { + int i, ndim = 0; + if (ctx->enc_type == 's' || ctx->enc_type == 'p') { + ctx->is_valid_array = ctx->head->field->type->ndim == 1; + ndim = 1; + if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { + PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %zu", + ctx->head->field->type->arraysize[0], ctx->enc_count); + return -1; + } + } + if (!ctx->is_valid_array) { + PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", + ctx->head->field->type->ndim, ndim); + return -1; + } + for (i = 0; i < ctx->head->field->type->ndim; i++) { + arraysize *= ctx->head->field->type->arraysize[i]; + } + ctx->is_valid_array = 0; + ctx->enc_count = 1; + } + group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); + do { + __Pyx_StructField* field = ctx->head->field; + __Pyx_TypeInfo* type = field->type; + if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { + size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); + } else { + size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); + } + if (ctx->enc_packmode == '@') { + size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); + size_t align_mod_offset; + if (align_at == 0) return -1; + align_mod_offset = ctx->fmt_offset % align_at; + if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; + if (ctx->struct_alignment == 0) + ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, + ctx->is_complex); + } + if (type->size != size || type->typegroup != group) { + if (type->typegroup == 'C' && type->fields != NULL) { + size_t parent_offset = ctx->head->parent_offset + field->offset; + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = parent_offset; + continue; + } + if ((type->typegroup == 'H' || group == 'H') && type->size == size) { + } else { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + } + offset = ctx->head->parent_offset + field->offset; + if (ctx->fmt_offset != offset) { + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", + (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); + return -1; + } + ctx->fmt_offset += size; + if (arraysize) + ctx->fmt_offset += (arraysize - 1) * size; + --ctx->enc_count; + while (1) { + if (field == &ctx->root) { + ctx->head = NULL; + if (ctx->enc_count != 0) { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + break; + } + ctx->head->field = ++field; + if (field->type == NULL) { + --ctx->head; + field = ctx->head->field; + continue; + } else if (field->type->typegroup == 'S') { + size_t parent_offset = ctx->head->parent_offset + field->offset; + if (field->type->fields->type == NULL) continue; + field = field->type->fields; + ++ctx->head; + ctx->head->field = field; + ctx->head->parent_offset = parent_offset; + break; + } else { + break; + } + } + } while (ctx->enc_count); + ctx->enc_type = 0; + ctx->is_complex = 0; + return 0; +} +static CYTHON_INLINE PyObject * +__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) +{ + const char *ts = *tsp; + int i = 0, number; + int ndim = ctx->head->field->type->ndim; +; + ++ts; + if (ctx->new_count != 1) { + PyErr_SetString(PyExc_ValueError, + "Cannot handle repeated arrays in format string"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + while (*ts && *ts != ')') { + switch (*ts) { + case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; + default: break; + } + number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) + return PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %d", + ctx->head->field->type->arraysize[i], number); + if (*ts != ',' && *ts != ')') + return PyErr_Format(PyExc_ValueError, + "Expected a comma in format string, got '%c'", *ts); + if (*ts == ',') ts++; + i++; + } + if (i != ndim) + return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", + ctx->head->field->type->ndim, i); + if (!*ts) { + PyErr_SetString(PyExc_ValueError, + "Unexpected end of format string, expected ')'"); + return NULL; + } + ctx->is_valid_array = 1; + ctx->new_count = 1; + *tsp = ++ts; + return Py_None; +} +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { + int got_Z = 0; + while (1) { + switch(*ts) { + case 0: + if (ctx->enc_type != 0 && ctx->head == NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + if (ctx->head != NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + return ts; + case ' ': + case '\r': + case '\n': + ++ts; + break; + case '<': + if (!__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '>': + case '!': + if (__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '=': + case '@': + case '^': + ctx->new_packmode = *ts++; + break; + case 'T': + { + const char* ts_after_sub; + size_t i, struct_count = ctx->new_count; + size_t struct_alignment = ctx->struct_alignment; + ctx->new_count = 1; + ++ts; + if (*ts != '{') { + PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + ctx->enc_count = 0; + ctx->struct_alignment = 0; + ++ts; + ts_after_sub = ts; + for (i = 0; i != struct_count; ++i) { + ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); + if (!ts_after_sub) return NULL; + } + ts = ts_after_sub; + if (struct_alignment) ctx->struct_alignment = struct_alignment; + } + break; + case '}': + { + size_t alignment = ctx->struct_alignment; + ++ts; + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + if (alignment && ctx->fmt_offset % alignment) { + ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); + } + } + return ts; + case 'x': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->fmt_offset += ctx->new_count; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->enc_packmode = ctx->new_packmode; + ++ts; + break; + case 'Z': + got_Z = 1; + ++ts; + if (*ts != 'f' && *ts != 'd' && *ts != 'g') { + __Pyx_BufFmt_RaiseUnexpectedChar('Z'); + return NULL; + } + case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': + case 'l': case 'L': case 'q': case 'Q': + case 'f': case 'd': case 'g': + case 'O': case 'p': + if (ctx->enc_type == *ts && got_Z == ctx->is_complex && + ctx->enc_packmode == ctx->new_packmode) { + ctx->enc_count += ctx->new_count; + ctx->new_count = 1; + got_Z = 0; + ++ts; + break; + } + case 's': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_count = ctx->new_count; + ctx->enc_packmode = ctx->new_packmode; + ctx->enc_type = *ts; + ctx->is_complex = got_Z; + ++ts; + ctx->new_count = 1; + got_Z = 0; + break; + case ':': + ++ts; + while(*ts != ':') ++ts; + ++ts; + break; + case '(': + if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; + break; + default: + { + int number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + ctx->new_count = (size_t)number; + } + } + } +} +static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) { + buf->buf = NULL; + buf->obj = NULL; + buf->strides = __Pyx_zeros; + buf->shape = __Pyx_zeros; + buf->suboffsets = __Pyx_minusones; +} +static CYTHON_INLINE int __Pyx_GetBufferAndValidate( + Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, + int nd, int cast, __Pyx_BufFmt_StackElem* stack) +{ + if (obj == Py_None || obj == NULL) { + __Pyx_ZeroBuffer(buf); + return 0; + } + buf->buf = NULL; + if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; + if (buf->ndim != nd) { + PyErr_Format(PyExc_ValueError, + "Buffer has wrong number of dimensions (expected %d, got %d)", + nd, buf->ndim); + goto fail; + } + if (!cast) { + __Pyx_BufFmt_Context ctx; + __Pyx_BufFmt_Init(&ctx, stack, dtype); + if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + } + if ((unsigned)buf->itemsize != dtype->size) { + PyErr_Format(PyExc_ValueError, + "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", + buf->itemsize, (buf->itemsize > 1) ? "s" : "", + dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); + goto fail; + } + if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; + return 0; +fail:; + __Pyx_ZeroBuffer(buf); + return -1; +} +static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { + if (info->buf == NULL) return; + if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; + __Pyx_ReleaseBuffer(info); +} + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { + PyObject *result; + ternaryfunc call = func->ob_type->tp_call; + if (unlikely(!call)) + return PyObject_Call(func, arg, kw); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = (*call)(func, arg, kw); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->curexc_type; + tmp_value = tstate->curexc_value; + tmp_tb = tstate->curexc_traceback; + tstate->curexc_type = type; + tstate->curexc_value = value; + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_Restore(type, value, tb); +#endif +} +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->curexc_type; + *value = tstate->curexc_value; + *tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(type, value, tb); +#endif +} + +#if PY_MAJOR_VERSION < 3 +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, + CYTHON_UNUSED PyObject *cause) { + Py_XINCREF(type); + if (!value || value == Py_None) + value = NULL; + else + Py_INCREF(value); + if (!tb || tb == Py_None) + tb = NULL; + else { + Py_INCREF(tb); + if (!PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto raise_error; + } + } + if (PyType_Check(type)) { +#if CYTHON_COMPILING_IN_PYPY + if (!value) { + Py_INCREF(Py_None); + value = Py_None; + } +#endif + PyErr_NormalizeException(&type, &value, &tb); + } else { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto raise_error; + } + value = type; + type = (PyObject*) Py_TYPE(type); + Py_INCREF(type); + if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto raise_error; + } + } + __Pyx_ErrRestore(type, value, tb); + return; +raise_error: + Py_XDECREF(value); + Py_XDECREF(type); + Py_XDECREF(tb); + return; +} +#else +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + PyObject* owned_instance = NULL; + if (tb == Py_None) { + tb = 0; + } else if (tb && !PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto bad; + } + if (value == Py_None) + value = 0; + if (PyExceptionInstance_Check(type)) { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto bad; + } + value = type; + type = (PyObject*) Py_TYPE(value); + } else if (PyExceptionClass_Check(type)) { + PyObject *instance_class = NULL; + if (value && PyExceptionInstance_Check(value)) { + instance_class = (PyObject*) Py_TYPE(value); + if (instance_class != type) { + if (PyObject_IsSubclass(instance_class, type)) { + type = instance_class; + } else { + instance_class = NULL; + } + } + } + if (!instance_class) { + PyObject *args; + if (!value) + args = PyTuple_New(0); + else if (PyTuple_Check(value)) { + Py_INCREF(value); + args = value; + } else + args = PyTuple_Pack(1, value); + if (!args) + goto bad; + owned_instance = PyObject_Call(type, args, NULL); + Py_DECREF(args); + if (!owned_instance) + goto bad; + value = owned_instance; + if (!PyExceptionInstance_Check(value)) { + PyErr_Format(PyExc_TypeError, + "calling %R should have returned an instance of " + "BaseException, not %R", + type, Py_TYPE(value)); + goto bad; + } + } + } else { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto bad; + } +#if PY_VERSION_HEX >= 0x03030000 + if (cause) { +#else + if (cause && cause != Py_None) { +#endif + PyObject *fixed_cause; + if (cause == Py_None) { + fixed_cause = NULL; + } else if (PyExceptionClass_Check(cause)) { + fixed_cause = PyObject_CallObject(cause, NULL); + if (fixed_cause == NULL) + goto bad; + } else if (PyExceptionInstance_Check(cause)) { + fixed_cause = cause; + Py_INCREF(fixed_cause); + } else { + PyErr_SetString(PyExc_TypeError, + "exception causes must derive from " + "BaseException"); + goto bad; + } + PyException_SetCause(value, fixed_cause); + } + PyErr_SetObject(type, value); + if (tb) { +#if CYTHON_COMPILING_IN_PYPY + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyErr_Fetch(tmp_type, tmp_value, tmp_tb); + Py_INCREF(tb); + PyErr_Restore(tmp_type, tmp_value, tb); + Py_XDECREF(tmp_tb); +#else + PyThreadState *tstate = PyThreadState_GET(); + PyObject* tmp_tb = tstate->curexc_traceback; + if (tb != tmp_tb) { + Py_INCREF(tb); + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_tb); + } +#endif + } +bad: + Py_XDECREF(owned_instance); + return; +} +#endif + +static void __Pyx_RaiseArgtupleInvalid( + const char* func_name, + int exact, + Py_ssize_t num_min, + Py_ssize_t num_max, + Py_ssize_t num_found) +{ + Py_ssize_t num_expected; + const char *more_or_less; + if (num_found < num_min) { + num_expected = num_min; + more_or_less = "at least"; + } else { + num_expected = num_max; + more_or_less = "at most"; + } + if (exact) { + more_or_less = "exactly"; + } + PyErr_Format(PyExc_TypeError, + "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", + func_name, more_or_less, num_expected, + (num_expected == 1) ? "" : "s", num_found); +} + +static void __Pyx_RaiseDoubleKeywordsError( + const char* func_name, + PyObject* kw_name) +{ + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION >= 3 + "%s() got multiple values for keyword argument '%U'", func_name, kw_name); + #else + "%s() got multiple values for keyword argument '%s'", func_name, + PyString_AsString(kw_name)); + #endif +} + +static int __Pyx_ParseOptionalKeywords( + PyObject *kwds, + PyObject **argnames[], + PyObject *kwds2, + PyObject *values[], + Py_ssize_t num_pos_args, + const char* function_name) +{ + PyObject *key = 0, *value = 0; + Py_ssize_t pos = 0; + PyObject*** name; + PyObject*** first_kw_arg = argnames + num_pos_args; + while (PyDict_Next(kwds, &pos, &key, &value)) { + name = first_kw_arg; + while (*name && (**name != key)) name++; + if (*name) { + values[name-argnames] = value; + continue; + } + name = first_kw_arg; + #if PY_MAJOR_VERSION < 3 + if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { + while (*name) { + if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) + && _PyString_Eq(**name, key)) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + if ((**argname == key) || ( + (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) + && _PyString_Eq(**argname, key))) { + goto arg_passed_twice; + } + argname++; + } + } + } else + #endif + if (likely(PyUnicode_Check(key))) { + while (*name) { + int cmp = (**name == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**name, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + int cmp = (**argname == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**argname, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) goto arg_passed_twice; + argname++; + } + } + } else + goto invalid_keyword_type; + if (kwds2) { + if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; + } else { + goto invalid_keyword; + } + } + return 0; +arg_passed_twice: + __Pyx_RaiseDoubleKeywordsError(function_name, key); + goto bad; +invalid_keyword_type: + PyErr_Format(PyExc_TypeError, + "%.200s() keywords must be strings", function_name); + goto bad; +invalid_keyword: + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION < 3 + "%.200s() got an unexpected keyword argument '%.200s'", + function_name, PyString_AsString(key)); + #else + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif +bad: + return -1; +} + +static void __Pyx_RaiseArgumentTypeInvalid(const char* name, PyObject *obj, PyTypeObject *type) { + PyErr_Format(PyExc_TypeError, + "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", + name, type->tp_name, Py_TYPE(obj)->tp_name); +} +static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, + const char *name, int exact) +{ + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (none_allowed && obj == Py_None) return 1; + else if (exact) { + if (likely(Py_TYPE(obj) == type)) return 1; + #if PY_MAJOR_VERSION == 2 + else if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; + #endif + } + else { + if (likely(PyObject_TypeCheck(obj, type))) return 1; + } + __Pyx_RaiseArgumentTypeInvalid(name, obj, type); + return 0; +} + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { + PyObject *self, *result; + PyCFunction cfunc; + cfunc = PyCFunction_GET_FUNCTION(func); + self = PyCFunction_GET_SELF(func); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = cfunc(self, arg); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_New(1); + if (unlikely(!args)) return NULL; + Py_INCREF(arg); + PyTuple_SET_ITEM(args, 0, arg); + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { +#ifdef __Pyx_CyFunction_USED + if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { +#else + if (likely(PyCFunction_Check(func))) { +#endif + if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { + return __Pyx_PyObject_CallMethO(func, arg); + } + } + return __Pyx__PyObject_CallOneArg(func, arg); +} +#else +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject* args = PyTuple_Pack(1, arg); + return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL; +} +#endif + +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { + PyObject *result; +#if CYTHON_COMPILING_IN_CPYTHON + result = PyDict_GetItem(__pyx_d, name); + if (likely(result)) { + Py_INCREF(result); + } else { +#else + result = PyObject_GetItem(__pyx_d, name); + if (!result) { + PyErr_Clear(); +#endif + result = __Pyx_GetBuiltinName(name); + } + return result; +} + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (likely(PyObject_TypeCheck(obj, type))) + return 1; + PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", + Py_TYPE(obj)->tp_name, type->tp_name); + return 0; +} + +static void __Pyx_RaiseBufferFallbackError(void) { + PyErr_SetString(PyExc_ValueError, + "Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!"); +} + +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); +} + +static CYTHON_INLINE int __Pyx_IterFinish(void) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + PyObject* exc_type = tstate->curexc_type; + if (unlikely(exc_type)) { + if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) { + PyObject *exc_value, *exc_tb; + exc_value = tstate->curexc_value; + exc_tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; + Py_DECREF(exc_type); + Py_XDECREF(exc_value); + Py_XDECREF(exc_tb); + return 0; + } else { + return -1; + } + } + return 0; +#else + if (unlikely(PyErr_Occurred())) { + if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { + PyErr_Clear(); + return 0; + } else { + return -1; + } + } + return 0; +#endif +} + +static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { + if (unlikely(retval)) { + Py_DECREF(retval); + __Pyx_RaiseTooManyValuesError(expected); + return -1; + } else { + return __Pyx_IterFinish(); + } + return 0; +} + +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { + PyObject *r; + if (!j) return NULL; + r = PyObject_GetItem(o, j); + Py_DECREF(j); + return r; +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck) { +#if CYTHON_COMPILING_IN_CPYTHON + if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o); + if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { + PyObject *r = PyList_GET_ITEM(o, i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck) { +#if