/* Generated by Cython 0.19.1 on Mon Apr 14 13:01:27 2014 */ #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 < 0x02040000 #error Cython requires Python 2.4+. #else #include /* For offsetof */ #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 PY_VERSION_HEX < 0x02050000 typedef int Py_ssize_t; #define PY_SSIZE_T_MAX INT_MAX #define PY_SSIZE_T_MIN INT_MIN #define PY_FORMAT_SIZE_T "" #define CYTHON_FORMAT_SSIZE_T "" #define PyInt_FromSsize_t(z) PyInt_FromLong(z) #define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o) #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \ (PyErr_Format(PyExc_TypeError, \ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \ (PyObject*)0)) #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \ !PyComplex_Check(o)) #define PyIndex_Check __Pyx_PyIndex_Check #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message) #define __PYX_BUILD_PY_SSIZE_T "i" #else #define __PYX_BUILD_PY_SSIZE_T "n" #define CYTHON_FORMAT_SSIZE_T "z" #define __Pyx_PyIndex_Check PyIndex_Check #endif #if PY_VERSION_HEX < 0x02060000 #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt) #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type) #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size) #define PyVarObject_HEAD_INIT(type, size) \ PyObject_HEAD_INIT(type) size, #define PyType_Modified(t) typedef struct { void *buf; PyObject *obj; Py_ssize_t len; Py_ssize_t itemsize; int readonly; int ndim; char *format; Py_ssize_t *shape; Py_ssize_t *strides; Py_ssize_t *suboffsets; void *internal; } Py_buffer; #define PyBUF_SIMPLE 0 #define PyBUF_WRITABLE 0x0001 #define PyBUF_FORMAT 0x0004 #define PyBUF_ND 0x0008 #define PyBUF_STRIDES (0x0010 | PyBUF_ND) #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES) #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES) #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES) #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES) #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE) #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE) typedef int (*getbufferproc)(PyObject *, Py_buffer *, int); typedef void (*releasebufferproc)(PyObject *, Py_buffer *); #endif #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, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #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) #endif #if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6 #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict") #endif #if PY_MAJOR_VERSION >= 3 #define Py_TPFLAGS_CHECKTYPES 0 #define Py_TPFLAGS_HAVE_INDEX 0 #endif #if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3) #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif #if PY_VERSION_HEX < 0x02060000 #define Py_TPFLAGS_HAVE_VERSION_TAG 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_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_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i])) #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_VERSION_HEX < 0x02060000 #define PyBytesObject PyStringObject #define PyBytes_Type PyString_Type #define PyBytes_Check PyString_Check #define PyBytes_CheckExact PyString_CheckExact #define PyBytes_FromString PyString_FromString #define PyBytes_FromStringAndSize PyString_FromStringAndSize #define PyBytes_FromFormat PyString_FromFormat #define PyBytes_DecodeEscape PyString_DecodeEscape #define PyBytes_AsString PyString_AsString #define PyBytes_AsStringAndSize PyString_AsStringAndSize #define PyBytes_Size PyString_Size #define PyBytes_AS_STRING PyString_AS_STRING #define PyBytes_GET_SIZE PyString_GET_SIZE #define PyBytes_Repr PyString_Repr #define PyBytes_Concat PyString_Concat #define PyBytes_ConcatAndDel PyString_ConcatAndDel #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_CheckExact(obj) || PyUnicode_CheckExact(obj) || \ PyString_Check(obj) || PyUnicode_Check(obj)) #define __Pyx_PyBaseString_CheckExact(obj) (Py_TYPE(obj) == &PyBaseString_Type) #endif #if PY_VERSION_HEX < 0x02060000 #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type) #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type) #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 #endif #if PY_MAJOR_VERSION >= 3 #define PyBoolObject PyLongObject #endif #if PY_VERSION_HEX < 0x03020000 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) || (PY_VERSION_HEX >= 0x03010300) #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b) #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value) #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b) #else #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0))) #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1))) #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \ (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \ (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1))) #endif #if PY_MAJOR_VERSION >= 3 #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) #endif #if PY_VERSION_HEX < 0x02050000 #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n))) #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a)) #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n))) #else #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n)) #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a)) #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n)) #endif #if PY_VERSION_HEX < 0x02050000 #define __Pyx_NAMESTR(n) ((char *)(n)) #define __Pyx_DOCSTR(n) ((char *)(n)) #else #define __Pyx_NAMESTR(n) (n) #define __Pyx_DOCSTR(n) (n) #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) #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 #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__MACS2__Poisson #define __PYX_HAVE_API__MACS2__Poisson #include "cPoisson.h" #include "string.h" #include "stdio.h" #include "pythread.h" #include "stdlib.h" #include "numpy/arrayobject.h" #include "numpy/ufuncobject.h" #include "khash.h" #include "math.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; /*proto*/ #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 static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); #define __Pyx_PyBytes_FromString PyBytes_FromString #define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(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_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) #define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((char*)s) #define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((char*)s) #define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((char*)s) #define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((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 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); static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*); #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() { PyObject* sys = NULL; PyObject* default_encoding = NULL; PyObject* ascii_chars_u = NULL; PyObject* ascii_chars_b = NULL; sys = PyImport_ImportModule("sys"); if (sys == NULL) goto bad; default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); if (default_encoding == NULL) goto bad; if (strcmp(PyBytes_AsString(default_encoding), "ascii") == 0) { __Pyx_sys_getdefaultencoding_not_ascii = 0; } else { const char* default_encoding_c = PyBytes_AS_STRING(default_encoding); 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 == NULL) goto bad; ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); if (ascii_chars_b == NULL || strncmp(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 '%s' is not a superset of ascii.", default_encoding_c); goto bad; } } Py_XDECREF(sys); Py_XDECREF(default_encoding); Py_XDECREF(ascii_chars_u); Py_XDECREF(ascii_chars_b); return 0; bad: Py_XDECREF(sys); 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() { PyObject* sys = NULL; PyObject* default_encoding = NULL; char* default_encoding_c; sys = PyImport_ImportModule("sys"); if (sys == NULL) goto bad; default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); if (default_encoding == NULL) goto bad; default_encoding_c = PyBytes_AS_STRING(default_encoding); __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c)); strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); Py_DECREF(sys); Py_DECREF(default_encoding); return 0; bad: Py_XDECREF(sys); Py_XDECREF(default_encoding); return -1; } #endif #endif #ifdef __GNUC__ /* Test for GCC > 2.95 */ #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) #define likely(x) __builtin_expect(!!(x), 1) #define unlikely(x) __builtin_expect(!!