CYTHON_COMPILING_IN_CPYTHON + if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o); + if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, + int is_list, int wraparound, int boundscheck) { +#if CYTHON_COMPILING_IN_CPYTHON + if (is_list || PyList_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); + if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) { + PyObject *r = PyList_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } + else if (PyTuple_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); + if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } else { + PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; + if (likely(m && m->sq_item)) { + if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { + Py_ssize_t l = m->sq_length(o); + if (likely(l >= 0)) { + i += l; + } else { + if (PyErr_ExceptionMatches(PyExc_OverflowError)) + PyErr_Clear(); + else + return NULL; + } + } + return m->sq_item(o, i); + } + } +#else + if (is_list || PySequence_Check(o)) { + return PySequence_GetItem(o, i); + } +#endif + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +} + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + +static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) { + PyTypeObject* type = Py_TYPE(obj); + while (type && type->tp_traverse != current_tp_traverse) + type = type->tp_base; + while (type && type->tp_traverse == current_tp_traverse) + type = type->tp_base; + if (type && type->tp_traverse) + return type->tp_traverse(obj, v, a); + return 0; +} + +static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) { + PyTypeObject* type = Py_TYPE(obj); + while (type && type->tp_clear != current_tp_clear) + type = type->tp_base; + while (type && type->tp_clear == current_tp_clear) + type = type->tp_base; + if (type && type->tp_clear) + type->tp_clear(obj); +} + +static int __Pyx_SetVtable(PyObject *dict, void *vtable) { +#if PY_VERSION_HEX >= 0x02070000 + PyObject *ob = PyCapsule_New(vtable, 0, 0); +#else + PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); +#endif + if (!ob) + goto bad; + if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0) + goto bad; + Py_DECREF(ob); + return 0; +bad: + Py_XDECREF(ob); + return -1; +} + +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { + int start = 0, mid = 0, end = count - 1; + if (end >= 0 && code_line > entries[end].code_line) { + return count; + } + while (start < end) { + mid = (start + end) / 2; + if (code_line < entries[mid].code_line) { + end = mid; + } else if (code_line > entries[mid].code_line) { + start = mid + 1; + } else { + return mid; + } + } + if (code_line <= entries[mid].code_line) { + return mid; + } else { + return mid + 1; + } +} +static PyCodeObject *__pyx_find_code_object(int code_line) { + PyCodeObject* code_object; + int pos; + if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { + return NULL; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { + return NULL; + } + code_object = __pyx_code_cache.entries[pos].code_object; + Py_INCREF(code_object); + return code_object; +} +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { + int pos, i; + __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; + if (unlikely(!code_line)) { + return; + } + if (unlikely(!entries)) { + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); + if (likely(entries)) { + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = 64; + __pyx_code_cache.count = 1; + entries[0].code_line = code_line; + entries[0].code_object = code_object; + Py_INCREF(code_object); + } + return; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { + PyCodeObject* tmp = entries[pos].code_object; + entries[pos].code_object = code_object; + Py_DECREF(tmp); + return; + } + if (__pyx_code_cache.count == __pyx_code_cache.max_count) { + int new_max = __pyx_code_cache.max_count + 64; + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( + __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); + if (unlikely(!entries)) { + return; + } + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = new_max; + } + for (i=__pyx_code_cache.count; i>pos; i--) { + entries[i] = entries[i-1]; + } + entries[pos].code_line = code_line; + entries[pos].code_object = code_object; + __pyx_code_cache.count++; + Py_INCREF(code_object); +} + +#include "compile.h" +#include "frameobject.h" +#include "traceback.h" +static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( + const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyObject *py_srcfile = 0; + PyObject *py_funcname = 0; + #if PY_MAJOR_VERSION < 3 + py_srcfile = PyString_FromString(filename); + #else + py_srcfile = PyUnicode_FromString(filename); + #endif + if (!py_srcfile) goto bad; + if (c_line) { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #else + py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #endif + } + else { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromString(funcname); + #else + py_funcname = PyUnicode_FromString(funcname); + #endif + } + if (!py_funcname) goto bad; + py_code = __Pyx_PyCode_New( + 0, + 0, + 0, + 0, + 0, + __pyx_empty_bytes, /*PyObject *code,*/ + __pyx_empty_tuple, /*PyObject *consts,*/ + __pyx_empty_tuple, /*PyObject *names,*/ + __pyx_empty_tuple, /*PyObject *varnames,*/ + __pyx_empty_tuple, /*PyObject *freevars,*/ + __pyx_empty_tuple, /*PyObject *cellvars,*/ + py_srcfile, /*PyObject *filename,*/ + py_funcname, /*PyObject *name,*/ + py_line, + __pyx_empty_bytes /*PyObject *lnotab*/ + ); + Py_DECREF(py_srcfile); + Py_DECREF(py_funcname); + return py_code; +bad: + Py_XDECREF(py_srcfile); + Py_XDECREF(py_funcname); + return NULL; +} +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyFrameObject *py_frame = 0; + py_code = __pyx_find_code_object(c_line ? c_line : py_line); + if (!py_code) { + py_code = __Pyx_CreateCodeObjectForTraceback( + funcname, c_line, py_line, filename); + if (!py_code) goto bad; + __pyx_insert_code_object(c_line ? c_line : py_line, py_code); + } + py_frame = PyFrame_New( + PyThreadState_GET(), /*PyThreadState *tstate,*/ + py_code, /*PyCodeObject *code,*/ + __pyx_d, /*PyObject *globals,*/ + 0 /*PyObject *locals*/ + ); + if (!py_frame) goto bad; + py_frame->f_lineno = py_line; + PyTraceBack_Here(py_frame); +bad: + Py_XDECREF(py_code); + Py_XDECREF(py_frame); +} + +#if PY_MAJOR_VERSION < 3 +static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { + if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); + PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); + return -1; +} +static void __Pyx_ReleaseBuffer(Py_buffer *view) { + PyObject *obj = view->obj; + if (!obj) return; + if (PyObject_CheckBuffer(obj)) { + PyBuffer_Release(view); + return; + } + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } + Py_DECREF(obj); + view->obj = NULL; +} +#endif + + + static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); + if (!empty_dict) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if (strchr(__Pyx_MODULE_NAME, '.')) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(1); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, 1); + #endif + if (!module) { + if (!PyErr_ExceptionMatches(PyExc_ImportError)) + goto bad; + PyErr_Clear(); + } + } + level = 0; + } + #endif + if (!module) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(level); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, level); + #endif + } + } +bad: + #if PY_VERSION_HEX < 0x03030000 + Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); + Py_XDECREF(empty_dict); + return module; +} + +#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \ + { \ + func_type value = func_value; \ + if (sizeof(target_type) < sizeof(func_type)) { \ + if (unlikely(value != (func_type) (target_type) value)) { \ + func_type zero = 0; \ + if (is_unsigned && unlikely(value < zero)) \ + goto raise_neg_overflow; \ + else \ + goto raise_overflow; \ + } \ + } \ + return (target_type) value; \ + } + +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + #include "longintrepr.h" + #endif +#endif + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { + const int neg_one = (int) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(int) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(int) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(int) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(int) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x)) + } else if (sizeof(int) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + int val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (int) -1; + } + } else { + int val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int"); + return (int) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int"); + return (int) -1; +} + +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { + const long neg_one = (long) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (long) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(long) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x)) + } else if (sizeof(long) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + long val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (long) -1; + } + } else { + long val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to long"); + return (long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to long"); + return (long) -1; +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(int) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); + } + } else { + if (sizeof(int) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); + } +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { + const long neg_one = (long) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(long) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(long) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); + } + } else { + if (sizeof(long) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(long), + little, !is_unsigned); + } +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value) { + const Py_intptr_t neg_one = (Py_intptr_t) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(Py_intptr_t) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(Py_intptr_t) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(Py_intptr_t) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); + } + } else { + if (sizeof(Py_intptr_t) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(Py_intptr_t) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(Py_intptr_t), + little, !is_unsigned); + } +} + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return ::std::complex< float >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return x + y*(__pyx_t_float_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + __pyx_t_float_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtf(z.real*z.real + z.imag*z.imag); + #else + return hypotf(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + float denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(a, a); + case 3: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, a); + case 4: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_absf(a); + theta = atan2f(a.imag, a.real); + } + lnr = logf(r); + z_r = expf(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosf(z_theta); + z.imag = z_r * sinf(z_theta); + return z; + } + #endif +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return ::std::complex< double >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return x + y*(__pyx_t_double_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + __pyx_t_double_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrt(z.real*z.real + z.imag*z.imag); + #else + return hypot(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(a, a); + case 3: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, a); + case 4: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_abs(a); + theta = atan2(a.imag, a.real); + } + lnr = log(r); + z_r = exp(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cos(z_theta); + z.imag = z_r * sin(z_theta); + return z; + } + #endif +#endif + +static int __Pyx_check_binary_version(void) { + char ctversion[4], rtversion[4]; + PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); + PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); + if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { + char message[200]; + PyOS_snprintf(message, sizeof(message), + "compiletime version %s of module '%.100s' " + "does not match runtime version %s", + ctversion, __Pyx_MODULE_NAME, rtversion); + return PyErr_WarnEx(NULL, message, 1); + } + return 0; +} + +#ifndef __PYX_HAVE_RT_ImportModule +#define __PYX_HAVE_RT_ImportModule +static PyObject *__Pyx_ImportModule(const char *name) { + PyObject *py_name = 0; + PyObject *py_module = 0; + py_name = __Pyx_PyIdentifier_FromString(name); + if (!py_name) + goto bad; + py_module = PyImport_Import(py_name); + Py_DECREF(py_name); + return py_module; +bad: + Py_XDECREF(py_name); + return 0; +} +#endif + +#ifndef __PYX_HAVE_RT_ImportType +#define __PYX_HAVE_RT_ImportType +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, + size_t size, int strict) +{ + PyObject *py_module = 0; + PyObject *result = 0; + PyObject *py_name = 0; + char warning[200]; + Py_ssize_t basicsize; +#ifdef Py_LIMITED_API + PyObject *py_basicsize; +#endif + py_module = __Pyx_ImportModule(module_name); + if (!py_module) + goto bad; + py_name = __Pyx_PyIdentifier_FromString(class_name); + if (!py_name) + goto bad; + result = PyObject_GetAttr(py_module, py_name); + Py_DECREF(py_name); + py_name = 0; + Py_DECREF(py_module); + py_module = 0; + if (!result) + goto bad; + if (!PyType_Check(result)) { + PyErr_Format(PyExc_TypeError, + "%.200s.%.200s is not a type object", + module_name, class_name); + goto bad; + } +#ifndef Py_LIMITED_API + basicsize = ((PyTypeObject *)result)->tp_basicsize; +#else + py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); + if (!py_basicsize) + goto bad; + basicsize = PyLong_AsSsize_t(py_basicsize); + Py_DECREF(py_basicsize); + py_basicsize = 0; + if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) + goto bad; +#endif + if (!strict && (size_t)basicsize > size) { + PyOS_snprintf(warning, sizeof(warning), + "%s.%s size changed, may indicate binary incompatibility", + module_name, class_name); + if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; + } + else if ((size_t)basicsize != size) { + PyErr_Format(PyExc_ValueError, + "%.200s.%.200s has the wrong size, try recompiling", + module_name, class_name); + goto bad; + } + return (PyTypeObject *)result; +bad: + Py_XDECREF(py_module); + Py_XDECREF(result); + return NULL; +} +#endif + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { + while (t->p) { + #if PY_MAJOR_VERSION < 3 + if (t->is_unicode) { + *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); + } else if (t->intern) { + *t->p = PyString_InternFromString(t->s); + } else { + *t->p = PyString_FromStringAndSize(t->s, t->n - 1); + } + #else + if (t->is_unicode | t->is_str) { + if (t->intern) { + *t->p = PyUnicode_InternFromString(t->s); + } else if (t->encoding) { + *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); + } else { + *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); + } + } else { + *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); + } + #endif + if (!*t->p) + return -1; + ++t; + } + return 0; +} + +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { + return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); +} +static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { + Py_ssize_t ignore; + return __Pyx_PyObject_AsStringAndSize(o, &ignore); +} +static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT + if ( +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + __Pyx_sys_getdefaultencoding_not_ascii && +#endif + PyUnicode_Check(o)) { +#if PY_VERSION_HEX < 0x03030000 + char* defenc_c; + PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); + if (!defenc) return NULL; + defenc_c = PyBytes_AS_STRING(defenc); +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + { + char* end = defenc_c + PyBytes_GET_SIZE(defenc); + char* c; + for (c = defenc_c; c < end; c++) { + if ((unsigned char) (*c) >= 128) { + PyUnicode_AsASCIIString(o); + return NULL; + } + } + } +#endif + *length = PyBytes_GET_SIZE(defenc); + return defenc_c; +#else + if (__Pyx_PyUnicode_READY(o) == -1) return NULL; +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + if (PyUnicode_IS_ASCII(o)) { + *length = PyUnicode_GET_LENGTH(o); + return PyUnicode_AsUTF8(o); + } else { + PyUnicode_AsASCIIString(o); + return NULL; + } +#else + return PyUnicode_AsUTF8AndSize(o, length); +#endif +#endif + } else +#endif +#if !CYTHON_COMPILING_IN_PYPY + if (PyByteArray_Check(o)) { + *length = PyByteArray_GET_SIZE(o); + return PyByteArray_AS_STRING(o); + } else +#endif + { + char* result; + int r = PyBytes_AsStringAndSize(o, &result, length); + if (unlikely(r < 0)) { + return NULL; + } else { + return result; + } + } +} +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { + int is_true = x == Py_True; + if (is_true | (x == Py_False) | (x == Py_None)) return is_true; + else return PyObject_IsTrue(x); +} +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { + PyNumberMethods *m; + const char *name = NULL; + PyObject *res = NULL; +#if PY_MAJOR_VERSION < 3 + if (PyInt_Check(x) || PyLong_Check(x)) +#else + if (PyLong_Check(x)) +#endif + return Py_INCREF(x), x; + m = Py_TYPE(x)->tp_as_number; +#if PY_MAJOR_VERSION < 3 + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Int(x); + } + else if (m && m->nb_long) { + name = "long"; + res = PyNumber_Long(x); + } +#else + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Long(x); + } +#endif + if (res) { +#if PY_MAJOR_VERSION < 3 + if (!PyInt_Check(res) && !PyLong_Check(res)) { +#else + if (!PyLong_Check(res)) { +#endif + PyErr_Format(PyExc_TypeError, + "__%.4s__ returned non-%.4s (type %.200s)", + name, name, Py_TYPE(res)->tp_name); + Py_DECREF(res); + return NULL; + } + } + else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_TypeError, + "an integer is required"); + } + return res; +} +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { + Py_ssize_t ival; + PyObject *x; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(b))) + return PyInt_AS_LONG(b); +#endif + if (likely(PyLong_CheckExact(b))) { + #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(b)) { + case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0]; + case 0: return 0; + case 1: return ((PyLongObject*)b)->ob_digit[0]; + } + #endif + #endif + return PyLong_AsSsize_t(b); + } + x = PyNumber_Index(b); + if (!x) return -1; + ival = PyInt_AsSsize_t(x); + Py_DECREF(x); + return ival; +} +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { + return PyInt_FromSize_t(ival); +} + + +#endif /* Py_PYTHON_H */ diff --git a/GPy/models/state_space_cython.pyx b/GPy/models/state_space_cython.pyx new file mode 100644 index 00000000..877f7e7c --- /dev/null +++ b/GPy/models/state_space_cython.pyx @@ -0,0 +1,947 @@ +# -*- coding: utf-8 -*- +""" +Contains some cython code for state space modelling. +""" +import numpy as np +cimport numpy as np +import scipy as sp +cimport cython + +DTYPE = np.float64 +DTYPE_int = np.int64 + +ctypedef np.float64_t DTYPE_t +ctypedef np.int64_t DTYPE_int_t + +# Template class for dynamic callables +cdef class Dynamic_Callables_Cython: + cpdef f_a(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] A): + raise NotImplemented("(cython) f_a is not implemented!") + + cpdef Ak(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] P): # returns state iteration matrix + raise NotImplemented("(cython) Ak is not implemented!") + + cpdef Qk(self, int k): + raise NotImplemented("(cython) Qk is not implemented!") + + cpdef Q_srk(self, int k): + raise NotImplemented("(cython) Q_srk is not implemented!") + + cpdef dAk(self, int k): + raise NotImplemented("(cython) dAk is not implemented!") + + cpdef dQk(self, int k): + raise NotImplemented("(cython) dQk is not implemented!") + + cpdef reset(self, bint compute_derivatives = False): + raise NotImplemented("(cython) reset is not implemented!") + +# Template class for measurement callables +cdef class Measurement_Callables_Cython: + cpdef f_h(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] Hk): + raise NotImplemented("(cython) f_a is not implemented!") + + cpdef Hk(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] P_pred): # returns state iteration matrix + raise NotImplemented("(cython) Hk is not implemented!") + + cpdef Rk(self, int k): + raise NotImplemented("(cython) Rk is not implemented!") + + cpdef R_isrk(self, int k): + raise NotImplemented("(cython) Q_srk is not implemented!") + + cpdef dHk(self, int k): + raise NotImplemented("(cython) dAk is not implemented!") + + cpdef dRk(self, int k): + raise NotImplemented("(cython) dQk is not implemented!") + + cpdef reset(self,compute_derivatives = False): + raise NotImplemented("(cython) reset is not implemented!") + +cdef class R_handling_Cython(Measurement_Callables_Cython): + """ + The calss handles noise matrix R. + """ + cdef: + np.ndarray R + np.ndarray index + int R_time_var_index + np.ndarray dR + bint svd_each_time + dict R_square_root + + def __init__(self, np.ndarray[DTYPE_t, ndim=3] R, np.ndarray[DTYPE_t, ndim=2] index, + int R_time_var_index, int p_unique_R_number, np.ndarray[DTYPE_t, ndim=3] dR = None): + """ + Input: + --------------- + R - array with noise on various steps. The result of preprocessing + the noise input. + + index - for each step of Kalman filter contains the corresponding index + in the array. + + R_time_var_index - another index in the array R. Computed earlier and passed here. + + unique_R_number - number of unique noise matrices below which square roots + are cached and above which they are computed each time. + + dR: 3D array[:, :, param_num] + derivative of R. Derivative is supported only when R do not change over time + + Output: + -------------- + Object which has two necessary functions: + f_R(k) + inv_R_square_root(k) + """ + + self.R = R + self.index = index + self.R_time_var_index = R_time_var_index + self.dR = dR + + cdef int unique_len = len(np.unique(index)) + + if (unique_len > p_unique_R_number): + self.svd_each_time = True + else: + self.svd_each_time = False + + self.R_square_root = {} + + cpdef Rk(self, int k): + return self.R[:,:, self.index[self.R_time_var_index, k]] + + + cpdef dRk(self,int k): + if self.dR is None: + raise ValueError("dR derivative is None") + + return self.dR # the same dirivative on each iteration + + cpdef R_isrk(self, int k): + """ + Function returns the inverse square root of R matrix on step k. + """ + cdef int ind = self.index[self.R_time_var_index, k] + cdef np.ndarray[DTYPE_t, ndim=2] R = self.R[:,:, ind ] + + cdef np.ndarray[DTYPE_t, ndim=2] inv_square_root + + cdef np.ndarray[DTYPE_t, ndim=2] U + cdef np.ndarray[DTYPE_t, ndim=1] S + cdef np.ndarray[DTYPE_t, ndim=2] Vh + + if (R.shape[0] == 1): # 1-D case handle simplier. No storage + # of the result, just compute it each time. + inv_square_root = np.sqrt( 1.0/R ) + else: + if self.svd_each_time: + + U,S,Vh = sp.linalg.svd( R,full_matrices=False, compute_uv=True, + overwrite_a=False,check_finite=True) + + inv_square_root = U * 1.0/np.sqrt(S) + else: + if ind in self.R_square_root: + inv_square_root = self.R_square_root[ind] + else: + U,S,Vh = sp.linalg.svd( R,full_matrices=False, compute_uv=True, + overwrite_a=False,check_finite=True) + + inv_square_root = U * 1.0/np.sqrt(S) + + self.R_square_root[ind] = inv_square_root + + return inv_square_root + + +cdef class Std_Measurement_Callables_Cython(R_handling_Cython): + + cdef: + np.ndarray H + int H_time_var_index + np.ndarray dH + + def __init__(self, np.ndarray[DTYPE_t, ndim=3] H, int H_time_var_index, + np.ndarray[DTYPE_t, ndim=3] R, np.ndarray[DTYPE_t, ndim=2] index, int R_time_var_index, + int unique_R_number, np.ndarray[DTYPE_t, ndim=3] dH = None, + np.ndarray[DTYPE_t, ndim=3] dR=None): + + super(Std_Measurement_Callables_Cython,self).__init__(R, index, R_time_var_index, unique_R_number,dR) + + self.H = H + self.H_time_var_index = H_time_var_index + self.dH = dH + + cpdef f_h(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] H): + """ + function (k, x_{k}, H_{k}). Measurement function. + k (iteration number), starts at 0 + x_{k} state + H_{k} Jacobian matrices of f_h. In the linear case it is exactly H_{k}. + """ + + return np.dot(H, m) + + cpdef Hk(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] P_pred): # returns state iteration matrix + """ + function (k, m, P) return Jacobian of measurement function, it is + passed into p_h. + k (iteration number), starts at 0 + m: point where Jacobian is evaluated + P: parameter for Jacobian, usually covariance matrix. + """ + + return self.H[:,:, self.index[self.H_time_var_index, k]] + + cpdef dHk(self,int k): + if self.dH is None: + raise ValueError("dH derivative is None") + + return self.dH # the same dirivative on each iteration + + + +cdef class Q_handling_Cython(Dynamic_Callables_Cython): + + cdef: + np.ndarray Q + np.ndarray index + int Q_time_var_index + np.ndarray dQ + dict Q_square_root + bint svd_each_time + + def __init__(self, np.ndarray[DTYPE_t, ndim=3] Q, np.ndarray[DTYPE_t, ndim=2] index, + int Q_time_var_index, int p_unique_Q_number, np.ndarray[DTYPE_t, ndim=3] dQ = None): + """ + Input: + --------------- + Q - array with noise on various steps. The result of preprocessing + the noise input. + + index - for each step of Kalman filter contains the corresponding index + in the array. + + Q_time_var_index - another index in the array R. Computed earlier and passed here. + + unique_Q_number - number of unique noise matrices below which square roots + are cached and above which they are computed each time. + + dQ: 3D array[:, :, param_num] + derivative of Q. Derivative is supported only when Q do not change over time + + Output: + -------------- + Object which has three necessary functions: + Qk(k) + dQk(k) + Q_srkt(k) + """ + + self.Q = Q + self.index = index + self.Q_time_var_index = Q_time_var_index + self.dQ = dQ + + cdef int unique_len = len(np.unique(index)) + + if (unique_len > p_unique_Q_number): + self.svd_each_time = True + else: + self.svd_each_time = False + + self.Q_square_root = {} + + + cpdef Qk(self, int k): + """ + function (k). Returns noise matrix of dynamic model on iteration k. + k (iteration number). starts at 0 + """ + return self.Q[:,:, self.index[self.Q_time_var_index, k]] + + cpdef dQk(self, int k): + if self.dQ is None: + raise ValueError("dQ derivative is None") + + return self.dQ # the same dirivative on each iteration + + cpdef Q_srk(self, int k): + """ + function (k). Returns the square root of noise matrix of dynamic model on iteration k. + k (iteration number). starts at 0 + + This function is implemented to use SVD prediction step. + """ + cdef int ind = self.index[self.Q_time_var_index, k] + cdef np.ndarray[DTYPE_t, ndim=2] Q = self.Q[:,:, ind] + + + cdef np.ndarray[DTYPE_t, ndim=2] square_root + + cdef np.ndarray[DTYPE_t, ndim=2] U + cdef np.ndarray[DTYPE_t, ndim=1] S + cdef np.ndarray[DTYPE_t, ndim=2] Vh + + if (Q.shape[0] == 1): # 1-D case handle simplier. No storage + # of the result, just compute it each time. + square_root = np.sqrt( Q ) + else: + if self.svd_each_time: + + U,S,Vh = sp.linalg.svd( Q,full_matrices=False, compute_uv=True, + overwrite_a=False,check_finite=True) + + square_root = U * np.sqrt(S) + else: + + if ind in self.Q_square_root: + square_root = self.Q_square_root[ind] + else: + U,S,Vh = sp.linalg.svd( Q,full_matrices=False, compute_uv=True, + overwrite_a=False,check_finite=True) + + square_root = U * np.sqrt(S) + + self.Q_square_root[ind] = square_root + + return square_root + +cdef class Std_Dynamic_Callables_Cython(Q_handling_Cython): + cdef: + np.ndarray A + int A_time_var_index + np.ndarray dA + + def __init__(self, np.ndarray[DTYPE_t, ndim=3] A, int A_time_var_index, + np.ndarray[DTYPE_t, ndim=3] Q, + np.ndarray[DTYPE_t, ndim=2] index, + int Q_time_var_index, int unique_Q_number, + np.ndarray[DTYPE_t, ndim=3] dA = None, + np.ndarray[DTYPE_t, ndim=3] dQ=None): + + super(Std_Dynamic_Callables_Cython,self).__init__(Q, index, Q_time_var_index, unique_Q_number,dQ) + + self.A = A + self.A_time_var_index = A_time_var_index + self.dA = dA + + cpdef f_a(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] A): + """ + f_a: function (k, x_{k-1}, A_{k}). Dynamic function. + k (iteration number), starts at 0 + x_{k-1} State from the previous step + A_{k} Jacobian matrices of f_a. In the linear case it is exactly A_{k}. + """ + + return np.dot(A,m) + + cpdef Ak(self, int k, np.ndarray[DTYPE_t, ndim=2] m_pred, np.ndarray[DTYPE_t, ndim=2] P_pred): # returns state iteration matrix + """ + function (k, m, P) return Jacobian of measurement function, it is + passed into p_h. + k (iteration number), starts at 0 + m: point where Jacobian is evaluated + P: parameter for Jacobian, usually covariance matrix. + """ + + return self.A[:,:, self.index[self.A_time_var_index, k]] + + cpdef dAk(self, int k): + if self.dA is None: + raise ValueError("dA derivative is None") + + return self.dA # the same dirivative on each iteration + + + cpdef reset(self, bint compute_derivatives=False): + """ + For reusing this object e.g. in smoother computation. It makes sence + because necessary matrices have been already computed for all + time steps. + """ + return self + +cdef class AQcompute_batch_Cython(Q_handling_Cython): + """ + Class for calculating matrices A, Q, dA, dQ of the discrete Kalman Filter + from the matrices F, L, Qc, P_ing, dF, dQc, dP_inf of the continuos state + equation. dt - time steps. + + It has the same interface as AQcompute_once. + + It computes matrices for all time steps. This object is used when + there are not so many (controlled by internal variable) + different time steps and storing all the matrices do not take too much memory. + + Since all the matrices are computed all together, this object can be used + in smoother without repeating the computations. + """ + #def __init__(self, F,L,Qc,dt,compute_derivatives=False, grad_params_no=None, P_inf=None, dP_inf=None, dF = None, dQc=None): + cdef: + np.ndarray As + np.ndarray Qs + np.ndarray dAs + np.ndarray dQs + np.ndarray reconstruct_indices + #long total_size_of_data + dict Q_svd_dict + int last_k + + def __init__(self, np.ndarray[DTYPE_t, ndim=3] As, np.ndarray[DTYPE_t, ndim=3] Qs, + np.ndarray[DTYPE_int_t, ndim=1] reconstruct_indices, + np.ndarray[DTYPE_t, ndim=4] dAs=None, + np.ndarray[DTYPE_t, ndim=4] dQs=None): + """ + Constructor. All necessary parameters are passed here and stored + in the opject. + + Input: + ------------------- + F, L, Qc, P_inf : matrices + Parameters of corresponding continuous state model + dt: array + All time steps + compute_derivatives: bool + Whether to calculate derivatives + + dP_inf, dF, dQc: 3D array + Derivatives if they are required + + Output: + ------------------- + + """ + + self.As = As + self.Qs = Qs + self.dAs = dAs + self.dQs = dQs + self.reconstruct_indices = reconstruct_indices + self.total_size_of_data = self.As.nbytes + self.Qs.nbytes +\ + (self.dAs.nbytes if (self.dAs is not None) else 0) +\ + (self.dQs.nbytes if (self.dQs is not None) else 0) +\ + (self.reconstruct_indices.nbytes if (self.reconstruct_indices is not None) else 0) + + self.Q_svd_dict = {} + self.last_k = 0 + # !!!Print statistics! Which object is created + # !!!Print statistics! Print sizes of matrices + cpdef f_a(self, int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] A): + """ + Dynamic model + """ + return np.dot(A, m) # default dynamic model + + cpdef reset(self, bint compute_derivatives=False): + """ + For reusing this object e.g. in smoother computation. It makes sence + because necessary matrices have been already computed for all + time steps. + """ + return self + + cpdef Ak(self,int k, np.ndarray[DTYPE_t, ndim=2] m, np.ndarray[DTYPE_t, ndim=2] P): + self.last_k = k + return self.As[:,:, self.reconstruct_indices[k]] + + cpdef Qk(self,int k): + self.last_k = k + return self.Qs[:,:, self.reconstruct_indices[k]] + + cpdef dAk(self, int k): + self.last_k = k + return self.dAs[:,:, :, self.reconstruct_indices[k]] + + cpdef dQk(self, int k): + self.last_k = k + return self.dQs[:,:, :, self.reconstruct_indices[k]] + + + cpdef Q_srk(self, int k): + """ + Square root of the noise matrix Q + """ + + cdef int matrix_index = self.reconstruct_indices[k] + cdef np.ndarray[DTYPE_t, ndim=2] square_root + + cdef np.ndarray[DTYPE_t, ndim=2] U + cdef np.ndarray[DTYPE_t, ndim=1] S + cdef np.ndarray[DTYPE_t, ndim=2] Vh + + if matrix_index in self.Q_svd_dict: + square_root = self.Q_svd_dict[matrix_index] + else: + U,S,Vh = sp.linalg.svd( self.Qs[:,:, matrix_index], + full_matrices=False, compute_uv=True, + overwrite_a=False, check_finite=False) + + square_root = U * np.sqrt(S) + self.Q_svd_dict[matrix_index] = square_root + + return square_root + +# def return_last(self): +# """ +# Function returns last available matrices. +# """ +# +# if (self.last_k is None): +# raise ValueError("Matrices are not computed.") +# else: +# ind = self.reconstruct_indices[self.last_k] +# A = self.As[:,:, ind] +# Q = self.Qs[:,:, ind] +# dA = self.dAs[:,:, :, ind] +# dQ = self.dQs[:,:, :, ind] +# +# return self.last_k, A, Q, dA, dQ + +@cython.boundscheck(False) +def _kalman_prediction_step_SVD_Cython(long k, np.ndarray[DTYPE_t, ndim=2] p_m , tuple p_P, + Dynamic_Callables_Cython p_dynamic_callables, + bint calc_grad_log_likelihood=False, + np.ndarray[DTYPE_t, ndim=3] p_dm = None, + np.ndarray[DTYPE_t, ndim=3] p_dP = None): + """ + Desctrete prediction function + + Input: + k:int + Iteration No. Starts at 0. Total number of iterations equal to the + number of measurements. + + p_m: matrix of size (state_dim, time_series_no) + Mean value from the previous step. For "multiple time series mode" + it is matrix, second dimension of which correspond to different + time series. + + p_P: tuple (Prev_cov, S, V) + Covariance matrix from the previous step and its SVD decomposition. + Prev_cov = V * S * V.T The tuple is (Prev_cov, S, V) + + p_a: function (k, x_{k-1}, A_{k}). Dynamic function. + k (iteration number), starts at 0 + x_{k-1} State from the previous step + A_{k} Jacobian matrices of f_a. In the linear case it is exactly A_{k}. + + p_f_A: function (k, m, P) return Jacobian of dynamic function, it is + passed into p_a. + k (iteration number), starts at 0 + m: point where Jacobian is evaluated + P: parameter for Jacobian, usually covariance matrix. + + p_f_Q: function (k). Returns noise matrix of dynamic model on iteration k. + k (iteration number). starts at 0 + + p_f_Qsr: function (k). Returns square root of noise matrix of the + dynamic model on iteration k. k (iteration number). starts at 0 + + calc_grad_log_likelihood: boolean + Whether to calculate gradient of the marginal likelihood + of the state-space model. If true then the next parameter must + provide the extra parameters for gradient calculation. + + p_dm: 3D array (state_dim, time_series_no, parameters_no) + Mean derivatives from the previous step. For "multiple time series mode" + it is 3D array, second dimension of which correspond to different + time series. + + p_dP: 3D array (state_dim, state_dim, parameters_no) + Mean derivatives from the previous step + + grad_calc_params_1: List or None + List with derivatives. The first component is 'f_dA' - function(k) + which returns the derivative of A. The second element is 'f_dQ' + - function(k). Function which returns the derivative of Q. + + Output: + ---------------------------- + m_pred, P_pred, dm_pred, dP_pred: metrices, 3D objects + Results of the prediction steps. + + """ + + # covariance from the previous step# p_prev_cov = v * S * V.T + cdef np.ndarray[DTYPE_t, ndim=2] Prev_cov = p_P[0] + cdef np.ndarray[DTYPE_t, ndim=1] S_old = p_P[1] + cdef np.ndarray[DTYPE_t, ndim=2] V_old = p_P[2] + #p_prev_cov_tst = np.dot(p_V, (p_S * p_V).T) # reconstructed covariance from the previous step + + # index correspond to values from previous iteration. + cdef np.ndarray[DTYPE_t, ndim=2] A = p_dynamic_callables.Ak(k,p_m,Prev_cov) # state transition matrix (or Jacobian) + cdef np.ndarray[DTYPE_t, ndim=2] Q = p_dynamic_callables.Qk(k) # state noise matrx. This is necessary for the square root calculation (next step) + cdef np.ndarray[DTYPE_t, ndim=2] Q_sr = p_dynamic_callables.Q_srk(k) + # Prediction step -> + cdef np.ndarray[DTYPE_t, ndim=2] m_pred = p_dynamic_callables.f_a(k, p_m, A) # predicted mean + + # coavariance prediction have changed: + cdef np.ndarray[DTYPE_t, ndim=2] svd_1_matr = np.vstack( ( (np.sqrt(S_old)* np.dot(A,V_old)).T , Q_sr.T) ) + res = sp.linalg.svd( svd_1_matr,full_matrices=False, compute_uv=True, + overwrite_a=False,check_finite=True) + # (U,S,Vh) + cdef np.ndarray[DTYPE_t, ndim=2] U = res[0] + cdef np.ndarray[DTYPE_t, ndim=1] S = res[1] + cdef np.ndarray[DTYPE_t, ndim=2] Vh = res[2] + # predicted variance computed by the regular method. For testing + #P_pred_tst = A.dot(Prev_cov).dot(A.T) + Q + cdef np.ndarray[DTYPE_t, ndim=2] V_new = Vh.T + cdef np.ndarray[DTYPE_t, ndim=1] S_new = S**2 + + cdef np.ndarray[DTYPE_t, ndim=2] P_pred = np.dot(V_new * S_new, V_new.T) # prediction covariance + #tuple P_pred = (P_pred, S_new, Vh.T) + # Prediction step <- + + # derivatives + cdef np.ndarray[DTYPE_t, ndim=3] dA_all_params + cdef np.ndarray[DTYPE_t, ndim=3] dQ_all_params + + cdef np.ndarray[DTYPE_t, ndim=3] dm_pred + cdef np.ndarray[DTYPE_t, ndim=3] dP_pred + + cdef int param_number + cdef int j + cdef tuple ret + + cdef np.ndarray[DTYPE_t, ndim=2] dA + cdef np.ndarray[DTYPE_t, ndim=2] dQ + if calc_grad_log_likelihood: + dA_all_params = p_dynamic_callables.dAk(k) # derivatives of A wrt parameters + dQ_all_params = p_dynamic_callables.dQk(k) # derivatives of Q wrt parameters + + param_number = p_dP.shape[2] + + # p_dm, p_dP - derivatives form the previoius step + dm_pred = np.empty((p_dm.shape[0], p_dm.shape[1], p_dm.shape[2]), dtype = DTYPE) + dP_pred = np.empty((p_dP.shape[0], p_dP.shape[1], p_dP.shape[2]), dtype = DTYPE) + + for j in range(param_number): + dA = dA_all_params[:,:,j] + dQ = dQ_all_params[:,:,j] + + dm_pred[:,:,j] = np.dot(dA, p_m) + np.dot(A, p_dm[:,:,j]) + # prediction step derivatives for current parameter: + + dP_pred[:,:,j] = np.dot( dA ,np.dot(Prev_cov, A.T)) + dP_pred[:,:,j] += dP_pred[:,:,j].T + dP_pred[:,:,j] += np.dot( A ,np.dot( p_dP[:,:,j] , A.T)) + dQ + + dP_pred[:,:,j] = 0.5*(dP_pred[:,:,j] + dP_pred[:,:,j].T) #symmetrize + else: + dm_pred = None + dP_pred = None + + ret = (P_pred, S_new, Vh.T) + return m_pred, ret, dm_pred, dP_pred + + + +@cython.boundscheck(False) +def _kalman_update_step_SVD_Cython(long k, np.ndarray[DTYPE_t, ndim=2] p_m, tuple p_P, + Measurement_Callables_Cython p_measurement_callables, + np.ndarray[DTYPE_t, ndim=2] measurement, + bint calc_log_likelihood= False, + bint calc_grad_log_likelihood=False, + np.ndarray[DTYPE_t, ndim=3] p_dm = None, + np.ndarray[DTYPE_t, ndim=3] p_dP = None): + """ + Input: + + k: int + Iteration No. Starts at 0. Total number of iterations equal to the + number of measurements. + + m_P: matrix of size (state_dim, time_series_no) + Mean value from the previous step. For "multiple time series mode" + it is matrix, second dimension of which correspond to different + time series. + + p_P: tuple (P_pred, S, V) + Covariance matrix from the prediction step and its SVD decomposition. + P_pred = V * S * V.T The tuple is (P_pred, S, V) + + p_h: function (k, x_{k}, H_{k}). Measurement function. + k (iteration number), starts at 0 + x_{k} state + H_{k} Jacobian matrices of f_h. In the linear case it is exactly H_{k}. + + p_f_H: function (k, m, P) return Jacobian of dynamic function, it is + passed into p_h. + k (iteration number), starts at 0 + m: point where Jacobian is evaluated + P: parameter for Jacobian, usually covariance matrix. + + p_f_R: function (k). Returns noise matrix of measurement equation + on iteration k. + k (iteration number). starts at 0 + + p_f_iRsr: function (k). Returns the square root of the noise matrix of + measurement equation on iteration k. + k (iteration number). starts at 0 + + measurement: (measurement_dim, time_series_no) matrix + One measurement used on the current update step. For + "multiple time series mode" it is matrix, second dimension of + which correspond to different time series. + + calc_log_likelihood: boolean + Whether to calculate marginal likelihood of the state-space model. + + calc_grad_log_likelihood: boolean + Whether to calculate gradient of the marginal likelihood + of the state-space model. If true then the next parameter must + provide the extra parameters for gradient calculation. + + p_dm: 3D array (state_dim, time_series_no, parameters_no) + Mean derivatives from the prediction step. For "multiple time series mode" + it is 3D array, second dimension of which correspond to different + time series. + + p_dP: array + Covariance derivatives from the prediction step. + + grad_calc_params_2: List or None + List with derivatives. The first component is 'f_dH' - function(k) + which returns the derivative of H. The second element is 'f_dR' + - function(k). Function which returns the derivative of R. + + Output: + ---------------------------- + m_upd, P_upd, dm_upd, dP_upd: metrices, 3D objects + Results of the prediction steps. + + log_likelihood_update: double or 1D array + Update to the log_likelihood from this step + + d_log_likelihood_update: (grad_params_no, time_series_no) matrix + Update to the gradient of log_likelihood, "multiple time series mode" + adds extra columns to the gradient. + + """ + + cdef np.ndarray[DTYPE_t, ndim=2] m_pred = p_m # from prediction step + #P_pred,S_pred,V_pred = p_P # from prediction step + cdef np.ndarray[DTYPE_t, ndim=2] P_pred = p_P[0] + cdef np.ndarray[DTYPE_t, ndim=1] S_pred = p_P[1] + cdef np.ndarray[DTYPE_t, ndim=2] V_pred = p_P[2] + + cdef np.ndarray[DTYPE_t, ndim=2] H = p_measurement_callables.Hk(k, m_pred, P_pred) + cdef np.ndarray[DTYPE_t, ndim=2] R = p_measurement_callables.Rk(k) + cdef np.ndarray[DTYPE_t, ndim=2] R_isr =p_measurement_callables.R_isrk(k) # square root of the inverse of R matrix + + cdef int time_series_no = p_m.shape[1] # number of time serieses + + cdef np.ndarray[DTYPE_t, ndim=2] log_likelihood_update # log_likelihood_update=None; + # Update step (only if there is data) + #if not np.any(np.isnan(measurement)): # TODO: if some dimensions are missing, do properly computations for other. + cdef np.ndarray[DTYPE_t, ndim=2] v = measurement-p_measurement_callables.f_h(k, m_pred, H) + + cdef np.ndarray[DTYPE_t, ndim=2] svd_2_matr = np.vstack( ( np.dot( R_isr.T, np.dot(H, V_pred)) , np.diag( 1.0/np.sqrt(S_pred) ) ) ) + + res = sp.linalg.svd( svd_2_matr,full_matrices=False, compute_uv=True, + overwrite_a=False,check_finite=True) + + #(U,S,Vh) + cdef np.ndarray[DTYPE_t, ndim=2] U = res[0] + cdef np.ndarray[DTYPE_t, ndim=1] S_svd = res[1] + cdef np.ndarray[DTYPE_t, ndim=2] Vh = res[2] + + # P_upd = U_upd S_upd**2 U_upd.T + cdef np.ndarray[DTYPE_t, ndim=2] U_upd = np.dot(V_pred, Vh.T) + cdef np.ndarray[DTYPE_t, ndim=1] S_upd = (1.0/S_svd)**2 + + cdef np.ndarray[DTYPE_t, ndim=2] P_upd = np.dot(U_upd * S_upd, U_upd.T) # update covariance + #P_upd = (P_upd,S_upd,U_upd) # tuple to pass to the next step + + # stil need to compute S and K for derivative computation + cdef np.ndarray[DTYPE_t, ndim=2] S = H.dot(P_pred).dot(H.T) + R + cdef np.ndarray[DTYPE_t, ndim=2] K + cdef bint measurement_dim_gt_one = False + if measurement.shape[0]==1: # measurements are one dimensional + if (S < 0): + raise ValueError("Kalman Filter Update SVD: S is negative step %i" % k ) + #import pdb; pdb.set_trace() + + K = P_pred.dot(H.T) / S + if calc_log_likelihood: + log_likelihood_update = -0.5 * ( np.log(2*np.pi) + np.log(S) + + v*v / S) + #log_likelihood_update = log_likelihood_update[0,0] # to make int + if np.any(np.isnan(log_likelihood_update)): # some member in P_pred is None. + raise ValueError("Nan values in likelihood update!") + else: + log_likelihood_update = None + #LL = None; islower = None + else: + measurement_dim_gt_one = True + raise ValueError("""Measurement dimension larger then 1 is currently not supported""") + + # Old method of computing updated covariance (for testing) -> + #P_upd_tst = K.dot(S).dot(K.T) + #P_upd_tst = 0.5*(P_upd_tst + P_upd_tst.T) + #P_upd_tst = P_pred - P_upd_tst# this update matrix is symmetric + # Old method of computing updated covariance (for testing) <- + cdef np.ndarray[DTYPE_t, ndim=3] dm_upd # dm_upd=None; + cdef np.ndarray[DTYPE_t, ndim=3] dP_upd # dP_upd=None; + cdef np.ndarray[DTYPE_t, ndim=2] d_log_likelihood_update # d_log_likelihood_update=None + + cdef np.ndarray[DTYPE_t, ndim=3] dm_pred_all_params + cdef np.ndarray[DTYPE_t, ndim=3] dP_pred_all_params + cdef int param_number + + cdef np.ndarray[DTYPE_t, ndim=3] dH_all_params + cdef np.ndarray[DTYPE_t, ndim=3] dR_all_params + + cdef int param + + cdef np.ndarray[DTYPE_t, ndim=2] dH, dR, dm_pred, dP_pred, dv, dS, tmp1, tmp2, tmp3, dK, tmp5 + cdef tuple ret + + if calc_grad_log_likelihood: + dm_pred_all_params = p_dm # derivativas of the prediction phase + dP_pred_all_params = p_dP + + param_number = p_dP.shape[2] + + dH_all_params = p_measurement_callables.dHk(k) + dR_all_params = p_measurement_callables.dRk(k) + + dm_upd = np.empty((dm_pred_all_params.shape[0], dm_pred_all_params.shape[1], dm_pred_all_params.shape[2]), dtype = DTYPE) + dP_upd = np.empty((dP_pred_all_params.shape[0], dP_pred_all_params.shape[1], dP_pred_all_params.shape[2]), dtype = DTYPE) + + # firts dimension parameter_no, second - time series number + d_log_likelihood_update = np.empty((param_number,time_series_no), dtype = DTYPE) + for param in range(param_number): + + dH = dH_all_params[:,:,param] + dR = dR_all_params[:,:,param] + + dm_pred = dm_pred_all_params[:,:,param] + dP_pred = dP_pred_all_params[:,:,param] + + # Terms in the likelihood derivatives + dv = - np.dot( dH, m_pred) - np.dot( H, dm_pred) + dS = np.dot(dH, np.dot( P_pred, H.T)) + dS += dS.T + dS += np.dot(H, np.dot( dP_pred, H.T)) + dR + + # TODO: maybe symmetrize dS + + tmp1 = H.T / S + tmp2 = dH.T / S + tmp3 = dS.T / S + + dK = np.dot( dP_pred, tmp1) + np.dot( P_pred, tmp2) - \ + np.dot( P_pred, np.dot( tmp1, tmp3 ) ) + + # terms required for the next step, save this for each parameter + dm_upd[:,:,param] = dm_pred + np.dot(dK, v) + np.dot(K, dv) + + dP_upd[:,:,param] = -np.dot(dK, np.dot(S, K.T)) + dP_upd[:,:,param] += dP_upd[:,:,param].T + dP_upd[:,:,param] += dP_pred - np.dot(K , np.dot( dS, K.T)) + + dP_upd[:,:,param] = 0.5*(dP_upd[:,:,param] + dP_upd[:,:,param].T) #symmetrize + # computing the likelihood change for each parameter: + tmp5 = v / S + + + d_log_likelihood_update[param,:] = -(0.5*np.sum(np.diag(tmp3)) + \ + np.sum(tmp5*dv, axis=0) - 0.5 * np.sum(tmp5 * np.dot(dS, tmp5), axis=0) ) + + # Compute the actual updates for mean of the states. Variance update + # is computed earlier. + else: + dm_upd = None + dP_upd = None + d_log_likelihood_update = None + + m_upd = m_pred + K.dot( v ) + + ret = (P_upd,S_upd,U_upd) + return m_upd, ret, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update + + +@cython.boundscheck(False) +def _cont_discr_kalman_filter_raw_Cython(int state_dim, Dynamic_Callables_Cython p_dynamic_callables, + Measurement_Callables_Cython p_measurement_callables, X, Y, + np.ndarray[DTYPE_t, ndim=2] m_init=None, np.ndarray[DTYPE_t, ndim=2] P_init=None, + p_kalman_filter_type='regular', + bint calc_log_likelihood=False, + bint calc_grad_log_likelihood=False, + int grad_params_no=0, + np.ndarray[DTYPE_t, ndim=3] dm_init=None, + np.ndarray[DTYPE_t, ndim=3] dP_init=None): + + cdef int steps_no = Y.shape[0] # number of steps in the Kalman Filter + cdef int time_series_no = Y.shape[2] # multiple time series mode + + # Allocate space for results + # Mean estimations. Initial values will be included + cdef np.ndarray[DTYPE_t, ndim=3] M = np.empty(((steps_no+1),state_dim,time_series_no), dtype=DTYPE) + M[0,:,:] = m_init # Initialize mean values + # Variance estimations. Initial values will be included + cdef np.ndarray[DTYPE_t, ndim=3] P = np.empty(((steps_no+1),state_dim,state_dim)) + P_init = 0.5*( P_init + P_init.T) # symmetrize initial covariance. In some ustable cases this is uiseful + P[0,:,:] = P_init # Initialize initial covariance matrix + + cdef np.ndarray[DTYPE_t, ndim=2] U + cdef np.ndarray[DTYPE_t, ndim=1] S + cdef np.ndarray[DTYPE_t, ndim=2] Vh + + U,S,Vh = sp.linalg.svd( P_init,full_matrices=False, compute_uv=True, + overwrite_a=False,check_finite=True) + S[ (S==0) ] = 1e-17 # allows to run algorithm for singular initial variance + cdef tuple P_upd = (P_init, S,U) + #log_likelihood = 0 + #grad_log_likelihood = np.zeros((grad_params_no,1)) + cdef np.ndarray[DTYPE_t, ndim=2] log_likelihood = np.zeros((1, time_series_no), dtype = DTYPE) #if calc_log_likelihood else None + cdef np.ndarray[DTYPE_t, ndim=2] grad_log_likelihood = np.zeros((grad_params_no, time_series_no), dtype = DTYPE) #if calc_grad_log_likelihood else None + + #setting initial values for derivatives update + cdef np.ndarray[DTYPE_t, ndim=3] dm_upd = dm_init + cdef np.ndarray[DTYPE_t, ndim=3] dP_upd = dP_init + # Main loop of the Kalman filter + cdef np.ndarray[DTYPE_t, ndim=2] prev_mean, k_measurment + cdef np.ndarray[DTYPE_t, ndim=2] m_pred, m_upd + cdef tuple P_pred + cdef np.ndarray[DTYPE_t, ndim=3] dm_pred, dP_pred + cdef np.ndarray[DTYPE_t, ndim=2] log_likelihood_update, d_log_likelihood_update + cdef int k + for k in range(0,steps_no): + # In this loop index for new estimations is (k+1), old - (k) + # This happened because initial values are stored at 0-th index. + #import pdb; pdb.set_trace() + + prev_mean = M[k,:,:] # mean from the previous step + + m_pred, P_pred, dm_pred, dP_pred = \ + _kalman_prediction_step_SVD_Cython(k, prev_mean ,P_upd, p_dynamic_callables, + calc_grad_log_likelihood, dm_upd, dP_upd) + + k_measurment = Y[k,:,:] + +# if np.any(np.isnan(k_measurment)): +# raise ValueError("Nan measurements are currently not supported") + + m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ + _kalman_update_step_SVD_Cython(k, m_pred , P_pred, p_measurement_callables, + k_measurment, calc_log_likelihood=calc_log_likelihood, + calc_grad_log_likelihood=calc_grad_log_likelihood, + p_dm = dm_pred, p_dP = dP_pred) + + if calc_log_likelihood: + log_likelihood += log_likelihood_update + + if calc_grad_log_likelihood: + grad_log_likelihood += d_log_likelihood_update + + M[k+1,:,:] = m_upd # separate mean value for each time series + P[k+1,:,:] = P_upd[0] + + return (M, P, log_likelihood, grad_log_likelihood, p_dynamic_callables.reset(False)) \ No newline at end of file diff --git a/GPy/models/state_space_main.py b/GPy/models/state_space_main.py index 39d5abe2..f8320f63 100644 --- a/GPy/models/state_space_main.py +++ b/GPy/models/state_space_main.py @@ -12,9 +12,466 @@ import numpy as np import scipy as sp import scipy.linalg as linalg - print_verbose = False +try: + import state_space_cython + cython_code_available = True + print("state_space: cython is available") +except ImportError as e: + cython_code_available = False + + +#cython_code_available = False +if cython_code_available: + print("state_space: cython is used") +else: + print("state_space: cython is NOT used") + +class Dynamic_Callables_Python(object): + + def f_a(self, k, m, A): + """ + p_a: function (k, x_{k-1}, A_{k}). Dynamic function. + k (iteration number), starts at 0 + x_{k-1} State from the previous step + A_{k} Jacobian matrices of f_a. In the linear case it is exactly A_{k}. + """ + + raise NotImplemented("f_a is not implemented!") + + def Ak(self, k,m,P): # returns state iteration matrix + """ + function (k, m, P) return Jacobian of dynamic function, it is passed into p_a. + k (iteration number), starts at 0 + m: point where Jacobian is evaluated + P: parameter for Jacobian, usually covariance matrix. + """ + + raise NotImplemented("Ak is not implemented!") + + def Qk(self, k): + """ + function (k). Returns noise matrix of dynamic model on iteration k. + k (iteration number). starts at 0 + """ + raise NotImplemented("Qk is not implemented!") + + def Q_srk(self, k): + """ + function (k). Returns the square root of noise matrix of dynamic model on iteration k. + k (iteration number). starts at 0 + + This function is implemented to use SVD prediction step. + """ + + raise NotImplemented("Q_srk is not implemented!") + + def dAk(self, k): + """ + function (k). Returns the derivative of A on iteration k. + k (iteration number). starts at 0 + """ + raise NotImplemented("dAk is not implemented!") + + def dQk(self, k): + """ + function (k). Returns the derivative of Q on iteration k. + k (iteration number). starts at 0 + """ + raise NotImplemented("dQk is not implemented!") + + def reset(self,compute_derivatives = False): + """ + Return the state of this object to the beginning of iteration (to k eq. 0) + """ + + raise NotImplemented("reset is not implemented!") + +if cython_code_available: + Dynamic_Callables_Class = state_space_cython.Dynamic_Callables_Cython +else: + Dynamic_Callables_Class = Dynamic_Callables_Python + + +class Measurement_Callables_Python(object): + def f_h(self, k, m_pred, Hk): + """ + function (k, x_{k}, H_{k}). Measurement function. + k (iteration number), starts at 0 + x_{k} state + H_{k} Jacobian matrices of f_h. In the linear case it is exactly H_{k}. + """ + + raise NotImplemented("f_a is not implemented!") + + def Hk(self, k,m_pred,P_pred): # returns state iteration matrix + """ + function (k, m, P) return Jacobian of measurement function, it is + passed into p_h. + k (iteration number), starts at 0 + m: point where Jacobian is evaluated + P: parameter for Jacobian, usually covariance matrix. + """ + + raise NotImplemented("Hk is not implemented!") + + def Rk(self, k): + """ + function (k). Returns noise matrix of measurement equation + on iteration k. + k (iteration number). starts at 0 + """ + raise NotImplemented("Rk is not implemented!") + + + def R_isrk(self, k): + """ + function (k). Returns the square root of the noise matrix of + measurement equation on iteration k. + k (iteration number). starts at 0 + + This function is implemented to use SVD prediction step. + """ + + raise NotImplemented("Q_srk is not implemented!") + + def dHk(self, k): + """ + function (k). Returns the derivative of H on iteration k. + k (iteration number). starts at 0 + """ + raise NotImplemented("dAk is not implemented!") + + def dRk(self, k): + """ + function (k). Returns the derivative of R on iteration k. + k (iteration number). starts at 0 + """ + raise NotImplemented("dQk is not implemented!") + + def reset(self,compute_derivatives = False): + """ + Return the state of this object to the beginning of iteration (to k eq. 0) + """ + + raise NotImplemented("reset is not implemented!") + +if cython_code_available: + Measurement_Callables_Class = state_space_cython.Measurement_Callables_Cython +else: + Measurement_Callables_Class = Measurement_Callables_Python + +class R_handling_Python(Measurement_Callables_Class): + """ + The calss handles noise matrix R. + """ + def __init__(self, R, index, R_time_var_index, unique_R_number, dR=None): + """ + Input: + --------------- + R - array with noise on various steps. The result of preprocessing + the noise input. + + index - for each step of Kalman filter contains the corresponding index + in the array. + + R_time_var_index - another index in the array R. Computed earlier and passed here. + + unique_R_number - number of unique noise matrices below which square roots + are cached and above which they are computed each time. + + dR: 3D array[:, :, param_num] + derivative of R. Derivative is supported only when R do not change over time + + Output: + -------------- + Object which has two necessary functions: + f_R(k) + inv_R_square_root(k) + """ + self.R = R + self.index = index + self.R_time_var_index = R_time_var_index + self.dR = dR + + if (len(np.unique(index)) > unique_R_number): + self.svd_each_time = True + else: + self.svd_each_time = False + + self.R_square_root = {} + + def Rk(self,k): + return self.R[:,:, self.index[self.R_time_var_index, k]] + + def dRk(self,k): + if self.dR is None: + raise ValueError("dR derivative is None") + + return self.dR # the same dirivative on each iteration + + def R_isrk(self, k): + """ + Function returns the inverse square root of R matrix on step k. + """ + ind = self.index[self.R_time_var_index, k] + R = self.R[:,:, ind ] + + if (R.shape[0] == 1): # 1-D case handle simplier. No storage + # of the result, just compute it each time. + inv_square_root = np.sqrt( 1.0/R ) + else: + if self.svd_each_time: + + (U,S,Vh) = sp.linalg.svd( R,full_matrices=False, compute_uv=True, + overwrite_a=False,check_finite=True) + + inv_square_root = U * 1.0/np.sqrt(S) + else: + if ind in self.R_square_root: + inv_square_root = self.R_square_root[ind] + else: + (U,S,Vh) = sp.linalg.svd( R,full_matrices=False, compute_uv=True, + overwrite_a=False,check_finite=True) + + inv_square_root = U * 1.0/np.sqrt(S) + + self.R_square_root[ind] = inv_square_root + + return inv_square_root + +if cython_code_available: + R_handling_Class = state_space_cython.R_handling_Cython +else: + R_handling_Class = R_handling_Python + +class Std_Measurement_Callables_Python(R_handling_Class): + + def __init__(self, H, H_time_var_index, R, index, R_time_var_index, unique_R_number, dH = None, dR=None): + super(Std_Measurement_Callables_Python,self).