(x), 0) #else /* __GNUC__ > 2 ... */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ > 2 ... */ #else /* __GNUC__ */ #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[] = { "Poisson.pyx", "numpy.pxd", "type.pxd", "bool.pxd", "complex.pxd", }; /* "numpy.pxd":723 * # 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; /* "numpy.pxd":724 * * 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; /* "numpy.pxd":725 * 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; /* "numpy.pxd":726 * 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; /* "numpy.pxd":730 * #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; /* "numpy.pxd":731 * * 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; /* "numpy.pxd":732 * 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; /* "numpy.pxd":733 * 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; /* "numpy.pxd":737 * #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; /* "numpy.pxd":738 * * 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; /* "numpy.pxd":747 * # 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; /* "numpy.pxd":748 * # 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; /* "numpy.pxd":749 * 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; /* "numpy.pxd":751 * 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; /* "numpy.pxd":752 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< * ctypedef npy_ulonglong ulonglong_t * */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; /* "numpy.pxd":753 * 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; /* "numpy.pxd":755 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< * ctypedef npy_uintp uintp_t * */ typedef npy_intp __pyx_t_5numpy_intp_t; /* "numpy.pxd":756 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< * * ctypedef npy_double float_t */ typedef npy_uintp __pyx_t_5numpy_uintp_t; /* "numpy.pxd":758 * 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; /* "numpy.pxd":759 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< * ctypedef npy_longdouble longdouble_t * */ typedef npy_double __pyx_t_5numpy_double_t; /* "numpy.pxd":760 * 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; #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_5MACS2_7Poisson_LogLR_Asym; struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail; struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff; struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym; /* "numpy.pxd":762 * 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; /* "numpy.pxd":763 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< * ctypedef npy_clongdouble clongdouble_t * */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; /* "numpy.pxd":764 * 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; /* "numpy.pxd":766 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< * * cdef inline object PyArray_MultiIterNew1(a): */ typedef npy_cdouble __pyx_t_5numpy_complex_t; /* "MACS2/Poisson.pyx":58 * * * cdef class LogLR_Asym: # <<<<<<<<<<<<<< * """Unit to calculate asymmetric log likelihood, and cache * results in a hashtable. */ struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym { PyObject_HEAD struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Asym *__pyx_vtab; kh_int64_t *logLR_table; }; /* "MACS2/Poisson.pyx":9 * from libc.math cimport log10, log * * cdef class P_Score_Upper_Tail: # <<<<<<<<<<<<<< * """Unit to calculate -log10 poisson_CDF of upper tail and cache * results in a hashtable. */ struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail { PyObject_HEAD struct __pyx_vtabstruct_5MACS2_7Poisson_P_Score_Upper_Tail *__pyx_vtab; kh_int64_t *pscore_table; }; /* "MACS2/Poisson.pyx":170 * * * cdef class LogLR_Diff: # <<<<<<<<<<<<<< * """Unit to calculate log likelihood for differential calling, and cache * results in a hashtable. */ struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff { PyObject_HEAD struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Diff *__pyx_vtab; kh_int64_t *logLR_table; }; /* "MACS2/Poisson.pyx":113 * * * cdef class LogLR_Sym: # <<<<<<<<<<<<<< * """Unit to calculate symmetric log likelihood, and cache * results in a hashtable. */ struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym { PyObject_HEAD struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Sym *__pyx_vtab; kh_int64_t *logLR_table; }; /* "MACS2/Poisson.pyx":58 * * * cdef class LogLR_Asym: # <<<<<<<<<<<<<< * """Unit to calculate asymmetric log likelihood, and cache * results in a hashtable. */ struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Asym { int (*check_cache)(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *, double, double, int __pyx_skip_dispatch); double (*get_logLR_asym)(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *, double, double, int __pyx_skip_dispatch); }; static struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Asym *__pyx_vtabptr_5MACS2_7Poisson_LogLR_Asym; /* "MACS2/Poisson.pyx":9 * from libc.math cimport log10, log * * cdef class P_Score_Upper_Tail: # <<<<<<<<<<<<<< * """Unit to calculate -log10 poisson_CDF of upper tail and cache * results in a hashtable. */ struct __pyx_vtabstruct_5MACS2_7Poisson_P_Score_Upper_Tail { int (*check_cache)(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *, int, double, int __pyx_skip_dispatch); double (*get_pscore)(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *, int, double, int __pyx_skip_dispatch); }; static struct __pyx_vtabstruct_5MACS2_7Poisson_P_Score_Upper_Tail *__pyx_vtabptr_5MACS2_7Poisson_P_Score_Upper_Tail; /* "MACS2/Poisson.pyx":170 * * * cdef class LogLR_Diff: # <<<<<<<<<<<<<< * """Unit to calculate log likelihood for differential calling, and cache * results in a hashtable. */ struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Diff { int (*check_cache)(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *, double, double, int __pyx_skip_dispatch); double (*get_logLR_diff)(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *, double, double, int __pyx_skip_dispatch); }; static struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Diff *__pyx_vtabptr_5MACS2_7Poisson_LogLR_Diff; /* "MACS2/Poisson.pyx":113 * * * cdef class LogLR_Sym: # <<<<<<<<<<<<<< * """Unit to calculate symmetric log likelihood, and cache * results in a hashtable. */ struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Sym { int (*check_cache)(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *, double, double, int __pyx_skip_dispatch); double (*get_logLR_sym)(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *, double, double, int __pyx_skip_dispatch); }; static struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Sym *__pyx_vtabptr_5MACS2_7Poisson_LogLR_Sym; #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); /*proto*/ #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__); \ } #else #define __Pyx_RefNannySetupContext(name, acquire_gil) \ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__) #endif #define __Pyx_RefNannyFinishContext() \ __Pyx_RefNanny->FinishContext(&__pyx_refnanny) #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__) #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__) #define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__) #define __Pyx_GIVEREF(r) __Pyx_RefNanny->GIVEREF(__pyx_refnanny, (PyObject *)(r), __LINE__) #define __Pyx_XINCREF(r) do { if((r) != NULL) {__Pyx_INCREF(r); }} while(0) #define __Pyx_XDECREF(r) do { if((r) != NULL) {__Pyx_DECREF(r); }} while(0) #define __Pyx_XGOTREF(r) do { if((r) != NULL) {__Pyx_GOTREF(r); }} while(0) #define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0) #else #define __Pyx_RefNannyDeclarations #define __Pyx_RefNannySetupContext(name, acquire_gil) #define __Pyx_RefNannyFinishContext() #define __Pyx_INCREF(r) Py_INCREF(r) #define __Pyx_DECREF(r) Py_DECREF(r) #define __Pyx_GOTREF(r) #define __Pyx_GIVEREF(r) #define __Pyx_XINCREF(r) Py_XINCREF(r) #define __Pyx_XDECREF(r) Py_XDECREF(r) #define __Pyx_XGOTREF(r) #define __Pyx_XGIVEREF(r) #endif /* CYTHON_REFNANNY */ #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) static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/ static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ const char* function_name); /*proto*/ 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); /*proto*/ static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict, const char* function_name, int kw_allowed); /*proto*/ #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 CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ static void __Pyx_WriteUnraisable(const char *name, int clineno, int lineno, const char *filename); /*proto*/ static PyObject *__Pyx_GetBuiltinName(PyObject *name); /*proto*/ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/ static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/ static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/ static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/ static CYTHON_INLINE npy_uint32 __Pyx_PyInt_from_py_npy_uint32(PyObject *); #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(__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 CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *); static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *); static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject *); static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject *); static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject *); static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject *); static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject *); static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject *); static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject *); static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject *); static CYTHON_INLINE long __Pyx_PyInt_AsLong(PyObject *); static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject *); static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *); static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *); 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); /*proto*/ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ 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); /*proto*/ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ /* Module declarations from 'cpython.version' */ /* Module declarations from 'cpython.ref' */ /* Module declarations from 'cpython.exc' */ /* Module declarations from 'cpython.module' */ /* Module declarations from 'cpython.mem' */ /* Module declarations from 'cpython.tuple' */ /* Module declarations from 'cpython.list' */ /* Module declarations from 'libc.string' */ /* Module declarations from 'libc.stdio' */ /* Module declarations from 'cpython.object' */ /* Module declarations from 'cpython.sequence' */ /* Module declarations from 'cpython.mapping' */ /* Module declarations from 'cpython.iterator' */ /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.type' */ static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; /* Module declarations from 'cpython.number' */ /* Module declarations from 'cpython.int' */ /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.bool' */ static PyTypeObject *__pyx_ptype_7cpython_4bool_bool = 0; /* Module declarations from 'cpython.long' */ /* Module declarations from 'cpython.float' */ /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.complex' */ static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0; /* Module declarations from 'cpython.string' */ /* Module declarations from 'cpython.unicode' */ /* Module declarations from 'cpython.dict' */ /* Module declarations from 'cpython.instance' */ /* Module declarations from 'cpython.function' */ /* Module declarations from 'cpython.method' */ /* Module declarations from 'cpython.weakref' */ /* Module declarations from 'cpython.getargs' */ /* Module declarations from 'cpython.pythread' */ /* Module declarations from 'cpython.pystate' */ /* Module declarations from 'cpython.cobject' */ /* Module declarations from 'cpython.oldbuffer' */ /* Module declarations from 'cpython.set' */ /* Module declarations from 'cpython.buffer' */ /* Module declarations from 'cpython.bytes' */ /* Module declarations from 'cpython.pycapsule' */ /* Module declarations from 'cpython' */ /* 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 'MACS2.khash' */ /* Module declarations from 'libc.math' */ /* Module declarations from 'MACS2.Poisson' */ static PyTypeObject *__pyx_ptype_5MACS2_7Poisson_LogLR_Asym = 0; static PyTypeObject *__pyx_ptype_5MACS2_7Poisson_P_Score_Upper_Tail = 0; static PyTypeObject *__pyx_ptype_5MACS2_7Poisson_LogLR_Diff = 0; static PyTypeObject *__pyx_ptype_5MACS2_7Poisson_LogLR_Sym = 0; #define __Pyx_MODULE_NAME "MACS2.Poisson" int __pyx_module_is_main_MACS2__Poisson = 0; /* Implementation of 'MACS2.Poisson' */ static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_RuntimeError; static int __pyx_pf_5MACS2_7Poisson_18P_Score_Upper_Tail___init__(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *__pyx_v_self, PyObject *__pyx_v_size_hint); /* proto */ static int __pyx_pf_5MACS2_7Poisson_18P_Score_Upper_Tail_2__cinit__(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *__pyx_v_self); /* proto */ static void __pyx_pf_5MACS2_7Poisson_18P_Score_Upper_Tail_4__dealloc__(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5MACS2_7Poisson_18P_Score_Upper_Tail_6check_cache(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *__pyx_v_self, int __pyx_v_x, double __pyx_v_l); /* proto */ static PyObject *__pyx_pf_5MACS2_7Poisson_18P_Score_Upper_Tail_8get_pscore(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *__pyx_v_self, int __pyx_v_x, double __pyx_v_l); /* proto */ static int __pyx_pf_5MACS2_7Poisson_10LogLR_Asym___init__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *__pyx_v_self, PyObject *__pyx_v_size_hint); /* proto */ static int __pyx_pf_5MACS2_7Poisson_10LogLR_Asym_2__cinit__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *__pyx_v_self); /* proto */ static void __pyx_pf_5MACS2_7Poisson_10LogLR_Asym_4__dealloc__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5MACS2_7Poisson_10LogLR_Asym_6check_cache(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *__pyx_v_self, double __pyx_v_x, double __pyx_v_y); /* proto */ static PyObject *__pyx_pf_5MACS2_7Poisson_10LogLR_Asym_8get_logLR_asym(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *__pyx_v_self, double __pyx_v_x, double __pyx_v_y); /* proto */ static int __pyx_pf_5MACS2_7Poisson_9LogLR_Sym___init__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *__pyx_v_self, PyObject *__pyx_v_size_hint); /* proto */ static int __pyx_pf_5MACS2_7Poisson_9LogLR_Sym_2__cinit__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *__pyx_v_self); /* proto */ static void __pyx_pf_5MACS2_7Poisson_9LogLR_Sym_4__dealloc__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5MACS2_7Poisson_9LogLR_Sym_6check_cache(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *__pyx_v_self, double __pyx_v_x, double __pyx_v_y); /* proto */ static PyObject *__pyx_pf_5MACS2_7Poisson_9LogLR_Sym_8get_logLR_sym(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *__pyx_v_self, double __pyx_v_x, double __pyx_v_y); /* proto */ static int __pyx_pf_5MACS2_7Poisson_10LogLR_Diff___init__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *__pyx_v_self, PyObject *__pyx_v_size_hint); /* proto */ static int __pyx_pf_5MACS2_7Poisson_10LogLR_Diff_2__cinit__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *__pyx_v_self); /* proto */ static void __pyx_pf_5MACS2_7Poisson_10LogLR_Diff_4__dealloc__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5MACS2_7Poisson_10LogLR_Diff_6check_cache(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *__pyx_v_self, double __pyx_v_x, double __pyx_v_y); /* proto */ static PyObject *__pyx_pf_5MACS2_7Poisson_10LogLR_Diff_8get_logLR_diff(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *__pyx_v_self, double __pyx_v_x, double __pyx_v_y); /* 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_5MACS2_7Poisson_LogLR_Asym(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5MACS2_7Poisson_P_Score_Upper_Tail(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5MACS2_7Poisson_LogLR_Diff(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_tp_new_5MACS2_7Poisson_LogLR_Sym(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static char __pyx_k_1[] = "ndarray is not C contiguous"; static char __pyx_k_3[] = "ndarray is not Fortran contiguous"; static char __pyx_k_5[] = "Non-native byte order not supported"; static char __pyx_k_7[] = "unknown dtype code in numpy.pxd (%d)"; static char __pyx_k_8[] = "Format string allocated too short, see comment in numpy.pxd"; static char __pyx_k_11[] = "Format string allocated too short."; static char __pyx_k__B[] = "B"; static char __pyx_k__H[] = "H"; static char __pyx_k__I[] = "I"; static char __pyx_k__L[] = "L"; static char __pyx_k__O[] = "O"; static char __pyx_k__Q[] = "Q"; 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__l[] = "l"; static char __pyx_k__q[] = "q"; static char __pyx_k__x[] = "x"; static char __pyx_k__y[] = "y"; static char __pyx_k__Zd[] = "Zd"; static char __pyx_k__Zf[] = "Zf"; static char __pyx_k__Zg[] = "Zg"; static char __pyx_k__range[] = "range"; static char __pyx_k____main__[] = "__main__"; static char __pyx_k____test__[] = "__test__"; static char __pyx_k__size_hint[] = "size_hint"; static char __pyx_k__ValueError[] = "ValueError"; static char __pyx_k__get_pscore[] = "get_pscore"; static char __pyx_k__check_cache[] = "check_cache"; static char __pyx_k__RuntimeError[] = "RuntimeError"; static char __pyx_k__get_logLR_sym[] = "get_logLR_sym"; static char __pyx_k____pyx_vtable__[] = "__pyx_vtable__"; static char __pyx_k__get_logLR_asym[] = "get_logLR_asym"; static char __pyx_k__get_logLR_diff[] = "get_logLR_diff"; static PyObject *__pyx_kp_u_1; static PyObject *__pyx_kp_u_11; static PyObject *__pyx_kp_u_3; static PyObject *__pyx_kp_u_5; static PyObject *__pyx_kp_u_7; static PyObject *__pyx_kp_u_8; static PyObject *__pyx_n_s__RuntimeError; static PyObject *__pyx_n_s__ValueError; static PyObject *__pyx_n_s____main__; static PyObject *__pyx_n_s____pyx_vtable__; static PyObject *__pyx_n_s____test__; static PyObject *__pyx_n_s__check_cache; static PyObject *__pyx_n_s__get_logLR_asym; static PyObject *__pyx_n_s__get_logLR_diff; static PyObject *__pyx_n_s__get_logLR_sym; static PyObject *__pyx_n_s__get_pscore; static PyObject *__pyx_n_s__l; static PyObject *__pyx_n_s__range; static PyObject *__pyx_n_s__size_hint; static PyObject *__pyx_n_s__x; static PyObject *__pyx_n_s__y; static PyObject *__pyx_int_1; static PyObject *__pyx_int_15; static PyObject *__pyx_k_tuple_2; static PyObject *__pyx_k_tuple_4; static PyObject *__pyx_k_tuple_6; static PyObject *__pyx_k_tuple_9; static PyObject *__pyx_k_tuple_10; static PyObject *__pyx_k_tuple_12; /* Python wrapper */ static int __pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static int __pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_size_hint = 0; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); { static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__size_hint,0}; PyObject* values[1] = {0}; values[0] = ((PyObject *)__pyx_int_1); if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__size_hint); if (value) { values[0] = value; kw_args--; } } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 16; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } } __pyx_v_size_hint = values[0]; } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__init__", 0, 0, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 16; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MACS2.Poisson.P_Score_Upper_Tail.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; __pyx_r = __pyx_pf_5MACS2_7Poisson_18P_Score_Upper_Tail___init__(((struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *)__pyx_v_self), __pyx_v_size_hint); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":16 * kh_int64_t *pscore_table # a hash where key is integr, value is float * * def __init__ ( self, size_hint = 1 ): # <<<<<<<<<<<<<< * if size_hint is not None: * kh_resize_int64( self.pscore_table, size_hint ) */ static int __pyx_pf_5MACS2_7Poisson_18P_Score_Upper_Tail___init__(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *__pyx_v_self, PyObject *__pyx_v_size_hint) { int __pyx_r; __Pyx_RefNannyDeclarations int __pyx_t_1; int __pyx_t_2; khint_t __pyx_t_3; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__init__", 0); /* "MACS2/Poisson.pyx":17 * * def __init__ ( self, size_hint = 1 ): * if size_hint is not None: # <<<<<<<<<<<<<< * kh_resize_int64( self.pscore_table, size_hint ) * */ __pyx_t_1 = (__pyx_v_size_hint != Py_None); __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { /* "MACS2/Poisson.pyx":18 * def __init__ ( self, size_hint = 1 ): * if size_hint is not None: * kh_resize_int64( self.pscore_table, size_hint ) # <<<<<<<<<<<<<< * * def __cinit__( self ): */ __pyx_t_3 = __Pyx_PyInt_from_py_npy_uint32(__pyx_v_size_hint); if (unlikely((__pyx_t_3 == (khint_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L1_error;} kh_resize_int64(__pyx_v_self->pscore_table, __pyx_t_3); goto __pyx_L3; } __pyx_L3:; __pyx_r = 0; goto __pyx_L0; __pyx_L1_error:; __Pyx_AddTraceback("MACS2.Poisson.P_Score_Upper_Tail.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = -1; __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static int __pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static int __pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) { __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;} if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 0))) return -1; __pyx_r = __pyx_pf_5MACS2_7Poisson_18P_Score_Upper_Tail_2__cinit__(((struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":20 * kh_resize_int64( self.pscore_table, size_hint ) * * def __cinit__( self ): # <<<<<<<<<<<<<< * self.pscore_table = kh_init_int64() * */ static int __pyx_pf_5MACS2_7Poisson_18P_Score_Upper_Tail_2__cinit__(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *__pyx_v_self) { int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__", 0); /* "MACS2/Poisson.pyx":21 * * def __cinit__( self ): * self.pscore_table = kh_init_int64() # <<<<<<<<<<<<<< * * def __dealloc__( self ): */ __pyx_v_self->pscore_table = kh_init_int64(); __pyx_r = 0; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static void __pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_5__dealloc__(PyObject *__pyx_v_self); /*proto*/ static void __pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_5__dealloc__(PyObject *__pyx_v_self) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); __pyx_pf_5MACS2_7Poisson_18P_Score_Upper_Tail_4__dealloc__(((struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); } /* "MACS2/Poisson.pyx":23 * self.pscore_table = kh_init_int64() * * def __dealloc__( self ): # <<<<<<<<<<<<<< * kh_destroy_int64(self.pscore_table) * */ static void __pyx_pf_5MACS2_7Poisson_18P_Score_Upper_Tail_4__dealloc__(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *__pyx_v_self) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__dealloc__", 0); /* "MACS2/Poisson.pyx":24 * * def __dealloc__( self ): * kh_destroy_int64(self.pscore_table) # <<<<<<<<<<<<<< * * cpdef bint check_cache ( self, int x, double l ): */ kh_destroy_int64(__pyx_v_self->pscore_table); __Pyx_RefNannyFinishContext(); } /* "MACS2/Poisson.pyx":26 * kh_destroy_int64(self.pscore_table) * * cpdef bint check_cache ( self, int x, double l ): # <<<<<<<<<<<<<< * """Check if the Poisson CDF(x|l) has been calculated and * cached. */ static PyObject *__pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_7check_cache(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static int __pyx_f_5MACS2_7Poisson_18P_Score_Upper_Tail_check_cache(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *__pyx_v_self, int __pyx_v_x, double __pyx_v_l, int __pyx_skip_dispatch) { khiter_t __pyx_v_k; long __pyx_v_key_value; int __pyx_r; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; int __pyx_t_5; Py_hash_t __pyx_t_6; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("check_cache", 0); /* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s__check_cache); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_7check_cache)) { __pyx_t_2 = PyInt_FromLong(__pyx_v_x); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = PyFloat_FromDouble(__pyx_v_l); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_2 = 0; __pyx_t_3 = 0; __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_r = __pyx_t_5; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L0; } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } /* "MACS2/Poisson.pyx":35 * long key_value * * key_value = hash( (x, l) ) # <<<<<<<<<<<<<< * k = kh_get_int64( self.pscore_table, key_value ) * return k != self.pscore_table.n_buckets */ __pyx_t_1 = PyInt_FromLong(__pyx_v_x); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_3 = PyFloat_FromDouble(__pyx_v_l); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_1 = 0; __pyx_t_3 = 0; __pyx_t_6 = PyObject_Hash(((PyObject *)__pyx_t_4)); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_v_key_value = __pyx_t_6; /* "MACS2/Poisson.pyx":36 * * key_value = hash( (x, l) ) * k = kh_get_int64( self.pscore_table, key_value ) # <<<<<<<<<<<<<< * return k != self.pscore_table.n_buckets * */ __pyx_v_k = kh_get_int64(__pyx_v_self->pscore_table, __pyx_v_key_value); /* "MACS2/Poisson.pyx":37 * key_value = hash( (x, l) ) * k = kh_get_int64( self.pscore_table, key_value ) * return k != self.pscore_table.n_buckets # <<<<<<<<<<<<<< * * cpdef double get_pscore ( self, int x, double l ): */ __pyx_r = (__pyx_v_k != __pyx_v_self->pscore_table->n_buckets); goto __pyx_L0; __pyx_r = 0; goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); __Pyx_WriteUnraisable("MACS2.Poisson.P_Score_Upper_Tail.check_cache", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static PyObject *__pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_7check_cache(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static char __pyx_doc_5MACS2_7Poisson_18P_Score_Upper_Tail_6check_cache[] = "Check if the Poisson CDF(x|l) has been calculated and\n cached.