__init__(R, index, R_time_var_index, unique_R_number,dR) + + self.H = H + self.H_time_var_index = H_time_var_index + self.dH = dH + def f_h(self, k, m, H): + """ + function (k, x_{k}, H_{k}). Measurement function. + k (iteration number), starts at 0 + x_{k} state + H_{k} Jacobian matrices of f_h. In the linear case it is exactly H_{k}. + """ + + return np.dot(H, m) + + def Hk(self, k,m_pred,P_pred): # returns state iteration matrix + """ + function (k, m, P) return Jacobian of measurement function, it is + passed into p_h. + k (iteration number), starts at 0 + m: point where Jacobian is evaluated + P: parameter for Jacobian, usually covariance matrix. + """ + + return self.H[:,:, self.index[self.H_time_var_index, k]] + + def dHk(self,k): + if self.dH is None: + raise ValueError("dH derivative is None") + + return self.dH # the same dirivative on each iteration + +if cython_code_available: + Std_Measurement_Callables_Class = state_space_cython.Std_Measurement_Callables_Cython +else: + Std_Measurement_Callables_Class = Std_Measurement_Callables_Python + +class Q_handling_Python(Dynamic_Callables_Class): + + def __init__(self, Q, index, Q_time_var_index, unique_Q_number, dQ = None): + """ + Input: + --------------- + R - array with noise on various steps. The result of preprocessing + the noise input. + + index - for each step of Kalman filter contains the corresponding index + in the array. + + R_time_var_index - another index in the array R. Computed earlier and passed here. + + unique_R_number - number of unique noise matrices below which square roots + are cached and above which they are computed each time. + + dQ: 3D array[:, :, param_num] + derivative of Q. Derivative is supported only when Q do not change over time + + Output: + -------------- + Object which has two necessary functions: + f_R(k) + inv_R_square_root(k) + """ + + self.Q = Q + self.index = index + self.Q_time_var_index = Q_time_var_index + self.dQ = dQ + + if (len(np.unique(index)) > unique_Q_number): + self.svd_each_time = True + else: + self.svd_each_time = False + + self.Q_square_root = {} + + + def Qk(self,k): + """ + function (k). Returns noise matrix of dynamic model on iteration k. + k (iteration number). starts at 0 + """ + return self.Q[:,:, self.index[self.Q_time_var_index, k]] + + def dQk(self,k): + if self.dQ is None: + raise ValueError("dQ derivative is None") + + return self.dQ # the same dirivative on each iteration + + def Q_srk(self,k): + """ + function (k). Returns the square root of noise matrix of dynamic model on iteration k. + k (iteration number). starts at 0 + + This function is implemented to use SVD prediction step. + """ + ind = self.index[self.Q_time_var_index, k] + Q = self.Q[:,:, ind] + + + if (Q.shape[0] == 1): # 1-D case handle simplier. No storage + # of the result, just compute it each time. + square_root = np.sqrt( Q ) + else: + if self.svd_each_time: + + (U,S,Vh) = sp.linalg.svd( Q,full_matrices=False, compute_uv=True, + overwrite_a=False,check_finite=True) + + square_root = U * np.sqrt(S) + else: + + if ind in self.Q_square_root: + square_root = self.Q_square_root[ind] + else: + (U,S,Vh) = sp.linalg.svd( Q,full_matrices=False, compute_uv=True, + overwrite_a=False,check_finite=True) + + square_root = U * np.sqrt(S) + + self.Q_square_root[ind] = square_root + + return square_root + +if cython_code_available: + Q_handling_Class = state_space_cython.Q_handling_Cython +else: + Q_handling_Class = Q_handling_Python + +class Std_Dynamic_Callables_Python(Q_handling_Class): + + def __init__(self, A, A_time_var_index, Q, index, Q_time_var_index, unique_Q_number, dA = None, dQ=None): + super(Std_Measurement_Callables_Python,self).__init__(Q, index, Q_time_var_index, unique_Q_number,dQ) + + self.A = A + self.A_time_var_index = A_time_var_index + self.dA = dA + + def f_a(self, k, m, A): + """ + f_a: function (k, x_{k-1}, A_{k}). Dynamic function. + k (iteration number), starts at 0 + x_{k-1} State from the previous step + A_{k} Jacobian matrices of f_a. In the linear case it is exactly A_{k}. + """ + + return np.dot(A,m) + + def Ak(self, k,m_pred,P_pred): # returns state iteration matrix + """ + function (k, m, P) return Jacobian of measurement function, it is + passed into p_h. + k (iteration number), starts at 0 + m: point where Jacobian is evaluated + P: parameter for Jacobian, usually covariance matrix. + """ + + return self.A[:,:, self.index[self.A_time_var_index, k]] + + def dAk(self,k): + if self.dA is None: + raise ValueError("dA derivative is None") + + return self.dA # the same dirivative on each iteration + +if cython_code_available: + Std_Dynamic_Callables_Class = state_space_cython.Std_Dynamic_Callables_Cython +else: + Std_Dynamic_Callables_Class = Std_Dynamic_Callables_Python + + +class AddMethodToClass(object): + + def __init__(self, func=None, tp='staticmethod'): + """ + Input: + -------------- + func: function to add + tp: string + Type of the method: normal, staticmethod, classmethod + """ + if func is None: + raise ValueError("Function can not be None") + + self.func = func + self.tp = tp + + def __get__(self, obj, klass=None,*args, **kwargs): + + if self.tp == 'staticmethod': + return self.func + elif self.tp == 'normal': + def newfunc(obj, *args, **kwargs): + return self.func + + elif self.tp == 'classmethod': + def newfunc(klass, *args, **kwargs): + return self.func + return newfunc + +class DescreteStateSpaceMeta(type): + """ + Substitute necessary methods from cython. + """ + + def __new__(typeclass, name, bases, attributes): + """ + After thos method the class object is created + """ + + if cython_code_available: + if '_kalman_prediction_step_SVD' in attributes: + attributes['_kalman_prediction_step_SVD'] = AddMethodToClass(state_space_cython._kalman_prediction_step_SVD_Cython) + + if '_kalman_update_step_SVD' in attributes: + attributes['_kalman_update_step_SVD'] = AddMethodToClass(state_space_cython._kalman_update_step_SVD_Cython) + + if '_cont_discr_kalman_filter_raw' in attributes: + attributes['_cont_discr_kalman_filter_raw'] = AddMethodToClass(state_space_cython._cont_discr_kalman_filter_raw_Cython) + + return super(DescreteStateSpaceMeta, typeclass).__new__(typeclass, name, bases, attributes) + class DescreteStateSpace(object): """ This class implents state-space inference for linear and non-linear @@ -37,9 +494,10 @@ class DescreteStateSpace(object): implementations are very similar. """ + __metaclass__ = DescreteStateSpaceMeta @staticmethod - def _reshape_input_data(shape): + def _reshape_input_data(shape, desired_dim=3): """ Static function returns the column-wise shape for for an input shape. @@ -47,23 +505,38 @@ class DescreteStateSpace(object): -------------- shape: tuple Shape of an input array, so that it is always a column. - + + desired_dim: int + desired shape of output. For Y data it should be 3 + (sample_no, dimension, ts_no). For X data - 2 (sample_no, 1) Output: -------------- new_shape: tuple New shape of the measurements array. Idea is that samples are - along dimension 0. + along dimension 0, sample dimension - dimension 1, different + time series - dimension 2. old_shape: tuple or None If the shape has been modified, return old shape, otherwise None """ if (len(shape) > 3): - raise ValueError("Input array is not supposed to be more than 3 dimensional") + raise ValueError("Input array is not supposed to be more than 3 dimensional.") + + if (len(shape) > desired_dim): + raise ValueError("Input array shape is more than desired shape.") elif len(shape) == 1: - return ((shape[0],1), shape) + if (desired_dim==3): + return ((shape[0],1,1), shape) # last dimension is the time serime_series_no + elif (desired_dim==2): + return ((shape[0],1), shape) + elif len(shape) == 2: - return ((shape[1],1), shape) if (shape[0] == 1) else (shape,None) # convert to column vector + if (desired_dim==3): + return ((shape[1],1,1), shape) if (shape[0] == 1) else ( (shape[0],shape[1],1), shape) # convert to column vector + elif (desired_dim==2): + return ((shape[1],1), shape) if (shape[0] == 1) else ( (shape[0],shape[1]), None) # convert to column vector + else: # len(shape) == 3 return (shape,None) # do nothing @@ -97,7 +570,7 @@ class DescreteStateSpace(object): Log_likelihood and Grad_log_likelihood have the corresponding dimensions then. 4) Calculation of Grad_log_likelihood is not supported if matrices A,Q, - H, or R changes overf time. (later may be changed) + H, or R changes over time. (later may be changed) 5) Measurement may include missing values. In this case update step is not done for this measurement. (later may be changed) @@ -208,10 +681,7 @@ class DescreteStateSpace(object): # Reshape and check measurements: Y.shape, old_Y_shape = cls._reshape_input_data(Y.shape) measurement_dim = Y.shape[1] - if len(Y.shape) == 2: - time_series_no = 1 # regular case - elif len(Y.shape) == 3: - time_series_no = Y.shape[2] # multiple time series mode + time_series_no = Y.shape[2] # multiple time series mode if ((len(p_A.shape) == 3) and (len(p_A.shape[2]) != 1)) or\ ((len(p_Q.shape) == 3) and (len(p_Q.shape[2]) != 1)) or\ @@ -256,14 +726,9 @@ class DescreteStateSpace(object): # m_init if m_init is None: - if (time_series_no == 1): - m_init = m_init = np.zeros((state_dim,1)) - else: - # multiple time series mode. - m_init = np.zeros((state_dim, time_series_no)) + m_init = np.zeros((state_dim, time_series_no)) else: - if (time_series_no == 1): - m_init = np.atleast_2d(m_init).T + m_init = np.atleast_2d(m_init).T # P_init if P_init is None: @@ -280,48 +745,36 @@ class DescreteStateSpace(object): c_p_Q = p_A.copy() # create a copy because this object is passed to the smoother c_index = index.copy() # create a copy because this object is passed to the smoother - fa = lambda k,m,A: np.dot(A, m) - f_A = lambda k,m,P: c_p_A[:,:, c_index[A_time_var_index, k]] - f_Q = lambda k: c_p_Q[:,:, c_index[Q_time_var_index, k]] - fh = lambda k,m,H: np.dot(H, m) - f_H = lambda k,m,P: p_H[:,:, index[H_time_var_index, k]] - f_R = lambda k: p_R[:,:, index[R_time_var_index, k]] - - grad_calc_params_pass_further = None if calc_grad_log_likelihood: if model_matrices_chage_with_time: raise ValueError("When computing likelihood gradient A and Q can not change over time.") - f_dA = cls._check_grad_state_matrices(grad_calc_params.get('dA'), state_dim, grad_params_no, which = 'dA') - f_dQ = cls._check_grad_state_matrices(grad_calc_params.get('dQ'), state_dim, grad_params_no, which = 'dQ') - f_dH = cls._check_grad_measurement_matrices(grad_calc_params.get('dH'), state_dim, grad_params_no, measurement_dim, which = 'dH') - f_dR = cls._check_grad_measurement_matrices(grad_calc_params.get('dR'), state_dim, grad_params_no, measurement_dim, which = 'dR') - + dA = cls._check_grad_state_matrices(grad_calc_params.get('dA'), state_dim, grad_params_no, which = 'dA') + dQ = cls._check_grad_state_matrices(grad_calc_params.get('dQ'), state_dim, grad_params_no, which = 'dQ') + dH = cls._check_grad_measurement_matrices(grad_calc_params.get('dH'), state_dim, grad_params_no, measurement_dim, which = 'dH') + dR = cls._check_grad_measurement_matrices(grad_calc_params.get('dR'), state_dim, grad_params_no, measurement_dim, which = 'dR') + dm_init = grad_calc_params.get('dm_init') if dm_init is None: - if (time_series_no == 1): - dm_init = np.zeros((state_dim,grad_params_no)) - else: - # multiple time series mode. Keep grad_params always as a last dimension - dm_init = np.zeros((state_dim, time_series_no, grad_params_no)) + dm_init = np.zeros((state_dim, time_series_no, grad_params_no)) dP_init = grad_calc_params.get('dP_init') if dP_init is None: dP_init = np.zeros((state_dim,state_dim,grad_params_no)) grad_calc_params_pass_further = {} - grad_calc_params_pass_further['f_dA'] = f_dA - grad_calc_params_pass_further['f_dQ'] = f_dQ - grad_calc_params_pass_further['f_dH'] = f_dH - grad_calc_params_pass_further['f_dR'] = f_dR grad_calc_params_pass_further['dm_init'] = dm_init grad_calc_params_pass_further['dP_init'] = dP_init - - (M, P,log_likelihood, grad_log_likelihood) = cls._kalman_algorithm_raw(state_dim, fa, f_A, f_Q, fh, f_H, f_R, Y, m_init, - P_init, calc_log_likelihood=calc_log_likelihood, - calc_grad_log_likelihood=calc_grad_log_likelihood, - grad_calc_params=grad_calc_params_pass_further) + + dynamic_callables = Std_Dynamic_Callables_Class(c_p_A, A_time_var_index, c_p_Q, c_index, Q_time_var_index, 20, dA, dQ) + measurement_callables = Std_Measurement_Callables_Class(p_H, H_time_var_index, p_R, index, R_time_var_index, 20, dH, dR) + + (M, P,log_likelihood, grad_log_likelihood) = cls._kalman_algorithm_raw(state_dim, dynamic_callables, + measurement_callables, Y, m_init, + P_init, calc_log_likelihood=calc_log_likelihood, + calc_grad_log_likelihood=calc_grad_log_likelihood, + grad_calc_params=grad_calc_params_pass_further) # restore shapes so that input parameters are unchenged if old_index_shape is not None: @@ -342,13 +795,8 @@ class DescreteStateSpace(object): if old_R_shape is not None: p_R.shape = old_R_shape # Return values - - matrs_for_smoother = {} - matrs_for_smoother['p_a'] = fa - matrs_for_smoother['p_f_A'] = f_A - matrs_for_smoother['p_f_Q'] = f_Q - - return (M, P,log_likelihood, grad_log_likelihood, matrs_for_smoother) + + return (M, P,log_likelihood, grad_log_likelihood, dynamic_callables) @classmethod def extended_kalman_filter(cls,p_state_dim, p_a, p_f_A, p_f_Q, p_h, p_f_H, p_f_R, Y, m_init=None, @@ -482,7 +930,21 @@ class DescreteStateSpace(object): else: if p_f_R(1).shape[0] != m_init.shape[0]: raise ValueError("p_f_R function returns matrix of wrong size") - + +# class dynamic_callables_class(Dynamic_Model_Callables): +# +# Ak = +# Qk = + + + class measurement_callables_class(R_handling_Class): + def __init__(self,R, index, R_time_var_index, unique_R_number): + super(measurement_callables_class,self).__init__(R, index, R_time_var_index, unique_R_number) + + Hk = AddMethodToClass(f_H) + f_h = AddMethodToClass(f_hl) + + (M, P,log_likelihood, grad_log_likelihood) = cls._kalman_algorithm_raw(p_state_dim, p_a, p_f_A, p_f_Q, p_h, p_f_H, p_f_R, Y, m_init, P_init, calc_log_likelihood, calc_grad_log_likelihood=False, grad_calc_params=None) @@ -505,7 +967,7 @@ class DescreteStateSpace(object): return (M, P) @classmethod - def _kalman_algorithm_raw(cls,state_dim, p_a, p_f_A, p_f_Q, p_h, p_f_H, p_f_R, Y, m_init, + def _kalman_algorithm_raw(cls,state_dim, p_dynamic_callables, p_measurement_callables, Y, m_init, P_init, calc_log_likelihood=False, calc_grad_log_likelihood=False, grad_calc_params=None): """ @@ -617,30 +1079,17 @@ class DescreteStateSpace(object): """ steps_no = Y.shape[0] # number of steps in the Kalman Filter - if len(Y.shape) == 2: - time_series_no = 1 # regular case - elif len(Y.shape) == 3: - time_series_no = Y.shape[2] # multiple time series mode + time_series_no = Y.shape[2] # multiple time series mode if calc_grad_log_likelihood: - grad_calc_params_1 = (grad_calc_params['f_dA'], grad_calc_params['f_dQ']) - grad_calc_params_2 = (grad_calc_params['f_dH'],grad_calc_params['f_dR']) - dm_init = grad_calc_params['dm_init']; dP_init = grad_calc_params['dP_init'] else: - grad_calc_params_1 = None - grad_calc_params_2 = None - dm_init = None; dP_init = None # Allocate space for results # Mean estimations. Initial values will be included - if (time_series_no == 1): # one time series mode - M = np.empty(((steps_no+1),state_dim)) - M[0,:] = np.squeeze(m_init) # Initialize mean values - else: # multiple time series mode - M = np.empty(((steps_no+1),state_dim,time_series_no)) - M[0,:,:] = m_init # Initialize mean values + M = np.empty(((steps_no+1),state_dim,time_series_no)) + M[0,:,:] = m_init # Initialize mean values # Variance estimations. Initial values will be included P = np.empty(((steps_no+1),state_dim,state_dim)) P[0,:,:] = P_init # Initialize initial covariance matrix @@ -655,22 +1104,24 @@ class DescreteStateSpace(object): for k in range(0,steps_no): # In this loop index for new estimations is (k+1), old - (k) # This happened because initial values are stored at 0-th index. + + prev_mean = M[k,:,:] # mean from the previous step - if (time_series_no == 1): # single time series mode - k_measurment = Y[k,:].T # measurement as column - else: # multiple time series mode - k_measurment = Y[k,:,:] - m_pred, P_pred, dm_pred, dP_pred = \ - cls._kalman_prediction_step(k, M[k,:] ,P[k,:,:], p_a, p_f_A, p_f_Q, + cls._kalman_prediction_step(k, prev_mean ,P[k,:,:], p_dynamic_callables, calc_grad_log_likelihood=calc_grad_log_likelihood, - p_dm = dm_upd, p_dP = dP_upd, grad_calc_params_1 = grad_calc_params_1) + p_dm = dm_upd, p_dP = dP_upd) + + k_measurment = Y[k,:,:] + + if np.any(np.isnan(k_measurment)): + raise ValueError("Nan measurements are currently not supported") m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ - cls._kalman_update_step(k, m_pred , P_pred, p_h, p_f_H, p_f_R, k_measurment, + cls._kalman_update_step(k, m_pred , P_pred, p_measurement_callables, k_measurment, calc_log_likelihood=calc_log_likelihood, calc_grad_log_likelihood=calc_grad_log_likelihood, - p_dm = dm_pred, p_dP = dP_pred, grad_calc_params_2 = grad_calc_params_2) + p_dm = dm_pred, p_dP = dP_pred) if calc_log_likelihood: log_likelihood += log_likelihood_update @@ -678,20 +1129,17 @@ class DescreteStateSpace(object): if calc_grad_log_likelihood: grad_log_likelihood += d_log_likelihood_update - if (time_series_no == 1): # single time series mode - M[k+1,:] = np.squeeze(m_upd) - else: # multiple time series mode - M[k+1,:,:] = m_upd # separate mean value for each time series + M[k+1,:,:] = m_upd # separate mean value for each time series P[k+1,:,:] = P_upd # !!!Print statistics! Print sizes of matrices # !!!Print statistics! Print iteration time base on another boolean variable - return (M, P, log_likelihood, grad_log_likelihood) + return (M, P, log_likelihood, grad_log_likelihood, p_dynamic_callables.reset(False)) @staticmethod - def _kalman_prediction_step(k, p_m , p_P, p_a, p_f_A, p_f_Q, calc_grad_log_likelihood=False, - p_dm = None, p_dP = None, grad_calc_params_1 = None): + def _kalman_prediction_step(k, p_m , p_P, p_dyn_model_callable, calc_grad_log_likelihood=False, + p_dm = None, p_dP = None): """ Desctrete prediction function @@ -708,20 +1156,9 @@ class DescreteStateSpace(object): p_P: Covariance matrix from the previous step. - p_a: function (k, x_{k-1}, A_{k}). Dynamic function. - k (iteration number), starts at 0 - x_{k-1} State from the previous step - A_{k} Jacobian matrices of f_a. In the linear case it is exactly A_{k}. + p_dyn_model_callable: class + - p_f_A: function (k, m, P) return Jacobian of dynamic function, it is - passed into p_a. - k (iteration number), starts at 0 - m: point where Jacobian is evaluated - P: parameter for Jacobian, usually covariance matrix. - - p_f_Q: function (k). Returns noise matrix of dynamic model on iteration k. - k (iteration number). starts at 0 - calc_grad_log_likelihood: boolean Whether to calculate gradient of the marginal likelihood of the state-space model. If true then the next parameter must @@ -735,40 +1172,25 @@ class DescreteStateSpace(object): p_dP: 3D array (state_dim, state_dim, parameters_no) Mean derivatives from the previous step - grad_calc_params_1: List or None - List with derivatives. The first component is 'f_dA' - function(k) - which returns the derivative of H. The second element is 'f_dQ' - - function(k). Function which returns the derivative of Q. - Output: ---------------------------- m_pred, P_pred, dm_pred, dP_pred: metrices, 3D objects Results of the prediction steps. """ - if len(p_m.shape)<2: - p_m.shape = (p_m.shape[0],1) - - #import pdb; pdb.set_trace() # index correspond to values from previous iteration. - A = p_f_A(k,p_m,p_P) # state transition matrix (or Jacobian) - Q = p_f_Q(k) # state noise matrix + A = p_dyn_model_callable.Ak(k,p_m,p_P) # state transition matrix (or Jacobian) + Q = p_dyn_model_callable.Qk(k) # state noise matrix - # Prediction step -> - m_pred = p_a(k, p_m, A) # predicted mean + m_pred = p_dyn_model_callable.f_a(k, p_m, A) # predicted mean P_pred = A.dot(p_P).dot(A.T) + Q # predicted variance # Prediction step <- - if (p_m.shape[1] > 1): - multiple_ts_mode = True - else: - multiple_ts_mode = False - if calc_grad_log_likelihood: - p_f_dA = grad_calc_params_1[0]; dA_all_params = p_f_dA(k) # derivatives of A wrt parameters - p_f_dQ = grad_calc_params_1[1]; dQ_all_params = p_f_dQ(k) # derivatives of Q wrt parameters + dA_all_params = p_dyn_model_callable.dAk(k) # derivatives of A wrt parameters + dQ_all_params = p_dyn_model_callable.dQk(k) # derivatives of Q wrt parameters param_number = p_dP.shape[2] @@ -781,15 +1203,10 @@ class DescreteStateSpace(object): dQ = dQ_all_params[:,:,j] dP = p_dP[:,:,j] - if (multiple_ts_mode == False): - dm = p_dm[:,j]; dm.shape = (dm.shape[0],1) - dm_pred[:,j] = np.squeeze(np.dot(dA, p_m) + np.dot(A, dm)) # dm can 3-dim (dim,ts,variable) - elif (multiple_ts_mode == True): # modification for several time series - dm = p_dm[:,:,j] - dm_pred[:,:,j] = np.dot(dA, p_m) + np.dot(A, dm) + dm = p_dm[:,:,j] + dm_pred[:,:,j] = np.dot(dA, p_m) + np.dot(A, dm) # prediction step derivatives for current parameter: - dP_pred[:,:,j] = np.dot( dA ,np.dot(p_P, A.T)) dP_pred[:,:,j] += dP_pred[:,:,j].T dP_pred[:,:,j] += np.dot( A ,np.dot(dP, A.T)) + dQ @@ -802,8 +1219,8 @@ class DescreteStateSpace(object): return m_pred, P_pred, dm_pred, dP_pred @staticmethod - def _kalman_prediction_step_SVD(k, p_m , p_P, p_a, p_f_A, p_f_Q, p_f_Qsr, calc_grad_log_likelihood=False, - p_dm = None, p_dP = None, grad_calc_params_1 = None): + def _kalman_prediction_step_SVD(k, p_m , p_P, p_dyn_model_callable, calc_grad_log_likelihood=False, + p_dm = None, p_dP = None): """ Desctrete prediction function @@ -821,22 +1238,7 @@ class DescreteStateSpace(object): Covariance matrix from the previous step and its SVD decomposition. Prev_cov = V * S * V.T The tuple is (Prev_cov, S, V) - p_a: function (k, x_{k-1}, A_{k}). Dynamic function. - k (iteration number), starts at 0 - x_{k-1} State from the previous step - A_{k} Jacobian matrices of f_a. In the linear case it is exactly A_{k}. - - p_f_A: function (k, m, P) return Jacobian of dynamic function, it is - passed into p_a. - k (iteration number), starts at 0 - m: point where Jacobian is evaluated - P: parameter for Jacobian, usually covariance matrix. - - p_f_Q: function (k). Returns noise matrix of dynamic model on iteration k. - k (iteration number). starts at 0 - - p_f_Qsr: function (k). Returns square root of noise matrix of the - dynamic model on iteration k. k (iteration number). starts at 0 + p_dyn_model_callable: object calc_grad_log_likelihood: boolean Whether to calculate gradient of the marginal likelihood @@ -851,19 +1253,12 @@ class DescreteStateSpace(object): p_dP: 3D array (state_dim, state_dim, parameters_no) Mean derivatives from the previous step - grad_calc_params_1: List or None - List with derivatives. The first component is 'f_dA' - function(k) - which returns the derivative of H. The second element is 'f_dQ' - - function(k). Function which returns the derivative of Q. - Output: ---------------------------- m_pred, P_pred, dm_pred, dP_pred: metrices, 3D objects Results of the prediction steps. """ - if len(p_m.shape)<2: - p_m.shape = (p_m.shape[0],1) # covariance from the previous step and its SVD decomposition # p_prev_cov = v * S * V.T @@ -871,11 +1266,11 @@ class DescreteStateSpace(object): #p_prev_cov_tst = np.dot(p_V, (p_S * p_V).T) # reconstructed covariance from the previous step # index correspond to values from previous iteration. - A = p_f_A(k,p_m,Prev_cov) # state transition matrix (or Jacobian) - Q = p_f_Q(k) # state noise matrx. This is necessary for the square root calculation (next step) - Q_sr = p_f_Qsr(k) + A = p_dyn_model_callable.Ak(k,p_m,Prev_cov) # state transition matrix (or Jacobian) + Q = p_dyn_model_callable.Qk(k) # state noise matrx. This is necessary for the square root calculation (next step) + Q_sr = p_dyn_model_callable.Q_srk(k) # Prediction step -> - m_pred = p_a(k, p_m, A) # predicted mean + m_pred = p_dyn_model_callable.f_a(k, p_m, A) # predicted mean # coavariance prediction have changed: svd_1_matr = np.vstack( ( (np.sqrt(S_old)* np.dot(A,V_old)).T , Q_sr.T) ) @@ -891,15 +1286,10 @@ class DescreteStateSpace(object): P_pred = (P_pred, S_new, Vh.T) # Prediction step <- - if (p_m.shape[1] > 1): - multiple_ts_mode = True - else: - multiple_ts_mode = False - # derivatives if calc_grad_log_likelihood: - p_f_dA = grad_calc_params_1[0]; dA_all_params = p_f_dA(k) # derivatives of A wrt parameters - p_f_dQ = grad_calc_params_1[1]; dQ_all_params = p_f_dQ(k) # derivatives of Q wrt parameters + dA_all_params = p_dyn_model_callable.dAk(k) # derivatives of A wrt parameters + dQ_all_params = p_dyn_model_callable.dQk(k) # derivatives of Q wrt parameters param_number = p_dP.shape[2] @@ -911,19 +1301,15 @@ class DescreteStateSpace(object): dA = dA_all_params[:,:,j] dQ = dQ_all_params[:,:,j] - dP = p_dP[:,:,j] - if (multiple_ts_mode == False): - dm = p_dm[:,j]; dm.shape = (dm.shape[0],1) - dm_pred[:,j] = np.squeeze(np.dot(dA, p_m) + np.dot(A, dm)) # dm can 3-dim (dim,ts,variable) - elif (multiple_ts_mode == True): # modification for several time series - dm = p_dm[:,:,j] - dm_pred[:,:,j] = np.dot(dA, p_m) + np.dot(A, dm) + #dP = p_dP[:,:,j] + #dm = p_dm[:,:,j] + dm_pred[:,:,j] = np.dot(dA, p_m) + np.dot(A, p_dm[:,:,j]) # prediction step derivatives for current parameter: dP_pred[:,:,j] = np.dot( dA ,np.dot(Prev_cov, A.T)) dP_pred[:,:,j] += dP_pred[:,:,j].T - dP_pred[:,:,j] += np.dot( A ,np.dot(dP, A.T)) + dQ + dP_pred[:,:,j] += np.dot( A ,np.dot(p_dP[:,:,j], A.T)) + dQ dP_pred[:,:,j] = 0.5*(dP_pred[:,:,j] + dP_pred[:,:,j].T) #symmetrize else: @@ -933,8 +1319,8 @@ class DescreteStateSpace(object): return m_pred, P_pred, dm_pred, dP_pred @staticmethod - def _kalman_update_step(k, p_m , p_P, p_h, p_f_H, p_f_R, measurement, calc_log_likelihood= False, - calc_grad_log_likelihood=False, p_dm = None, p_dP = None, grad_calc_params_2 = None): + def _kalman_update_step(k, p_m , p_P, p_meas_model_callable, measurement, calc_log_likelihood= False, + calc_grad_log_likelihood=False, p_dm = None, p_dP = None): """ Input: @@ -950,21 +1336,8 @@ class DescreteStateSpace(object): p_P: Covariance matrix from the prediction step. - p_h: function (k, x_{k}, H_{k}). Measurement function. - k (iteration number), starts at 0 - x_{k} state - H_{k} Jacobian matrices of f_h. In the linear case it is exactly H_{k}. + p_meas_model_callable: object - p_f_H: function (k, m, P) return Jacobian of dynamic function, it is - passed into p_h. - k (iteration number), starts at 0 - m: point where Jacobian is evaluated - P: parameter for Jacobian, usually covariance matrix. - - p_f_R: function (k). Returns noise matrix of measurement equation - on iteration k. - k (iteration number). starts at 0 - measurement: (measurement_dim, time_series_no) matrix One measurement used on the current update step. For "multiple time series mode" it is matrix, second dimension of @@ -986,11 +1359,6 @@ class DescreteStateSpace(object): p_dP: array Covariance derivatives from the prediction step. - grad_calc_params_2: List or None - List with derivatives. The first component is 'f_dH' - function(k) - which returns the derivative of H. The second element is 'f_dR' - - function(k). Function which returns the derivative of R. - Output: ---------------------------- m_upd, P_upd, dm_upd, dP_upd: metrices, 3D objects @@ -1008,135 +1376,119 @@ class DescreteStateSpace(object): m_pred = p_m # from prediction step P_pred = p_P # from prediction step - H = p_f_H(k, m_pred, P_pred) - R = p_f_R(k) - - if (p_m.shape[1] > 1): - multiple_ts_mode = True - time_series_no = p_m.shape[1] # number of time serieses - else: - time_series_no = 1 - multiple_ts_mode = False + H = p_meas_model_callable.Hk(k, m_pred, P_pred) + R = p_meas_model_callable.Rk(k) + time_series_no = p_m.shape[1] # number of time serieses + log_likelihood_update=None; dm_upd=None; dP_upd=None; d_log_likelihood_update=None # Update step (only if there is data) - if not np.any(np.isnan(measurement)): # TODO: if some dimensions are missing, do properly computations for other. - v = measurement-p_h(k, m_pred, H) - S = H.dot(P_pred).dot(H.T) + R - if measurement.shape[0]==1: # measurements are one dimensional - if (S < 0): - raise ValueError("Kalman Filter Update: S is negative step %i" % k ) - #import pdb; pdb.set_trace() - - K = P_pred.dot(H.T) / S - if calc_log_likelihood: - log_likelihood_update = -0.5 * ( np.log(2*np.pi) + np.log(S) + - v*v / S) - #log_likelihood_update = log_likelihood_update[0,0] # to make int - if np.any(np.isnan(log_likelihood_update)): # some member in P_pred is None. - raise ValueError("Nan values in likelihood update!") - LL = None; islower = None - else: - LL,islower = linalg.cho_factor(S) - K = linalg.cho_solve((LL,islower), H.dot(P_pred.T)).T + #if not np.any(np.isnan(measurement)): # TODO: if some dimensions are missing, do properly computations for other. + v = measurement-p_meas_model_callable.f_h(k, m_pred, H) + S = H.dot(P_pred).dot(H.T) + R + if measurement.shape[0]==1: # measurements are one dimensional + if (S < 0): + raise ValueError("Kalman Filter Update: S is negative step %i" % k ) + #import pdb; pdb.set_trace() - if calc_log_likelihood: - log_likelihood_update = -0.5 * ( v.shape[0]*np.log(2*np.pi) + - 2*np.sum( np.log(np.diag(LL)) ) +\ - np.sum((linalg.cho_solve((LL,islower),v)) * v, axis = 0) ) # diagonal of v.T*S^{-1}*v - #log_likelihood_update = log_likelihood_update[0,0] # to make int - - - if calc_grad_log_likelihood: - dm_pred_all_params = p_dm # derivativas of the prediction phase - dP_pred_all_params = p_dP - - param_number = p_dP.shape[2] - - p_f_dH = grad_calc_params_2[0]; dH_all_params = p_f_dH(k) - p_f_dR = grad_calc_params_2[1]; dR_all_params = p_f_dR(k) - - dm_upd = np.empty(dm_pred_all_params.shape) - dP_upd = np.empty(dP_pred_all_params.shape) - - # firts dimension parameter_no, second - time series number - d_log_likelihood_update = np.empty((param_number,time_series_no)) - for param in range(param_number): - - dH = dH_all_params[:,:,param] - dR = dR_all_params[:,:,param] - - if (multiple_ts_mode == False): - dm_pred = dm_pred_all_params[:,param] - else: - dm_pred = dm_pred_all_params[:,:,param] - - - dP_pred = dP_pred_all_params[:,:,param] - - # Terms in the likelihood derivatives - dv = - np.dot( dH, m_pred) - np.dot( H, dm_pred) - dS = np.dot(dH, np.dot( P_pred, H.T)) - dS += dS.T - dS += np.dot(H, np.dot( dP_pred, H.T)) + dR - - # TODO: maybe symmetrize dS - - #dm and dP for the next stem - if LL is not None: # the state vector is not a scalar - tmp1 = linalg.cho_solve((LL,islower), H).T - tmp2 = linalg.cho_solve((LL,islower), dH).T - tmp3 = linalg.cho_solve((LL,islower), dS).T - else: # the state vector is a scalar - tmp1 = H.T / S - tmp2 = dH.T / S - tmp3 = dS.T / S - - dK = np.dot( dP_pred, tmp1) + np.dot( P_pred, tmp2) - \ - np.dot( P_pred, np.dot( tmp1, tmp3 ) ) - - # terms required for the next step, save this for each parameter - if (multiple_ts_mode == False): - dm_upd[:,param] = dm_pred + np.squeeze(np.dot(dK, v) + np.dot(K, dv)) - else: - dm_upd[:,:,param] = dm_pred + np.dot(dK, v) + np.dot(K, dv) - - dP_upd[:,:,param] = -np.dot(dK, np.dot(S, K.T)) - dP_upd[:,:,param] += dP_upd[:,:,param].T - dP_upd[:,:,param] += dP_pred - np.dot(K , np.dot( dS, K.T)) - - dP_upd[:,:,param] = 0.5*(dP_upd[:,:,param] + dP_upd[:,:,param].T) #symmetrize - # computing the likelihood change for each parameter: - if LL is not None: # the state vector is not 1D - #tmp4 = linalg.cho_solve((LL,islower), dv) - tmp5 = linalg.cho_solve((LL,islower), v) - else: # the state vector is a scalar - #tmp4 = dv / S - tmp5 = v / S - - - d_log_likelihood_update[param,:] = -(0.5*np.sum(np.diag(tmp3)) + \ - np.sum(tmp5*dv, axis=0) - 0.5 * np.sum(tmp5 * np.dot(dS, tmp5), axis=0) ) - - # Before - #d_log_likelihood_update[param,0] = -(0.5*np.sum(np.diag(tmp3)) + \ - #np.dot(tmp5.T, dv) - 0.5 * np.dot(tmp5.T ,np.dot(dS, tmp5)) ) - - - - # Compute the actual updates for mean and variance of the states. - m_upd = m_pred + K.dot( v ) + K = P_pred.dot(H.T) / S + if calc_log_likelihood: + log_likelihood_update = -0.5 * ( np.log(2*np.pi) + np.log(S) + + v*v / S) + #log_likelihood_update = log_likelihood_update[0,0] # to make int + if np.any(np.isnan(log_likelihood_update)): # some member in P_pred is None. + raise ValueError("Nan values in likelihood update!") + LL = None; islower = None + else: + LL,islower = linalg.cho_factor(S) + K = linalg.cho_solve((LL,islower), H.dot(P_pred.T)).T - # Covariance update and ensure it is symmetric - P_upd = K.dot(S).dot(K.T) - P_upd = 0.5*(P_upd + P_upd.T) - P_upd = P_pred - P_upd# this update matrix is symmetric + if calc_log_likelihood: + log_likelihood_update = -0.5 * ( v.shape[0]*np.log(2*np.pi) + + 2*np.sum( np.log(np.diag(LL)) ) +\ + np.sum((linalg.cho_solve((LL,islower),v)) * v, axis = 0) ) # diagonal of v.T*S^{-1}*v + + if calc_grad_log_likelihood: + dm_pred_all_params = p_dm # derivativas of the prediction phase + dP_pred_all_params = p_dP + + param_number = p_dP.shape[2] + + dH_all_params = p_meas_model_callable.dHk(k) + dR_all_params = p_meas_model_callable.dRk(k) + + dm_upd = np.empty(dm_pred_all_params.shape) + dP_upd = np.empty(dP_pred_all_params.shape) + + # firts dimension parameter_no, second - time series number + d_log_likelihood_update = np.empty((param_number,time_series_no)) + for param in range(param_number): + + dH = dH_all_params[:,:,param] + dR = dR_all_params[:,:,param] + + dm_pred = dm_pred_all_params[:,:,param] + dP_pred = dP_pred_all_params[:,:,param] + + # Terms in the likelihood derivatives + dv = - np.dot( dH, m_pred) - np.dot( H, dm_pred) + dS = np.dot(dH, np.dot( P_pred, H.T)) + dS += dS.T + dS += np.dot(H, np.dot( dP_pred, H.T)) + dR + + # TODO: maybe symmetrize dS + + #dm and dP for the next stem + if LL is not None: # the state vector is not a scalar + tmp1 = linalg.cho_solve((LL,islower), H).T + tmp2 = linalg.cho_solve((LL,islower), dH).T + tmp3 = linalg.cho_solve((LL,islower), dS).T + else: # the state vector is a scalar + tmp1 = H.T / S + tmp2 = dH.T / S + tmp3 = dS.T / S + + dK = np.dot( dP_pred, tmp1) + np.dot( P_pred, tmp2) - \ + np.dot( P_pred, np.dot( tmp1, tmp3 ) ) + + # terms required for the next step, save this for each parameter + dm_upd[:,:,param] = dm_pred + np.dot(dK, v) + np.dot(K, dv) + + dP_upd[:,:,param] = -np.dot(dK, np.dot(S, K.T)) + dP_upd[:,:,param] += dP_upd[:,:,param].T + dP_upd[:,:,param] += dP_pred - np.dot(K , np.dot( dS, K.T)) + + dP_upd[:,:,param] = 0.5*(dP_upd[:,:,param] + dP_upd[:,:,param].T) #symmetrize + # computing the likelihood change for each parameter: + if LL is not None: # the state vector is not 1D + #tmp4 = linalg.cho_solve((LL,islower), dv) + tmp5 = linalg.cho_solve((LL,islower), v) + else: # the state vector is a scalar + #tmp4 = dv / S + tmp5 = v / S + + + d_log_likelihood_update[param,:] = -(0.5*np.sum(np.diag(tmp3)) + \ + np.sum(tmp5*dv, axis=0) - 0.5 * np.sum(tmp5 * np.dot(dS, tmp5), axis=0) ) + # Before + #d_log_likelihood_update[param,0] = -(0.5*np.sum(np.diag(tmp3)) + \ + #np.dot(tmp5.T, dv) - 0.5 * np.dot(tmp5.T ,np.dot(dS, tmp5)) ) + + + + # Compute the actual updates for mean and variance of the states. + m_upd = m_pred + K.dot( v ) + + # Covariance update and ensure it is symmetric + P_upd = K.dot(S).dot(K.T) + P_upd = 0.5*(P_upd + P_upd.T) + P_upd = P_pred - P_upd# this update matrix is symmetric - return m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update + return m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update @staticmethod - def _kalman_update_step_SVD(k, p_m , p_P, p_h, p_f_H, p_f_R, p_f_iRsr, measurement, calc_log_likelihood= False, - calc_grad_log_likelihood=False, p_dm = None, p_dP = None, grad_calc_params_2 = None): + def _kalman_update_step_SVD(k, p_m , p_P, p_meas_model_callable, measurement, calc_log_likelihood= False, + calc_grad_log_likelihood=False, p_dm = None, p_dP = None): """ Input: @@ -1158,7 +1510,7 @@ class DescreteStateSpace(object): x_{k} state H_{k} Jacobian matrices of f_h. In the linear case it is exactly H_{k}. - p_f_H: function (k, m, P) return