\n \n "; static PyObject *__pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_7check_cache(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_v_x; double __pyx_v_l; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("check_cache (wrapper)", 0); { static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__x,&__pyx_n_s__l,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__x)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__l)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("check_cache", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "check_cache") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; } else { values[0] = PyTuple_GET_ITEM(__pyx_args, 0); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); } __pyx_v_x = __Pyx_PyInt_AsInt(values[0]); if (unlikely((__pyx_v_x == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_l = __pyx_PyFloat_AsDouble(values[1]); if (unlikely((__pyx_v_l == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("check_cache", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MACS2.Poisson.P_Score_Upper_Tail.check_cache", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; __pyx_r = __pyx_pf_5MACS2_7Poisson_18P_Score_Upper_Tail_6check_cache(((struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *)__pyx_v_self), __pyx_v_x, __pyx_v_l); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":26 * kh_destroy_int64(self.pscore_table) * * cpdef bint check_cache ( self, int x, double l ): # <<<<<<<<<<<<<< * """Check if the Poisson CDF(x|l) has been calculated and * cached. */ static PyObject *__pyx_pf_5MACS2_7Poisson_18P_Score_Upper_Tail_6check_cache(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *__pyx_v_self, int __pyx_v_x, double __pyx_v_l) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("check_cache", 0); __Pyx_XDECREF(__pyx_r); __pyx_t_1 = __Pyx_PyBool_FromLong(((struct __pyx_vtabstruct_5MACS2_7Poisson_P_Score_Upper_Tail *)__pyx_v_self->__pyx_vtab)->check_cache(__pyx_v_self, __pyx_v_x, __pyx_v_l, 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_AddTraceback("MACS2.Poisson.P_Score_Upper_Tail.check_cache", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":39 * return k != self.pscore_table.n_buckets * * cpdef double get_pscore ( self, int x, double l ): # <<<<<<<<<<<<<< * cdef: * khiter_t k # index got in the table; translated from hash key */ static PyObject *__pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_9get_pscore(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static double __pyx_f_5MACS2_7Poisson_18P_Score_Upper_Tail_get_pscore(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *__pyx_v_self, int __pyx_v_x, double __pyx_v_l, int __pyx_skip_dispatch) { khiter_t __pyx_v_k; int __pyx_v_ret; double __pyx_v_val; long __pyx_v_key_value; double __pyx_r; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; double __pyx_t_5; Py_hash_t __pyx_t_6; int __pyx_t_7; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("get_pscore", 0); /* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s__get_pscore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_9get_pscore)) { __pyx_t_2 = PyInt_FromLong(__pyx_v_x); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = PyFloat_FromDouble(__pyx_v_l); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_2 = 0; __pyx_t_3 = 0; __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_t_5 = __pyx_PyFloat_AsDouble(__pyx_t_3); if (unlikely((__pyx_t_5 == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_r = __pyx_t_5; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L0; } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } /* "MACS2/Poisson.pyx":42 * cdef: * khiter_t k # index got in the table; translated from hash key * int ret = 0 # <<<<<<<<<<<<<< * double val * long key_value # hash key */ __pyx_v_ret = 0; /* "MACS2/Poisson.pyx":45 * double val * long key_value # hash key * key_value = hash( (x, l) ) # <<<<<<<<<<<<<< * k = kh_get_int64(self.pscore_table, key_value) # translate hash key to index * if k != self.pscore_table.n_buckets: #kh_exist_int64( self.pscore_table, k ): */ __pyx_t_1 = PyInt_FromLong(__pyx_v_x); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_3 = PyFloat_FromDouble(__pyx_v_l); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_1 = 0; __pyx_t_3 = 0; __pyx_t_6 = PyObject_Hash(((PyObject *)__pyx_t_4)); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 45; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_v_key_value = __pyx_t_6; /* "MACS2/Poisson.pyx":46 * long key_value # hash key * key_value = hash( (x, l) ) * k = kh_get_int64(self.pscore_table, key_value) # translate hash key to index # <<<<<<<<<<<<<< * if k != self.pscore_table.n_buckets: #kh_exist_int64( self.pscore_table, k ): * return self.pscore_table.vals[k] */ __pyx_v_k = kh_get_int64(__pyx_v_self->pscore_table, __pyx_v_key_value); /* "MACS2/Poisson.pyx":47 * key_value = hash( (x, l) ) * k = kh_get_int64(self.pscore_table, key_value) # translate hash key to index * if k != self.pscore_table.n_buckets: #kh_exist_int64( self.pscore_table, k ): # <<<<<<<<<<<<<< * return self.pscore_table.vals[k] * else: */ __pyx_t_7 = ((__pyx_v_k != __pyx_v_self->pscore_table->n_buckets) != 0); if (__pyx_t_7) { /* "MACS2/Poisson.pyx":48 * k = kh_get_int64(self.pscore_table, key_value) # translate hash key to index * if k != self.pscore_table.n_buckets: #kh_exist_int64( self.pscore_table, k ): * return self.pscore_table.vals[k] # <<<<<<<<<<<<<< * else: * # calculate and cache */ __pyx_r = (__pyx_v_self->pscore_table->vals[__pyx_v_k]); goto __pyx_L0; goto __pyx_L3; } /*else*/ { /* "MACS2/Poisson.pyx":51 * else: * # calculate and cache * val = -1 * log10_poisson_cdf ( x, l, 0 ) # <<<<<<<<<<<<<< * k = kh_put_int64( self.pscore_table, key_value, &ret ) * self.pscore_table.keys[ k ] = key_value */ __pyx_v_val = (-1.0 * log10_poisson_cdf(__pyx_v_x, __pyx_v_l, 0)); /* "MACS2/Poisson.pyx":52 * # calculate and cache * val = -1 * log10_poisson_cdf ( x, l, 0 ) * k = kh_put_int64( self.pscore_table, key_value, &ret ) # <<<<<<<<<<<<<< * self.pscore_table.keys[ k ] = key_value * self.pscore_table.vals[ k ] = val */ __pyx_v_k = kh_put_int64(__pyx_v_self->pscore_table, __pyx_v_key_value, (&__pyx_v_ret)); /* "MACS2/Poisson.pyx":53 * val = -1 * log10_poisson_cdf ( x, l, 0 ) * k = kh_put_int64( self.pscore_table, key_value, &ret ) * self.pscore_table.keys[ k ] = key_value # <<<<<<<<<<<<<< * self.pscore_table.vals[ k ] = val * return val */ (__pyx_v_self->pscore_table->keys[__pyx_v_k]) = __pyx_v_key_value; /* "MACS2/Poisson.pyx":54 * k = kh_put_int64( self.pscore_table, key_value, &ret ) * self.pscore_table.keys[ k ] = key_value * self.pscore_table.vals[ k ] = val # <<<<<<<<<<<<<< * return val * */ (__pyx_v_self->pscore_table->vals[__pyx_v_k]) = __pyx_v_val; /* "MACS2/Poisson.pyx":55 * self.pscore_table.keys[ k ] = key_value * self.pscore_table.vals[ k ] = val * return val # <<<<<<<<<<<<<< * * */ __pyx_r = __pyx_v_val; goto __pyx_L0; } __pyx_L3:; __pyx_r = 0; goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); __Pyx_WriteUnraisable("MACS2.Poisson.P_Score_Upper_Tail.get_pscore", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static PyObject *__pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_9get_pscore(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static PyObject *__pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_9get_pscore(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_v_x; double __pyx_v_l; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("get_pscore (wrapper)", 0); { static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__x,&__pyx_n_s__l,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__x)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__l)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("get_pscore", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "get_pscore") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; } else { values[0] = PyTuple_GET_ITEM(__pyx_args, 0); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); } __pyx_v_x = __Pyx_PyInt_AsInt(values[0]); if (unlikely((__pyx_v_x == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_l = __pyx_PyFloat_AsDouble(values[1]); if (unlikely((__pyx_v_l == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("get_pscore", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MACS2.Poisson.P_Score_Upper_Tail.get_pscore", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; __pyx_r = __pyx_pf_5MACS2_7Poisson_18P_Score_Upper_Tail_8get_pscore(((struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *)__pyx_v_self), __pyx_v_x, __pyx_v_l); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":39 * return k != self.pscore_table.n_buckets * * cpdef double get_pscore ( self, int x, double l ): # <<<<<<<<<<<<<< * cdef: * khiter_t k # index got in the table; translated from hash key */ static PyObject *__pyx_pf_5MACS2_7Poisson_18P_Score_Upper_Tail_8get_pscore(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *__pyx_v_self, int __pyx_v_x, double __pyx_v_l) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("get_pscore", 0); __Pyx_XDECREF(__pyx_r); __pyx_t_1 = PyFloat_FromDouble(((struct __pyx_vtabstruct_5MACS2_7Poisson_P_Score_Upper_Tail *)__pyx_v_self->__pyx_vtab)->get_pscore(__pyx_v_self, __pyx_v_x, __pyx_v_l, 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_AddTraceback("MACS2.Poisson.P_Score_Upper_Tail.get_pscore", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static int __pyx_pw_5MACS2_7Poisson_10LogLR_Asym_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static int __pyx_pw_5MACS2_7Poisson_10LogLR_Asym_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_size_hint = 0; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); { static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__size_hint,0}; PyObject* values[1] = {0}; values[0] = ((PyObject *)__pyx_int_1); if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__size_hint); if (value) { values[0] = value; kw_args--; } } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } } __pyx_v_size_hint = values[0]; } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__init__", 0, 0, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MACS2.Poisson.LogLR_Asym.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; __pyx_r = __pyx_pf_5MACS2_7Poisson_10LogLR_Asym___init__(((struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *)__pyx_v_self), __pyx_v_size_hint); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":65 * kh_int64_t *logLR_table # a hash where key is integr, value is float * * def __init__ ( self, size_hint = 1 ): # <<<<<<<<<<<<<< * if size_hint is not None: * kh_resize_int64( self.logLR_table, size_hint ) */ static int __pyx_pf_5MACS2_7Poisson_10LogLR_Asym___init__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *__pyx_v_self, PyObject *__pyx_v_size_hint) { int __pyx_r; __Pyx_RefNannyDeclarations int __pyx_t_1; int __pyx_t_2; khint_t __pyx_t_3; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__init__", 0); /* "MACS2/Poisson.pyx":66 * * def __init__ ( self, size_hint = 1 ): * if size_hint is not None: # <<<<<<<<<<<<<< * kh_resize_int64( self.logLR_table, size_hint ) * */ __pyx_t_1 = (__pyx_v_size_hint != Py_None); __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { /* "MACS2/Poisson.pyx":67 * def __init__ ( self, size_hint = 1 ): * if size_hint is not None: * kh_resize_int64( self.logLR_table, size_hint ) # <<<<<<<<<<<<<< * * def __cinit__( self ): */ __pyx_t_3 = __Pyx_PyInt_from_py_npy_uint32(__pyx_v_size_hint); if (unlikely((__pyx_t_3 == (khint_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 67; __pyx_clineno = __LINE__; goto __pyx_L1_error;} kh_resize_int64(__pyx_v_self->logLR_table, __pyx_t_3); goto __pyx_L3; } __pyx_L3:; __pyx_r = 0; goto __pyx_L0; __pyx_L1_error:; __Pyx_AddTraceback("MACS2.Poisson.LogLR_Asym.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = -1; __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static int __pyx_pw_5MACS2_7Poisson_10LogLR_Asym_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static int __pyx_pw_5MACS2_7Poisson_10LogLR_Asym_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) { __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;} if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 0))) return -1; __pyx_r = __pyx_pf_5MACS2_7Poisson_10LogLR_Asym_2__cinit__(((struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":69 * kh_resize_int64( self.logLR_table, size_hint ) * * def __cinit__( self ): # <<<<<<<<<<<<<< * self.logLR_table = kh_init_int64() * */ static int __pyx_pf_5MACS2_7Poisson_10LogLR_Asym_2__cinit__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *__pyx_v_self) { int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__", 0); /* "MACS2/Poisson.pyx":70 * * def __cinit__( self ): * self.logLR_table = kh_init_int64() # <<<<<<<<<<<<<< * * def __dealloc__( self ): */ __pyx_v_self->logLR_table = kh_init_int64(); __pyx_r = 0; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static void __pyx_pw_5MACS2_7Poisson_10LogLR_Asym_5__dealloc__(PyObject *__pyx_v_self); /*proto*/ static void __pyx_pw_5MACS2_7Poisson_10LogLR_Asym_5__dealloc__(PyObject *__pyx_v_self) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); __pyx_pf_5MACS2_7Poisson_10LogLR_Asym_4__dealloc__(((struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); } /* "MACS2/Poisson.pyx":72 * self.logLR_table = kh_init_int64() * * def __dealloc__( self ): # <<<<<<<<<<<<<< * kh_destroy_int64(self.logLR_table) * */ static void __pyx_pf_5MACS2_7Poisson_10LogLR_Asym_4__dealloc__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *__pyx_v_self) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__dealloc__", 0); /* "MACS2/Poisson.pyx":73 * * def __dealloc__( self ): * kh_destroy_int64(self.logLR_table) # <<<<<<<<<<<<<< * * cpdef bint check_cache ( self, double x, double y ): */ kh_destroy_int64(__pyx_v_self->logLR_table); __Pyx_RefNannyFinishContext(); } /* "MACS2/Poisson.pyx":75 * kh_destroy_int64(self.logLR_table) * * cpdef bint check_cache ( self, double x, double y ): # <<<<<<<<<<<<<< * """Check if the logLR of enrich:x background:y; has been * calculated and cached. */ static PyObject *__pyx_pw_5MACS2_7Poisson_10LogLR_Asym_7check_cache(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static int __pyx_f_5MACS2_7Poisson_10LogLR_Asym_check_cache(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *__pyx_v_self, double __pyx_v_x, double __pyx_v_y, int __pyx_skip_dispatch) { khiter_t __pyx_v_k; long __pyx_v_key_value; int __pyx_r; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; int __pyx_t_5; Py_hash_t __pyx_t_6; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("check_cache", 0); /* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s__check_cache); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_5MACS2_7Poisson_10LogLR_Asym_7check_cache)) { __pyx_t_2 = PyFloat_FromDouble(__pyx_v_x); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = PyFloat_FromDouble(__pyx_v_y); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_2 = 0; __pyx_t_3 = 0; __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_r = __pyx_t_5; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L0; } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } /* "MACS2/Poisson.pyx":84 * long key_value * * key_value = hash( (x, y) ) # <<<<<<<<<<<<<< * k = kh_get_int64( self.logLR_table, key_value ) * return k != self.logLR_table.n_buckets */ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_x); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_3 = PyFloat_FromDouble(__pyx_v_y); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_1 = 0; __pyx_t_3 = 0; __pyx_t_6 = PyObject_Hash(((PyObject *)__pyx_t_4)); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_v_key_value = __pyx_t_6; /* "MACS2/Poisson.pyx":85 * * key_value = hash( (x, y) ) * k = kh_get_int64( self.logLR_table, key_value ) # <<<<<<<<<<<<<< * return k != self.logLR_table.n_buckets * */ __pyx_v_k = kh_get_int64(__pyx_v_self->logLR_table, __pyx_v_key_value); /* "MACS2/Poisson.pyx":86 * key_value = hash( (x, y) ) * k = kh_get_int64( self.logLR_table, key_value ) * return k != self.logLR_table.n_buckets # <<<<<<<<<<<<<< * * cpdef double get_logLR_asym ( self, double x, double y ): */ __pyx_r = (__pyx_v_k != __pyx_v_self->logLR_table->n_buckets); goto __pyx_L0; __pyx_r = 0; goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); __Pyx_WriteUnraisable("MACS2.Poisson.LogLR_Asym.check_cache", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static PyObject *__pyx_pw_5MACS2_7Poisson_10LogLR_Asym_7check_cache(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static char __pyx_doc_5MACS2_7Poisson_10LogLR_Asym_6check_cache[] = "Check if the logLR of enrich:x background:y; has been\n calculated and cached.\n \n "; static PyObject *__pyx_pw_5MACS2_7Poisson_10LogLR_Asym_7check_cache(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { double __pyx_v_x; double __pyx_v_y; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("check_cache (wrapper)", 0); { static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__x,&__pyx_n_s__y,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__x)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__y)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("check_cache", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "check_cache") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; } else { values[0] = PyTuple_GET_ITEM(__pyx_args, 0); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); } __pyx_v_x = __pyx_PyFloat_AsDouble(values[0]); if (unlikely((__pyx_v_x == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_y = __pyx_PyFloat_AsDouble(values[1]); if (unlikely((__pyx_v_y == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("check_cache", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MACS2.Poisson.LogLR_Asym.check_cache", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; __pyx_r = __pyx_pf_5MACS2_7Poisson_10LogLR_Asym_6check_cache(((struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *)__pyx_v_self), __pyx_v_x, __pyx_v_y); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":75 * kh_destroy_int64(self.logLR_table) * * cpdef bint check_cache ( self, double x, double y ): # <<<<<<<<<<<<<< * """Check if the logLR of enrich:x background:y; has been * calculated and cached. */ static PyObject *__pyx_pf_5MACS2_7Poisson_10LogLR_Asym_6check_cache(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *__pyx_v_self, double __pyx_v_x, double __pyx_v_y) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("check_cache", 0); __Pyx_XDECREF(__pyx_r); __pyx_t_1 = __Pyx_PyBool_FromLong(((struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Asym *)__pyx_v_self->__pyx_vtab)->check_cache(__pyx_v_self, __pyx_v_x, __pyx_v_y, 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_AddTraceback("MACS2.Poisson.LogLR_Asym.check_cache", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":88 * return k != self.logLR_table.n_buckets * * cpdef double get_logLR_asym ( self, double x, double y ): # <<<<<<<<<<<<<< * cdef: * khiter_t k # index got in the table; translated from hash key */ static PyObject *__pyx_pw_5MACS2_7Poisson_10LogLR_Asym_9get_logLR_asym(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static double __pyx_f_5MACS2_7Poisson_10LogLR_Asym_get_logLR_asym(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *__pyx_v_self, double __pyx_v_x, double __pyx_v_y, int __pyx_skip_dispatch) { khiter_t __pyx_v_k; int __pyx_v_ret; double __pyx_v_val; long __pyx_v_key_value; double __pyx_r; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; double __pyx_t_5; Py_hash_t __pyx_t_6; int __pyx_t_7; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("get_logLR_asym", 0); /* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s__get_logLR_asym); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_5MACS2_7Poisson_10LogLR_Asym_9get_logLR_asym)) { __pyx_t_2 = PyFloat_FromDouble(__pyx_v_x); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = PyFloat_FromDouble(__pyx_v_y); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_2 = 0; __pyx_t_3 = 0; __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_t_5 = __pyx_PyFloat_AsDouble(__pyx_t_3); if (unlikely((__pyx_t_5 == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_r = __pyx_t_5; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L0; } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } /* "MACS2/Poisson.pyx":91 * cdef: * khiter_t k # index got in the table; translated from hash key * int ret = 0 # <<<<<<<<<<<<<< * double val * long key_value # hash key */ __pyx_v_ret = 0; /* "MACS2/Poisson.pyx":94 * double val * long key_value # hash key * key_value = hash( (x, y) ) # <<<<<<<<<<<<<< * k = kh_get_int64(self.logLR_table, key_value) # translate hash key to index * if k != self.logLR_table.n_buckets: #kh_exist_int64( self.pscore_table, k ): */ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_x); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_3 = PyFloat_FromDouble(__pyx_v_y); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_1 = 0; __pyx_t_3 = 0; __pyx_t_6 = PyObject_Hash(((PyObject *)__pyx_t_4)); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_v_key_value = __pyx_t_6; /* "MACS2/Poisson.pyx":95 * long key_value # hash key * key_value = hash( (x, y) ) * k = kh_get_int64(self.logLR_table, key_value) # translate hash key to index # <<<<<<<<<<<<<< * if k != self.logLR_table.n_buckets: #kh_exist_int64( self.pscore_table, k ): * return self.logLR_table.vals[k] */ __pyx_v_k = kh_get_int64(__pyx_v_self->logLR_table, __pyx_v_key_value); /* "MACS2/Poisson.pyx":96 * key_value = hash( (x, y) ) * k = kh_get_int64(self.logLR_table, key_value) # translate hash key to index * if k != self.logLR_table.n_buckets: #kh_exist_int64( self.pscore_table, k ): # <<<<<<<<<<<<<< * return self.logLR_table.vals[k] * else: */ __pyx_t_7 = ((__pyx_v_k != __pyx_v_self->logLR_table->n_buckets) != 0); if (__pyx_t_7) { /* "MACS2/Poisson.pyx":97 * k = kh_get_int64(self.logLR_table, key_value) # translate hash key to index * if k != self.logLR_table.n_buckets: #kh_exist_int64( self.pscore_table, k ): * return self.logLR_table.vals[k] # <<<<<<<<<<<<<< * else: * # calculate and cache */ __pyx_r = (__pyx_v_self->logLR_table->vals[__pyx_v_k]); goto __pyx_L0; goto __pyx_L3; } /*else*/ { /* "MACS2/Poisson.pyx":100 * else: * # calculate and cache * if x > y: # <<<<<<<<<<<<<< * val = (x*(log10(x)-log10(y))+y-x) * elif x < y: */ __pyx_t_7 = ((__pyx_v_x > __pyx_v_y) != 0); if (__pyx_t_7) { /* "MACS2/Poisson.pyx":101 * # calculate and cache * if x > y: * val = (x*(log10(x)-log10(y))+y-x) # <<<<<<<<<<<<<< * elif x < y: * val = (x*(-log10(x)+log10(y))-y+x) */ __pyx_v_val = (((__pyx_v_x * (log10(__pyx_v_x) - log10(__pyx_v_y))) + __pyx_v_y) - __pyx_v_x); goto __pyx_L4; } /* "MACS2/Poisson.pyx":102 * if x > y: * val = (x*(log10(x)-log10(y))+y-x) * elif x < y: # <<<<<<<<<<<<<< * val = (x*(-log10(x)+log10(y))-y+x) * else: */ __pyx_t_7 = ((__pyx_v_x < __pyx_v_y) != 0); if (__pyx_t_7) { /* "MACS2/Poisson.pyx":103 * val = (x*(log10(x)-log10(y))+y-x) * elif x < y: * val = (x*(-log10(x)+log10(y))-y+x) # <<<<<<<<<<<<<< * else: * val = 0 */ __pyx_v_val = (((__pyx_v_x * ((-log10(__pyx_v_x)) + log10(__pyx_v_y))) - __pyx_v_y) + __pyx_v_x); goto __pyx_L4; } /*else*/ { /* "MACS2/Poisson.pyx":105 * val = (x*(-log10(x)+log10(y))-y+x) * else: * val = 0 # <<<<<<<<<<<<<< * * k = kh_put_int64( self.logLR_table, key_value, &ret ) */ __pyx_v_val = 0.0; } __pyx_L4:; /* "MACS2/Poisson.pyx":107 * val = 0 * * k = kh_put_int64( self.logLR_table, key_value, &ret ) # <<<<<<<<<<<<<< * self.logLR_table.keys[ k ] = key_value * self.logLR_table.vals[ k ] = val */ __pyx_v_k = kh_put_int64(__pyx_v_self->logLR_table, __pyx_v_key_value, (&__pyx_v_ret)); /* "MACS2/Poisson.pyx":108 * * k = kh_put_int64( self.logLR_table, key_value, &ret ) * self.logLR_table.keys[ k ] = key_value # <<<<<<<<<<<<<< * self.logLR_table.vals[ k ] = val * return val */ (__pyx_v_self->logLR_table->keys[__pyx_v_k]) = __pyx_v_key_value; /* "MACS2/Poisson.pyx":109 * k = kh_put_int64( self.logLR_table, key_value, &ret ) * self.logLR_table.keys[ k ] = key_value * self.logLR_table.vals[ k ] = val # <<<<<<<<<<<<<< * return val * */ (__pyx_v_self->logLR_table->vals[__pyx_v_k]) = __pyx_v_val; /* "MACS2/Poisson.pyx":110 * self.logLR_table.keys[ k ] = key_value * self.logLR_table.vals[ k ] = val * return val # <<<<<<<<<<<<<< * * */ __pyx_r = __pyx_v_val; goto __pyx_L0; } __pyx_L3:; __pyx_r = 0; goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); __Pyx_WriteUnraisable("MACS2.Poisson.LogLR_Asym.get_logLR_asym", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static PyObject *__pyx_pw_5MACS2_7Poisson_10LogLR_Asym_9get_logLR_asym(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static PyObject *__pyx_pw_5MACS2_7Poisson_10LogLR_Asym_9get_logLR_asym(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { double __pyx_v_x; double __pyx_v_y; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("get_logLR_asym (wrapper)", 0); { static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__x,&__pyx_n_s__y,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__x)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__y)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("get_logLR_asym", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "get_logLR_asym") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; } else { values[0] = PyTuple_GET_ITEM(__pyx_args, 0); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); } __pyx_v_x = __pyx_PyFloat_AsDouble(values[0]); if (unlikely((__pyx_v_x == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_y = __pyx_PyFloat_AsDouble(values[1]); if (unlikely((__pyx_v_y == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("get_logLR_asym", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MACS2.Poisson.LogLR_Asym.get_logLR_asym", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; __pyx_r = __pyx_pf_5MACS2_7Poisson_10LogLR_Asym_8get_logLR_asym(((struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *)__pyx_v_self), __pyx_v_x, __pyx_v_y); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":88 * return k != self.logLR_table.n_buckets * * cpdef double get_logLR_asym ( self, double x, double y ): # <<<<<<<<<<<<<< * cdef: * khiter_t k # index got in the table; translated from hash key */ static PyObject *__pyx_pf_5MACS2_7Poisson_10LogLR_Asym_8get_logLR_asym(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *__pyx_v_self, double __pyx_v_x, double __pyx_v_y) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("get_logLR_asym", 0); __Pyx_XDECREF(__pyx_r); __pyx_t_1 = PyFloat_FromDouble(((struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Asym *)__pyx_v_self->__pyx_vtab)->get_logLR_asym(__pyx_v_self, __pyx_v_x, __pyx_v_y, 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_AddTraceback("MACS2.Poisson.LogLR_Asym.get_logLR_asym", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static int __pyx_pw_5MACS2_7Poisson_9LogLR_Sym_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static int __pyx_pw_5MACS2_7Poisson_9LogLR_Sym_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_size_hint = 0; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); { static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__size_hint,0}; PyObject* values[1] = {0}; values[0] = ((PyObject *)__pyx_int_1); if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__size_hint); if (value) { values[0] = value; kw_args--; } } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } } __pyx_v_size_hint = values[0]; } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__init__", 0, 0, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MACS2.Poisson.LogLR_Sym.