Jacobian of dynamic function, it is + p_f_H: function (k, m, P) return Jacobian of measurement function, it is passed into p_h. k (iteration number), starts at 0 m: point where Jacobian is evaluated @@ -1212,145 +1564,130 @@ class DescreteStateSpace(object): """ + #import pdb; pdb.set_trace() + m_pred = p_m # from prediction step P_pred,S_pred,V_pred = p_P # from prediction step - H = p_f_H(k, m_pred, P_pred) - R = p_f_R(k) - R_isr = p_f_iRsr(k) # square root of the inverse of R matrix + H = p_meas_model_callable.Hk(k, m_pred, P_pred) + R = p_meas_model_callable.Rk(k) + R_isr = p_meas_model_callable.R_isrk(k) # square root of the inverse of R matrix - if (p_m.shape[1] > 1): - multiple_ts_mode = True - time_series_no = p_m.shape[1] # number of time serieses - else: - time_series_no = 1 - multiple_ts_mode = False + time_series_no = p_m.shape[1] # number of time serieses log_likelihood_update=None; dm_upd=None; dP_upd=None; d_log_likelihood_update=None # Update step (only if there is data) - if not np.any(np.isnan(measurement)): # TODO: if some dimensions are missing, do properly computations for other. - v = measurement-p_h(k, m_pred, H) - - svd_2_matr = np.vstack( ( np.dot( R_isr.T, np.dot(H, V_pred)) , np.diag( 1.0/np.sqrt(S_pred) ) ) ) - - (U,S,Vh) = sp.linalg.svd( svd_2_matr,full_matrices=False, compute_uv=True, - overwrite_a=False,check_finite=True) - - # P_upd = U_upd S_upd**2 U_upd.T - U_upd = np.dot(V_pred, Vh.T) - S_upd = (1.0/S)**2 - - P_upd = np.dot(U_upd * S_upd, U_upd.T) # update covariance - P_upd = (P_upd,S_upd,U_upd) # tuple to pass to the next step + #if not np.any(np.isnan(measurement)): # TODO: if some dimensions are missing, do properly computations for other. + v = measurement-p_meas_model_callable.f_h(k, m_pred, H) + + svd_2_matr = np.vstack( ( np.dot( R_isr.T, np.dot(H, V_pred)) , np.diag( 1.0/np.sqrt(S_pred) ) ) ) - # stil need to compute S and K for derivative computation - S = H.dot(P_pred).dot(H.T) + R - if measurement.shape[0]==1: # measurements are one dimensional - if (S < 0): - raise ValueError("Kalman Filter Update SVD: S is negative step %i" % k ) - #import pdb; pdb.set_trace() - - K = P_pred.dot(H.T) / S - if calc_log_likelihood: - log_likelihood_update = -0.5 * ( np.log(2*np.pi) + np.log(S) + - v*v / S) - #log_likelihood_update = log_likelihood_update[0,0] # to make int - if np.any(np.isnan(log_likelihood_update)): # some member in P_pred is None. - raise ValueError("Nan values in likelihood update!") - LL = None; islower = None - else: - raise ValueError("""Measurement dimension larger then 1 is currently not supported""") + (U,S,Vh) = sp.linalg.svd( svd_2_matr,full_matrices=False, compute_uv=True, + overwrite_a=False,check_finite=True) + + # P_upd = U_upd S_upd**2 U_upd.T + U_upd = np.dot(V_pred, Vh.T) + S_upd = (1.0/S)**2 + + P_upd = np.dot(U_upd * S_upd, U_upd.T) # update covariance + P_upd = (P_upd,S_upd,U_upd) # tuple to pass to the next step + + # stil need to compute S and K for derivative computation + S = H.dot(P_pred).dot(H.T) + R + if measurement.shape[0]==1: # measurements are one dimensional + if (S < 0): + raise ValueError("Kalman Filter Update SVD: S is negative step %i" % k ) + #import pdb; pdb.set_trace() + + K = P_pred.dot(H.T) / S + if calc_log_likelihood: + log_likelihood_update = -0.5 * ( np.log(2*np.pi) + np.log(S) + + v*v / S) + if np.any(np.isnan(log_likelihood_update)): # some member in P_pred is None. + raise ValueError("Nan values in likelihood update!") + LL = None; islower = None + else: + raise ValueError("""Measurement dimension larger then 1 is currently not supported""") + + # Old method of computing updated covariance (for testing) -> + #P_upd_tst = K.dot(S).dot(K.T) + #P_upd_tst = 0.5*(P_upd_tst + P_upd_tst.T) + #P_upd_tst = P_pred - P_upd_tst# this update matrix is symmetric + # Old method of computing updated covariance (for testing) <- + + if calc_grad_log_likelihood: + dm_pred_all_params = p_dm # derivativas of the prediction phase + dP_pred_all_params = p_dP - # Old method of computing updated covariance (for testing) -> - #P_upd_tst = K.dot(S).dot(K.T) - #P_upd_tst = 0.5*(P_upd_tst + P_upd_tst.T) - #P_upd_tst = P_pred - P_upd_tst# this update matrix is symmetric - # Old method of computing updated covariance (for testing) <- + param_number = p_dP.shape[2] - if calc_grad_log_likelihood: - dm_pred_all_params = p_dm # derivativas of the prediction phase - dP_pred_all_params = p_dP - - param_number = p_dP.shape[2] - - p_f_dH = grad_calc_params_2[0]; dH_all_params = p_f_dH(k) - p_f_dR = grad_calc_params_2[1]; dR_all_params = p_f_dR(k) - - dm_upd = np.empty(dm_pred_all_params.shape) - dP_upd = np.empty(dP_pred_all_params.shape) - - # firts dimension parameter_no, second - time series number - d_log_likelihood_update = np.empty((param_number,time_series_no)) - for param in range(param_number): - - dH = dH_all_params[:,:,param] - dR = dR_all_params[:,:,param] - - if (multiple_ts_mode == False): - dm_pred = dm_pred_all_params[:,param] - else: - dm_pred = dm_pred_all_params[:,:,param] - - - dP_pred = dP_pred_all_params[:,:,param] - - # Terms in the likelihood derivatives - dv = - np.dot( dH, m_pred) - np.dot( H, dm_pred) - dS = np.dot(dH, np.dot( P_pred, H.T)) - dS += dS.T - dS += np.dot(H, np.dot( dP_pred, H.T)) + dR - - # TODO: maybe symmetrize dS - - #dm and dP for the next stem - if LL is not None: # the state vector is not a scalar - tmp1 = linalg.cho_solve((LL,islower), H).T - tmp2 = linalg.cho_solve((LL,islower), dH).T - tmp3 = linalg.cho_solve((LL,islower), dS).T - else: # the state vector is a scalar - tmp1 = H.T / S - tmp2 = dH.T / S - tmp3 = dS.T / S - - dK = np.dot( dP_pred, tmp1) + np.dot( P_pred, tmp2) - \ - np.dot( P_pred, np.dot( tmp1, tmp3 ) ) - - # terms required for the next step, save this for each parameter - if (multiple_ts_mode == False): - dm_upd[:,param] = dm_pred + np.squeeze(np.dot(dK, v) + np.dot(K, dv)) - else: - dm_upd[:,:,param] = dm_pred + np.dot(dK, v) + np.dot(K, dv) - - dP_upd[:,:,param] = -np.dot(dK, np.dot(S, K.T)) - dP_upd[:,:,param] += dP_upd[:,:,param].T - dP_upd[:,:,param] += dP_pred - np.dot(K , np.dot( dS, K.T)) - - dP_upd[:,:,param] = 0.5*(dP_upd[:,:,param] + dP_upd[:,:,param].T) #symmetrize - # computing the likelihood change for each parameter: - if LL is not None: # the state vector is not 1D - #tmp4 = linalg.cho_solve((LL,islower), dv) - tmp5 = linalg.cho_solve((LL,islower), v) - else: # the state vector is a scalar - #tmp4 = dv / S - tmp5 = v / S - - - d_log_likelihood_update[param,:] = -(0.5*np.sum(np.diag(tmp3)) + \ - np.sum(tmp5*dv, axis=0) - 0.5 * np.sum(tmp5 * np.dot(dS, tmp5), axis=0) ) - - # Before - #d_log_likelihood_update[param,0] = -(0.5*np.sum(np.diag(tmp3)) + \ - #np.dot(tmp5.T, dv) - 0.5 * np.dot(tmp5.T ,np.dot(dS, tmp5)) ) - - # Compute the actual updates for mean of the states. Variance update - # is computed earlier. - m_upd = m_pred + K.dot( v ) + dH_all_params = p_meas_model_callable.dHk(k) + dR_all_params = p_meas_model_callable.dRk(k) - return m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update + dm_upd = np.empty(dm_pred_all_params.shape) + dP_upd = np.empty(dP_pred_all_params.shape) + + # firts dimension parameter_no, second - time series number + d_log_likelihood_update = np.empty((param_number,time_series_no)) + for param in range(param_number): + + dH = dH_all_params[:,:,param] + dR = dR_all_params[:,:,param] + + dm_pred = dm_pred_all_params[:,:,param] + dP_pred = dP_pred_all_params[:,:,param] + + # Terms in the likelihood derivatives + dv = - np.dot( dH, m_pred) - np.dot( H, dm_pred) + dS = np.dot(dH, np.dot( P_pred, H.T)) + dS += dS.T + dS += np.dot(H, np.dot( dP_pred, H.T)) + dR + + # TODO: maybe symmetrize dS + + #dm and dP for the next stem + if LL is not None: # the state vector is not a scalar + tmp1 = linalg.cho_solve((LL,islower), H).T + tmp2 = linalg.cho_solve((LL,islower), dH).T + tmp3 = linalg.cho_solve((LL,islower), dS).T + else: # the state vector is a scalar + tmp1 = H.T / S + tmp2 = dH.T / S + tmp3 = dS.T / S + + dK = np.dot( dP_pred, tmp1) + np.dot( P_pred, tmp2) - \ + np.dot( P_pred, np.dot( tmp1, tmp3 ) ) + + # terms required for the next step, save this for each parameter + dm_upd[:,:,param] = dm_pred + np.dot(dK, v) + np.dot(K, dv) + + dP_upd[:,:,param] = -np.dot(dK, np.dot(S, K.T)) + dP_upd[:,:,param] += dP_upd[:,:,param].T + dP_upd[:,:,param] += dP_pred - np.dot(K , np.dot( dS, K.T)) + + dP_upd[:,:,param] = 0.5*(dP_upd[:,:,param] + dP_upd[:,:,param].T) #symmetrize + # computing the likelihood change for each parameter: + if LL is not None: # the state vector is not 1D + tmp5 = linalg.cho_solve((LL,islower), v) + else: # the state vector is a scalar + tmp5 = v / S + + + d_log_likelihood_update[param,:] = -(0.5*np.sum(np.diag(tmp3)) + \ + np.sum(tmp5*dv, axis=0) - 0.5 * np.sum(tmp5 * np.dot(dS, tmp5), axis=0) ) + # Before + #d_log_likelihood_update[param,0] = -(0.5*np.sum(np.diag(tmp3)) + \ + #np.dot(tmp5.T, dv) - 0.5 * np.dot(tmp5.T ,np.dot(dS, tmp5)) ) + + # Compute the actual updates for mean of the states. Variance update + # is computed earlier. + m_upd = m_pred + K.dot( v ) + + return m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update @staticmethod def _rts_smoother_update_step(k, p_m , p_P, p_m_pred, p_P_pred, p_m_prev_step, - p_P_prev_step, p_f_A): + p_P_prev_step, p_dynamic_callables): """ Rauch–Tung–Striebel(RTS) update step @@ -1385,13 +1722,8 @@ class DescreteStateSpace(object): P: parameter for Jacobian, usually covariance matrix. """ - if len(p_m.shape)<2: - p_m.shape = (p_m.shape[0],1) - - if len(p_m_prev_step.shape)<2: - p_m_prev_step.shape = (p_m_prev_step.shape[0],1) - - A = p_f_A(k,p_m,p_P) # state transition matrix (or Jacobian) + + A = p_dynamic_callables.Ak(k,p_m,p_P) # state transition matrix (or Jacobian) tmp = np.dot( A, p_P.T) if A.shape[0] == 1: # 1D states @@ -1402,14 +1734,10 @@ class DescreteStateSpace(object): G = linalg.cho_solve((LL,islower),tmp).T except: # It happende that p_P_pred has several near zero eigenvalues - # hence the Cholessky method does not work. + # hence the Cholesky method does not work. res = sp.linalg.lstsq(p_P_pred, tmp) G = res[0].T - #import pdb; pdb.set_trace() - #pass - - - + m_upd = p_m + G.dot( p_m_prev_step-p_m_pred ) P_upd = p_P + G.dot( p_P_prev_step-p_P_pred).dot(G.T) @@ -1418,7 +1746,7 @@ class DescreteStateSpace(object): return m_upd, P_upd, G @classmethod - def rts_smoother(cls,state_dim, p_a, p_f_A, p_f_Q, filter_means, + def rts_smoother(cls,state_dim, p_dynamic_callables, filter_means, filter_covars): """ This function implements Rauch–Tung–Striebel(RTS) smoother algorithm @@ -1474,12 +1802,19 @@ class DescreteStateSpace(object): m_pred, P_pred, tmp1, tmp2 = \ cls._kalman_prediction_step(k, filter_means[k,:], - filter_covars[k,:,:], p_a, p_f_A, p_f_Q, + filter_covars[k,:,:], p_dynamic_callables, calc_grad_log_likelihood=False) + p_m = filter_means[k,:] + if len(p_m.shape)<2: + p_m.shape = (p_m.shape[0],1) + + p_m_prev_step = M[k+1,:] + if len(p_m_prev_step.shape)<2: + p_m_prev_step.shape = (p_m_prev_step.shape[0],1) m_upd, P_upd, G_tmp = cls._rts_smoother_update_step(k, - filter_means[k,:] ,filter_covars[k,:,:], - m_pred, P_pred, M[k+1,:] ,P[k+1,:,:], p_f_A) + p_m ,filter_covars[k,:,:], + m_pred, P_pred, p_m_prev_step ,P[k+1,:,:], p_dynamic_callables) M[k,:] = np.squeeze(m_upd) P[k,:,:] = P_upd @@ -1684,12 +2019,12 @@ class DescreteStateSpace(object): else: dM = np.ones((1,1,1)) * dM - if not isinstance(dM, types.FunctionType): - f_dM = lambda k: dM - else: - f_dM = dM +# if not isinstance(dM, types.FunctionType): +# f_dM = lambda k: dM +# else: +# f_dM = dM - return f_dM + return dM @staticmethod @@ -1746,114 +2081,19 @@ class DescreteStateSpace(object): raise ValueError("When computing likelihood gradient wrong dH dimension.") else: dM = np.ones((1,1,1)) * dM - if not isinstance(dM, types.FunctionType): - f_dM = lambda k: dM - else: - f_dM = dM + +# if not isinstance(dM, types.FunctionType): +# f_dM = lambda k: dM +# else: +# f_dM = dM - return f_dM + return dM class Struct(object): pass -def inverse_square_root(R, tol=1e-14): - """ - The function computes the square root of the matrix inverse. - - Input: - ------------------ - R - given matrix - tol - smallest value of the singular number below which the inversion - of S must be handeled specially. - Output: - ------------------- - inv_square_root - square root of the inverse - """ - - if (R.shape[0] == 1): # matrix M is (1x1) - inv_square_root = np.sqrt(R) - else: - (U,S,Vh) = sp.linalg.svd( R,full_matrices=False, compute_uv=True, - overwrite_a=False,check_finite=True) - if (np.abs(S) < tol): - raise ValueError("""Inverse Square Root: Measurement noise matrix - is singular. Handling is not implemented.""") - inv_square_root = U * 1.0/np.sqrt(S) - - return inv_square_root - -class R_handling(): - """ - The calss handles noise matrix R. - """ - def __init__(self, R, index, R_time_var_index, unique_R_number): - """ - Input: - --------------- - R - array with noise on various steps. The result of preprocessing - the noise input. - - index - for each step of Kalman filter contains the corresponding index - in the array. - - unique_R_number - number of unique noise matrices below which square roots - are cached and above which they are computed each time. - - R_time_var_index - another index in the array R. Computed earlier and passed here. - - Output: - -------------- - Object which has two necessary functions: - f_R(k) - inv_R_square_root(k) - """ - self.R = R - self.index = index - self.R_time_var_index = R_time_var_index - - if (len(np.unique(index)) > unique_R_number): - self.svd_each_time = True - else: - self.svd_each_time = False - - self.R_square_root = {} - - def f_R(self,k): - return self.R[:,:, self.index[self.R_time_var_index, k]] - - def f_iRsr(self, k): - """ - Function returns the inverse square root of R matrix on step k. - """ - R = self.R[:,:, self.index[self.R_time_var_index, k]] - - if (self.R.shape[0] == 1): # 1-D case handle simplier. No storage - # of the result, just compute it each time. - inv_square_root = np.sqrt( 1.0/R ) - else: - if self.svd_each_time: - - (U,S,Vh) = sp.linalg.svd( R,full_matrices=False, compute_uv=True, - overwrite_a=False,check_finite=True) - - inv_square_root = U * 1.0/np.sqrt(S) - else: - ind = self.index[self.R_time_var_index, k] - if ind in self.R_square_root: - inv_square_root = self.R_square_root[ind] - else: - (U,S,Vh) = sp.linalg.svd( R,full_matrices=False, compute_uv=True, - overwrite_a=False,check_finite=True) - - inv_square_root = U * 1.0/np.sqrt(S) - - self.R_square_root[ind] = inv_square_root - - return inv_square_root - - class ContDescrStateSpace(DescreteStateSpace): """ Class for continuous-discrete Kalman filter. State equation is @@ -1864,7 +2104,7 @@ class ContDescrStateSpace(DescreteStateSpace): """ - class AQcompute_once(object): + class AQcompute_once(Q_handling_Class): """ Class for calculating matrices A, Q, dA, dQ of the discrete Kalman Filter from the matrices F, L, Qc, P_ing, dF, dQc, dP_inf of the continuos state @@ -1919,13 +2159,21 @@ class ContDescrStateSpace(DescreteStateSpace): self.last_k = 0 self.last_k_computed = False - self.Ak = None - self.Qk = None - self.dAk = None - self.dQk = None + self.v_Ak = None + self.v_Qk = None + self.v_dAk = None + self.v_dQk = None self.square_root_computed = False # !!!Print statistics! Which object is created + + def f_a(self, k,m,A): + """ + Dynamic model + """ + + return np.dot(A, m) # default dynamic model + def _recompute_for_new_k(self,k): """ Computes the necessary matrices for an index k and store the results. @@ -1941,26 +2189,26 @@ class ContDescrStateSpace(DescreteStateSpace): A, Q, dA dQ on step k """ if (self.last_k != k) or (self.last_k_computed == False): - Ak,Qk, tmp, dAk, dQk = ContDescrStateSpace.lti_sde_to_descrete(self.F, + v_Ak,v_Qk, tmp, v_dAk, v_dQk = ContDescrStateSpace.lti_sde_to_descrete(self.F, self.L,self.Qc,self.dt[k],self.compute_derivatives, grad_params_no=self.grad_params_no, P_inf=self.P_inf, dP_inf=self.dP_inf, dF=self.dF, dQc=self.dQc) self.last_k = k self.last_k_computed = True - self.Ak = Ak - self.Qk = Qk - self.dAk = dAk - self.dQk = dQk + self.v_Ak = v_Ak + self.v_Qk = v_Qk + self.v_dAk = v_dAk + self.v_dQk = v_dQk self.Q_square_root_computed = False else: - Ak = self.Ak - Qk = self.Qk - dAk = self.dAk - dQk = self.dQk + v_Ak = self.v_Ak + v_Qk = self.v_Qk + v_dAk = self.v_dAk + v_dQk = self.v_dQk # !!!Print statistics! Print sizes of matrices - return Ak,Qk, dAk, dQk + return v_Ak,v_Qk, v_dAk, v_dQk def reset(self, compute_derivatives): """ @@ -1977,30 +2225,30 @@ class ContDescrStateSpace(DescreteStateSpace): return self - def f_A(self,k,m,P): - Ak,Qk, dAk, dQk = self._recompute_for_new_k(k) - return Ak + def Ak(self,k,m,P): + v_Ak,v_Qk, v_dAk, v_dQk = self._recompute_for_new_k(k) + return v_Ak - def f_Q(self,k): - Ak,Qk, dAk, dQk = self._recompute_for_new_k(k) - return Qk + def Qk(self,k): + v_Ak,v_Qk, v_dAk, v_dQk = self._recompute_for_new_k(k) + return v_Qk - def f_dA(self, k): - Ak,Qk, dAk, dQk = self._recompute_for_new_k(k) - return dAk + def dAk(self, k): + v_Ak,v_Qk, v_dAk, v_dQk = self._recompute_for_new_k(k) + return v_dAk - def f_dQ(self, k): - Ak,Qk, dAk, dQk = self._recompute_for_new_k(k) - return dQk + def dQk(self, k): + v_Ak,v_Qk, v_dAk, v_dQk = self._recompute_for_new_k(k) + return v_dQk - def f_Qsr(self,k): + def Q_srk(self,k): """ Square root of the noise matrix Q """ if ((self.last_k == k) and (self.last_k_computed == True)): if not self.Q_square_root_computed: - (U, S, Vh) = sp.linalg.svd( self.Qk, full_matrices=False, compute_uv=True, overwrite_a=False, check_finite=False) + (U, S, Vh) = sp.linalg.svd( self.v_Qk, full_matrices=False, compute_uv=True, overwrite_a=False, check_finite=False) square_root = U * np.sqrt(S) self.square_root_computed = True self.Q_square_root = square_root @@ -2019,14 +2267,14 @@ class ContDescrStateSpace(DescreteStateSpace): raise ValueError("Matrices are not computed.") else: k = self.last_k - A = self.Ak - Q = self.Qk - dA = self.dAk - dQ = self.dQk + A = self.v_Ak + Q = self.v_Qk + dA = self.v_dAk + dQ = self.v_dQk return k, A, Q, dA, dQ - class AQcompute_batch(object): + class AQcompute_batch_Python(Q_handling_Class): """ Class for calculating matrices A, Q, dA, dQ of the discrete Kalman Filter from the matrices F, L, Qc, P_ing, dF, dQc, dP_inf of the continuos state @@ -2077,10 +2325,17 @@ class ContDescrStateSpace(DescreteStateSpace): (self.reconstruct_indices.nbytes if (self.reconstruct_indices is not None) else 0) self.Q_svd_dict = {} - self.last_k = None + self.last_k = None # !!!Print statistics! Which object is created # !!!Print statistics! Print sizes of matrices - def reset(self, compute_derivatives): + + def f_a(self, k,m,A): + """ + Dynamic model + """ + return np.dot(A, m) # default dynamic model + + def reset(self, compute_derivatives=False): """ For reusing this object e.g. in smoother computation. It makes sence because necessary matrices have been already computed for all @@ -2088,24 +2343,24 @@ class ContDescrStateSpace(DescreteStateSpace): """ return self - def f_A(self,k,m,P): + def Ak(self,k,m,P): self.last_k = k return self.As[:,:, self.reconstruct_indices[k]] - def f_Q(self,k): + def Qk(self,k): self.last_k = k return self.Qs[:,:, self.reconstruct_indices[k]] - def f_dA(self,k): + def dAk(self,k): self.last_k = k return self.dAs[:,:, :, self.reconstruct_indices[k]] - def f_dQ(self,k): + def dQk(self,k): self.last_k = k return self.dQs[:,:, :, self.reconstruct_indices[k]] - def f_Qsr(self,k): + def Q_srk(self,k): """ Square root of the noise matrix Q """ @@ -2143,7 +2398,7 @@ class ContDescrStateSpace(DescreteStateSpace): p_kalman_filter_type='regular', calc_log_likelihood=False, calc_grad_log_likelihood=False, - grad_params_no=None, grad_calc_params=None): + grad_params_no=0, grad_calc_params=None): """ This function implements the continuous-discrete Kalman Filter algorithm These notations for the State-Space model are assumed: @@ -2285,7 +2540,7 @@ class ContDescrStateSpace(DescreteStateSpace): p_H = np.atleast_1d(p_H) p_R = np.atleast_1d(p_R) - X.shape, old_X_shape = cls._reshape_input_data(X.shape) # represent as column + X.shape, old_X_shape = cls._reshape_input_data(X.shape, 2) # represent as column if (X.shape[1] != 1): raise ValueError("Only one dimensional X data is supported.") @@ -2330,14 +2585,9 @@ class ContDescrStateSpace(DescreteStateSpace): (p_R, old_R_shape) = cls._check_SS_matrix(p_R, state_dim, measurement_dim, which='R') if m_init is None: - if (time_series_no == 1): - m_init = m_init = np.zeros((state_dim,1)) - else: - # multiple time series mode. - m_init = np.zeros((state_dim, time_series_no)) + m_init = np.zeros((state_dim, time_series_no)) else: - if (time_series_no == 1): - m_init = np.atleast_2d(m_init).T + m_init = np.atleast_2d(m_init).T if P_init is None: P_init = P_inf.copy() @@ -2351,10 +2601,10 @@ class ContDescrStateSpace(DescreteStateSpace): # Parameters: # k - number of Kalman filter iteration # m - vector for calculating matrices. Required for EKF. Not used here. - f_h = lambda k,m,H: np.dot(H, m) - f_H = lambda k,m,P: p_H[:,:, index[H_time_var_index, k]] + # f_hl = lambda k,m,H: np.dot(H, m) + # f_H = lambda k,m,P: p_H[:,:, index[H_time_var_index, k]] #f_R = lambda k: p_R[:,:, index[R_time_var_index, k]] - o_R = R_handling( p_R, index, R_time_var_index, 20) + #o_R = R_handling( p_R, index, R_time_var_index, 20) if calc_grad_log_likelihood: @@ -2367,11 +2617,8 @@ class ContDescrStateSpace(DescreteStateSpace): dm_init = grad_calc_params.get('dm_init') # Initial values for the Kalman Filter if dm_init is None: - if time_series_no == 1: - dm_init = np.zeros( (state_dim,grad_params_no) ) - else: - # multiple time series mode. Keep grad_params always as a last dimension - dm_init = np.zeros( (state_dim, time_series_no, grad_params_no) ) + # multiple time series mode. Keep grad_params always as a last dimension + dm_init = np.zeros( (state_dim, time_series_no, grad_params_no) ) dP_init = grad_calc_params.get('dP_init') # Initial values for the Kalman Filter if dP_init is None: @@ -2386,14 +2633,23 @@ class ContDescrStateSpace(DescreteStateSpace): dm_init = None dP_init = None + measurement_callables = Std_Measurement_Callables_Class(p_H, H_time_var_index, p_R, index, R_time_var_index, 20, dH, dR) + #import pdb; pdb.set_trace() + + dynamic_callables = cls._cont_to_discrete_object(X, F, L, Qc, compute_derivatives=calc_grad_log_likelihood, + grad_params_no=grad_params_no, + P_inf=P_inf, dP_inf=dP_inf, dF = dF, dQc=dQc) + if print_verbose: print("General: run Continuos-Discrete Kalman Filter") # Also for dH, dR and probably for all derivatives - (M, P, log_likelihood, grad_log_likelihood, AQcomp) = cls._cont_discr_kalman_filter_raw(state_dim,F, L, Qc, P_inf, - f_h, f_H, o_R, X, Y, m_init=m_init, P_init=P_init, p_kalman_filter_type=p_kalman_filter_type, + (M, P, log_likelihood, grad_log_likelihood, AQcomp) = cls._cont_discr_kalman_filter_raw(state_dim, + dynamic_callables, measurement_callables, + X, Y, m_init=m_init, P_init=P_init, + p_kalman_filter_type=p_kalman_filter_type, calc_log_likelihood=calc_log_likelihood, - calc_grad_log_likelihood=calc_grad_log_likelihood, grad_params_no=grad_params_no, dP_inf=dP_inf, - dF = dF, dQc=dQc, dH=dH, dR=dR, dm_init=dm_init, dP_init=dP_init) + calc_grad_log_likelihood=calc_grad_log_likelihood, grad_params_no=grad_params_no, + dm_init=dm_init, dP_init=dP_init) if old_index_shape is not None: index.shape = old_index_shape @@ -2413,12 +2669,11 @@ class ContDescrStateSpace(DescreteStateSpace): return (M, P, log_likelihood, grad_log_likelihood, AQcomp) @classmethod - def _cont_discr_kalman_filter_raw(cls,state_dim,F,L,Qc, P_inf, f_h, f_H, p_R, X, Y, + def _cont_discr_kalman_filter_raw(cls,state_dim, p_dynamic_callables, p_measurement_callables, X, Y, m_init=None, P_init=None, p_kalman_filter_type='regular', calc_log_likelihood=False, - calc_grad_log_likelihood=False, grad_params_no=None, dP_inf=None, - dF = None, dQc=None, dH=None, dR=None, dm_init=None, dP_init=None): + calc_grad_log_likelihood=False, grad_params_no=None, dm_init=None, dP_init=None): """ General filtering algorithm for inference in the continuos-discrete state-space model: @@ -2504,32 +2759,14 @@ class ContDescrStateSpace(DescreteStateSpace): """ + #import pdb; pdb.set_trace() steps_no = Y.shape[0] # number of steps in the Kalman Filter - if len(Y.shape) == 2: - time_series_no = 1 # regular case - elif len(Y.shape) == 3: - time_series_no = Y.shape[2] # multiple time series mode + time_series_no = Y.shape[2] # multiple time series mode - # Return object which computes A, Q and possibly derivatives on the way, pass the derivative matrices not functions - AQcomp = cls._cont_to_discrete_object(X, F,L,Qc,compute_derivatives=calc_grad_log_likelihood, - grad_params_no=grad_params_no, - P_inf=P_inf, dP_inf=(dP_inf(0) if calc_grad_log_likelihood else None), - dF = (dF(0) if calc_grad_log_likelihood else None), - dQc=(dQc(0) if calc_grad_log_likelihood else None)) - - # Functions required for discrete Kalman filter. Other requirements - # are: fh, p_H, p_R - provided as parameters - # p_A, p_Q - provided by the object AQcomp. - f_a = lambda k,m,A: np.dot(A, m) # state dynamic model - # Allocate space for results # Mean estimations. Initial values will be included - if (time_series_no == 1): # one time series mode - M = np.empty(((steps_no+1),state_dim)) - M[0,:] = np.squeeze(m_init) # Initialize mean values # ??? why here squeze and in discrete case no squeeze - else: # multiple time series mode - M = np.empty(((steps_no+1),state_dim,time_series_no)) - M[0,:,:] = m_init # Initialize mean values + M = np.empty(((steps_no+1),state_dim,time_series_no)) + M[0,:,:] = m_init # Initialize mean values # Variance estimations. Initial values will be included P = np.empty(((steps_no+1),state_dim,state_dim)) P_init = 0.5*( P_init + P_init.T) # symmetrize initial covariance. In some ustable cases this is uiseful @@ -2553,31 +2790,33 @@ class ContDescrStateSpace(DescreteStateSpace): for k in range(0,steps_no): # In this loop index for new estimations is (k+1), old - (k) # This happened because initial values are stored at 0-th index. - - if (time_series_no == 1): # single time series mode - k_measurment = Y[k,:].T # measurement as column - else: # multiple time series mode - k_measurment = Y[k,:,:] - #import pdb; pdb.set_trace() + + prev_mean = M[k,:,:] # mean from the previous step + if p_kalman_filter_type == 'svd': m_pred, P_pred, dm_pred, dP_pred = \ - cls._kalman_prediction_step_SVD(k, M[k,:] ,P_upd, f_a, AQcomp.f_A, AQcomp.f_Q, AQcomp.f_Qsr, + cls._kalman_prediction_step_SVD(k, prev_mean ,P_upd, p_dynamic_callables, calc_grad_log_likelihood=calc_grad_log_likelihood, - p_dm = dm_upd, p_dP = dP_upd, grad_calc_params_1 = (AQcomp.f_dA, AQcomp.f_dQ) ) + p_dm = dm_upd, p_dP = dP_upd ) else: m_pred, P_pred, dm_pred, dP_pred = \ - cls._kalman_prediction_step(k, M[k,:] ,P[k,:,:], f_a, AQcomp.f_A, AQcomp.f_Q, + cls._kalman_prediction_step(k, M[k,:] ,P[k,:,:], p_dynamic_callables, calc_grad_log_likelihood=calc_grad_log_likelihood, - p_dm = dm_upd, p_dP = dP_upd, grad_calc_params_1 = (AQcomp.f_dA, AQcomp.f_dQ) ) + p_dm = dm_upd, p_dP = dP_upd ) #import pdb; pdb.set_trace() + k_measurment = Y[k,:,:] + + if np.any(np.isnan(k_measurment)): + raise ValueError("Nan measurements are currently not supported") + if p_kalman_filter_type == 'svd': m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ - cls._kalman_update_step_SVD(k, m_pred , P_pred, f_h, f_H, p_R.f_R, p_R.f_iRsr, + cls._kalman_update_step_SVD(k, m_pred , P_pred, p_measurement_callables, k_measurment, calc_log_likelihood=calc_log_likelihood, calc_grad_log_likelihood=calc_grad_log_likelihood, - p_dm = dm_pred, p_dP = dP_pred, grad_calc_params_2 = (dH, dR)) + p_dm = dm_pred, p_dP = dP_pred ) # m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ @@ -2591,10 +2830,10 @@ class ContDescrStateSpace(DescreteStateSpace): # P_upd = (P_upd, S,U) else: m_upd, P_upd, log_likelihood_update, dm_upd, dP_upd, d_log_likelihood_update = \ - cls._kalman_update_step(k, m_pred , P_pred, f_h, f_H, p_R.f_R, k_measurment, + cls._kalman_update_step(k, m_pred , P_pred, p_measurement_callables, k_measurment, calc_log_likelihood=calc_log_likelihood, calc_grad_log_likelihood=calc_grad_log_likelihood, - p_dm = dm_pred, p_dP = dP_pred, grad_calc_params_2 = (dH, dR)) + p_dm = dm_pred, p_dP = dP_pred ) if calc_log_likelihood: log_likelihood += log_likelihood_update @@ -2602,10 +2841,7 @@ class ContDescrStateSpace(DescreteStateSpace): if calc_grad_log_likelihood: grad_log_likelihood += d_log_likelihood_update - if (time_series_no == 1): - M[k+1,:] = np.squeeze(m_upd) - else: - M[k+1,:,:] = m_upd # separate mean value for each time series + M[k+1,:,:] = m_upd # separate mean value for each time series if p_kalman_filter_type == 'svd': P[k+1,:,:] = P_upd[0] @@ -2614,11 +2850,11 @@ class ContDescrStateSpace(DescreteStateSpace): #print("kf it: %i" % k) # !!!Print statistics! Print sizes of matrices # !!!Print statistics! Print iteration time base on another boolean variable - return (M, P, log_likelihood, grad_log_likelihood, AQcomp.reset(False)) + return (M, P, log_likelihood, grad_log_likelihood, p_dynamic_callables.reset(False)) @classmethod def cont_discr_rts_smoother(cls,state_dim, filter_means, filter_covars, - AQcomp=None, X=None, F=None,L=None,Qc=None): + p_dynamic_callables=None, X=None, F=None,L=None,Qc=None): """ Continuos-discrete Rauch–Tung–Striebel(RTS) smoother. @@ -2641,7 +2877,7 @@ class ContDescrStateSpace(DescreteStateSpace): filter_covars: (no_steps+1, state_dim, state_dim) 3D array Results of the Kalman Filter covariance estimation. - AQcomp: object or None + Dynamic_callables: object or None Object form the filter phase which provides functions for computing A, Q, dA, dQ fro discrete model from the continuos model. @@ -2658,12 +2894,11 @@ class ContDescrStateSpace(DescreteStateSpace): Smoothed estimates of the state covariances """ - if AQcomp is None: # make this object from scratch - AQcomp = cls._cont_to_discrete_object(cls, X, F,L,Qc,compute_derivatives=False, - grad_params_no=None, P_inf=None, dP_inf=None, dF = None, dQc=None) - f_a = lambda k,m,A: np.dot(A, m) # state dynamic model - + if p_dynamic_callables is None: # make this object from scratch + p_dynamic_callables = cls._cont_to_discrete_object(cls, X, F,L,Qc,f_a,compute_derivatives=False, + grad_params_no=None, P_inf=None, dP_inf=None, dF = None, dQc=None) + no_steps = filter_covars.shape[0]-1# number of steps (minus initial covariance) M = np.empty(filter_means.shape) # smoothed means @@ -2672,23 +2907,25 @@ class ContDescrStateSpace(DescreteStateSpace): if print_verbose: print("General: run Continuos-Discrete Kalman Smoother") - M[-1,:] = filter_means[-1,:] + M[-1,:,:] = filter_means[-1,:,:] P[-1,:,:] = filter_covars[-1,:,:] for k in range(no_steps-1,-1,-1): + prev_mean = filter_means[k,:] # mean from the previous step m_pred, P_pred, tmp1, tmp2 = \ - cls._kalman_prediction_step(k, filter_means[k,:], - filter_covars[k,:,:], f_a, AQcomp.f_A, AQcomp.f_Q, + cls._kalman_prediction_step(k, prev_mean, + filter_covars[k,:,:], p_dynamic_callables, calc_grad_log_likelihood=False) - + p_m = filter_means[k,:] + p_m_prev_step = M[(k+1),:] + m_upd, P_upd, tmp_G = cls._rts_smoother_update_step(k, - filter_means[k,:] ,filter_covars[k,:,:], - m_pred, P_pred, M[(k+1),:] ,P[(k+1),:,:], AQcomp.f_A) + p_m ,filter_covars[k,:,:], + m_pred, P_pred, p_m_prev_step ,P[(k+1),:,:], p_dynamic_callables) - M[k,:] = np.squeeze(m_upd) + M[k,:,:] = m_upd P[k,:,:] = P_upd # Return values - return (M, P) @classmethod @@ -2708,6 +2945,8 @@ class ContDescrStateSpace(DescreteStateSpace): X, F, L, Qc: matrices Continuous model matrices + f_a: function + Dynamic Function is attached to the Dynamic_Model_Callables class compute_derivatives: boolean Whether to compute derivatives @@ -2733,7 +2972,19 @@ class ContDescrStateSpace(DescreteStateSpace): unique_indices = np.unique(np.round(dt, decimals=unique_round_decimals)) number_unique_indices = len(unique_indices) - if number_unique_indices > threshold_number_of_unique_time_steps: + #import pdb; pdb.set_trace() + if cython_code_available: + class AQcompute_batch(state_space_cython.AQcompute_batch_Cython): + def __init__(self, F,L,Qc,dt,compute_derivatives=False, grad_params_no=None, P_inf=None, dP_inf=None, dF = None, dQc=None): + As, Qs, reconstruct_indices, dAs, dQs = ContDescrStateSpace.lti_sde_to_descrete(F, + L,Qc,dt,compute_derivatives, + grad_params_no=grad_params_no, P_inf=P_inf, dP_inf=dP_inf, dF=dF, dQc=dQc) + + super(AQcompute_batch,self).__init__(As, Qs, reconstruct_indices, dAs,dQs) + else: + AQcompute_batch = cls.AQcompute_batch_Python + + if number_unique_indices > threshold_number_of_unique_time_steps: AQcomp = cls.AQcompute_once(F,L,Qc, dt,compute_derivatives=compute_derivatives, grad_params_no=grad_params_no, P_inf=P_inf, dP_inf=dP_inf, dF=dF, dQc=dQc) if print_verbose: @@ -2741,7 +2992,7 @@ class ContDescrStateSpace(DescreteStateSpace): print("CDO: Number of different time steps: %i" % (number_unique_indices,) ) else: - AQcomp = cls.AQcompute_batch(F,L,Qc,dt,compute_derivatives=compute_derivatives, + AQcomp = AQcompute_batch(F,L,Qc,dt,compute_derivatives=compute_derivatives, grad_params_no=grad_params_no, P_inf=P_inf, dP_inf=dP_inf, dF=dF, dQc=dQc) if print_verbose: print("CDO: Continue-to-discrete BATCH object is created.") @@ -2926,9 +3177,22 @@ def matrix_exponent(M): Mexp = np.array( ((np.exp(M[0,0]) ,),) ) else: # matrix is larger - Mexp = linalg.expm(M) - if np.any(np.isnan(Mexp)): - Mexp = linalg.expm3(M) + method = None + try: + Mexp = linalg.expm(M) + method = 1 + except (FloatingPointError, ValueError) as e: + Mexp = linalg.expm3(M) + method = 2 + finally: + if np.any(np.isnan(Mexp)): + if method == 2: + raise ValueError("Matrix Exponent is not computed 1") + else: + Mexp = linalg.expm3(M) + method = 2 + if np.any(np.isnan(Mexp)): + raise ValueError("Matrix Exponent is not computed 2") return Mexp diff --git a/GPy/models/state_space_new.py b/GPy/models/state_space_new.py index 48675fdf..324f8522 100644 --- a/GPy/models/state_space_new.py +++ b/GPy/models/state_space_new.py @@ -43,6 +43,8 @@ class StateSpace(Model): assert self.output_dim == 1, "State space methods for single outputs only" self.kalman_filter_type = kalman_filter_type + self.kalman_filter_type = 'svd' # temp test + # Make sure the observations are ordered in time sort_index = np.argsort(X[:,0]) @@ -70,7 +72,9 @@ class StateSpace(Model): """ Parameters have now changed """ - + np.set_printoptions(16) + print(self.param_array) + #import pdb; pdb.set_trace() # Get the model matrices from the kernel (F,L,Qc,H,P_inf, P0, dFt,dQct,dP_inft, dP0t) = self.kern.sde() @@ -116,6 +120,15 @@ class StateSpace(Model): grad_params_no=grad_params_no, grad_calc_params=grad_calc_params) + #import pdb; pdb.set_trace() + + if np.any( np.isfinite(log_likelihood) == False): + import pdb; pdb.set_trace() + + if np.any( np.isfinite(grad_log_likelihood) == False): + import pdb; pdb.set_trace() + #print(grad_log_likelihood) + grad_log_likelihood_sum = np.sum(grad_log_likelihood,axis=1) grad_log_likelihood_sum.shape = (grad_log_likelihood_sum.shape[0],1) self._log_marginal_likelihood = np.sum( log_likelihood,axis=1 ) @@ -190,27 +203,39 @@ class StateSpace(Model): F,L,Qc,H,float(self.Gaussian_noise.variance),P_inf,self.X,Y,m_init=None, P_init=P0, p_kalman_filter_type = kalman_filter_type, calc_log_likelihood=False, - calc_grad_log_likelihood=False) + calc_grad_log_likelihood=False) + +# (filter_means, filter_covs, log_likelihood, +# grad_log_likelihood,SmootherMatrObject) = ssm.ContDescrStateSpace.cont_discr_kalman_filter(F,L,Qc,H, +# float(self.Gaussian_noise.variance),P_inf,self.X,self.Y,m_init=None, +# P_init=P0, p_kalman_filter_type = kalman_filter_type, calc_log_likelihood=True, +# calc_grad_log_likelihood=True, +# grad_params_no=grad_params_no, +# grad_calc_params=grad_calc_params) + # Run the Rauch-Tung-Striebel smoother if not filteronly: (M, P) = ssm.ContDescrStateSpace.cont_discr_rts_smoother(state_dim, M, P, - AQcomp=SmootherMatrObject, X=X, F=F,L=L,Qc=Qc) + p_dynamic_callables=SmootherMatrObject, X=X, F=F,L=L,Qc=Qc) # remove initial values - M = M[1:,:] + M = M[1:,:,:] P = P[1:,:,:] # Put the data back in the original order - M = M[return_inverse,:] + M = M[return_inverse,:,:] P = P[return_inverse,:,:] # Only return the values for Xnew if not predict_only_training: - M = M[self.num_data:,:] + M = M[self.num_data:,:,:] P = P[self.num_data:,:,:] - + # Calculate the mean and variance - m = np.dot(M,H.T) + # after einsum m has dimension in 3D (sample_num, dim_no,time_series_no) + m = np.einsum('ijl,kj', M, H)# np.dot(M,H.T) + m.shape = (m.shape[0], m.shape[1]) # remove the third dimension + V = np.einsum('ij,ajk,kl', H, P, H.T) V.shape = (V.shape[0], V.shape[1]) # remove the third dimension diff --git a/setup.py b/setup.py index fee4a10d..9e0a2bf2 100644 --- a/setup.py +++ b/setup.py @@ -94,6 +94,10 @@ ext_mods = [Extension(name='GPy.kern.src.stationary_cython', Extension(name='GPy.kern.src.coregionalize_cython', sources=['GPy/kern/src/coregionalize_cython.c'], include_dirs=[np.get_include(),'.'], + extra_compile_args=compile_flags), + Extension(name='GPy.models.state_space_cython', + sources=['GPy/models/state_space_cython.c'], + include_dirs=[np.get_include(),'.'], extra_compile_args=compile_flags)] setup(name = 'GPy',