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; __pyx_r = __pyx_pf_5MACS2_7Poisson_9LogLR_Sym___init__(((struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *)__pyx_v_self), __pyx_v_size_hint); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":122 * kh_int64_t *logLR_table # a hash where key is integr, value is float * * def __init__ ( self, size_hint = 1 ): # <<<<<<<<<<<<<< * if size_hint is not None: * kh_resize_int64( self.logLR_table, size_hint ) */ static int __pyx_pf_5MACS2_7Poisson_9LogLR_Sym___init__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *__pyx_v_self, PyObject *__pyx_v_size_hint) { int __pyx_r; __Pyx_RefNannyDeclarations int __pyx_t_1; int __pyx_t_2; khint_t __pyx_t_3; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__init__", 0); /* "MACS2/Poisson.pyx":123 * * def __init__ ( self, size_hint = 1 ): * if size_hint is not None: # <<<<<<<<<<<<<< * kh_resize_int64( self.logLR_table, size_hint ) * */ __pyx_t_1 = (__pyx_v_size_hint != Py_None); __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { /* "MACS2/Poisson.pyx":124 * def __init__ ( self, size_hint = 1 ): * if size_hint is not None: * kh_resize_int64( self.logLR_table, size_hint ) # <<<<<<<<<<<<<< * * def __cinit__( self ): */ __pyx_t_3 = __Pyx_PyInt_from_py_npy_uint32(__pyx_v_size_hint); if (unlikely((__pyx_t_3 == (khint_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;} kh_resize_int64(__pyx_v_self->logLR_table, __pyx_t_3); goto __pyx_L3; } __pyx_L3:; __pyx_r = 0; goto __pyx_L0; __pyx_L1_error:; __Pyx_AddTraceback("MACS2.Poisson.LogLR_Sym.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = -1; __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static int __pyx_pw_5MACS2_7Poisson_9LogLR_Sym_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static int __pyx_pw_5MACS2_7Poisson_9LogLR_Sym_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) { __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;} if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 0))) return -1; __pyx_r = __pyx_pf_5MACS2_7Poisson_9LogLR_Sym_2__cinit__(((struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":126 * kh_resize_int64( self.logLR_table, size_hint ) * * def __cinit__( self ): # <<<<<<<<<<<<<< * self.logLR_table = kh_init_int64() * */ static int __pyx_pf_5MACS2_7Poisson_9LogLR_Sym_2__cinit__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *__pyx_v_self) { int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__", 0); /* "MACS2/Poisson.pyx":127 * * def __cinit__( self ): * self.logLR_table = kh_init_int64() # <<<<<<<<<<<<<< * * def __dealloc__( self ): */ __pyx_v_self->logLR_table = kh_init_int64(); __pyx_r = 0; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static void __pyx_pw_5MACS2_7Poisson_9LogLR_Sym_5__dealloc__(PyObject *__pyx_v_self); /*proto*/ static void __pyx_pw_5MACS2_7Poisson_9LogLR_Sym_5__dealloc__(PyObject *__pyx_v_self) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); __pyx_pf_5MACS2_7Poisson_9LogLR_Sym_4__dealloc__(((struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); } /* "MACS2/Poisson.pyx":129 * self.logLR_table = kh_init_int64() * * def __dealloc__( self ): # <<<<<<<<<<<<<< * kh_destroy_int64(self.logLR_table) * */ static void __pyx_pf_5MACS2_7Poisson_9LogLR_Sym_4__dealloc__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *__pyx_v_self) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__dealloc__", 0); /* "MACS2/Poisson.pyx":130 * * def __dealloc__( self ): * kh_destroy_int64(self.logLR_table) # <<<<<<<<<<<<<< * * cpdef bint check_cache ( self, double x, double y ): */ kh_destroy_int64(__pyx_v_self->logLR_table); __Pyx_RefNannyFinishContext(); } /* "MACS2/Poisson.pyx":132 * kh_destroy_int64(self.logLR_table) * * cpdef bint check_cache ( self, double x, double y ): # <<<<<<<<<<<<<< * """Check if the logLR of enrich:x background:y; has been * calculated and cached. */ static PyObject *__pyx_pw_5MACS2_7Poisson_9LogLR_Sym_7check_cache(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static int __pyx_f_5MACS2_7Poisson_9LogLR_Sym_check_cache(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *__pyx_v_self, double __pyx_v_x, double __pyx_v_y, int __pyx_skip_dispatch) { khiter_t __pyx_v_k; long __pyx_v_key_value; int __pyx_r; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; int __pyx_t_5; Py_hash_t __pyx_t_6; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("check_cache", 0); /* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s__check_cache); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_5MACS2_7Poisson_9LogLR_Sym_7check_cache)) { __pyx_t_2 = PyFloat_FromDouble(__pyx_v_x); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = PyFloat_FromDouble(__pyx_v_y); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_2 = 0; __pyx_t_3 = 0; __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_r = __pyx_t_5; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L0; } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } /* "MACS2/Poisson.pyx":141 * long key_value * * key_value = hash( (x, y) ) # <<<<<<<<<<<<<< * k = kh_get_int64( self.logLR_table, key_value ) * return k != self.logLR_table.n_buckets */ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_x); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_3 = PyFloat_FromDouble(__pyx_v_y); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_1 = 0; __pyx_t_3 = 0; __pyx_t_6 = PyObject_Hash(((PyObject *)__pyx_t_4)); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_v_key_value = __pyx_t_6; /* "MACS2/Poisson.pyx":142 * * key_value = hash( (x, y) ) * k = kh_get_int64( self.logLR_table, key_value ) # <<<<<<<<<<<<<< * return k != self.logLR_table.n_buckets * */ __pyx_v_k = kh_get_int64(__pyx_v_self->logLR_table, __pyx_v_key_value); /* "MACS2/Poisson.pyx":143 * key_value = hash( (x, y) ) * k = kh_get_int64( self.logLR_table, key_value ) * return k != self.logLR_table.n_buckets # <<<<<<<<<<<<<< * * cpdef double get_logLR_sym ( self, double x, double y ): */ __pyx_r = (__pyx_v_k != __pyx_v_self->logLR_table->n_buckets); goto __pyx_L0; __pyx_r = 0; goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); __Pyx_WriteUnraisable("MACS2.Poisson.LogLR_Sym.check_cache", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static PyObject *__pyx_pw_5MACS2_7Poisson_9LogLR_Sym_7check_cache(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static char __pyx_doc_5MACS2_7Poisson_9LogLR_Sym_6check_cache[] = "Check if the logLR of enrich:x background:y; has been\n calculated and cached.\n \n "; static PyObject *__pyx_pw_5MACS2_7Poisson_9LogLR_Sym_7check_cache(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { double __pyx_v_x; double __pyx_v_y; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("check_cache (wrapper)", 0); { static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__x,&__pyx_n_s__y,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__x)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__y)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("check_cache", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "check_cache") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; } else { values[0] = PyTuple_GET_ITEM(__pyx_args, 0); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); } __pyx_v_x = __pyx_PyFloat_AsDouble(values[0]); if (unlikely((__pyx_v_x == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_y = __pyx_PyFloat_AsDouble(values[1]); if (unlikely((__pyx_v_y == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("check_cache", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MACS2.Poisson.LogLR_Sym.check_cache", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; __pyx_r = __pyx_pf_5MACS2_7Poisson_9LogLR_Sym_6check_cache(((struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *)__pyx_v_self), __pyx_v_x, __pyx_v_y); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":132 * kh_destroy_int64(self.logLR_table) * * cpdef bint check_cache ( self, double x, double y ): # <<<<<<<<<<<<<< * """Check if the logLR of enrich:x background:y; has been * calculated and cached. */ static PyObject *__pyx_pf_5MACS2_7Poisson_9LogLR_Sym_6check_cache(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *__pyx_v_self, double __pyx_v_x, double __pyx_v_y) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("check_cache", 0); __Pyx_XDECREF(__pyx_r); __pyx_t_1 = __Pyx_PyBool_FromLong(((struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Sym *)__pyx_v_self->__pyx_vtab)->check_cache(__pyx_v_self, __pyx_v_x, __pyx_v_y, 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_AddTraceback("MACS2.Poisson.LogLR_Sym.check_cache", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":145 * return k != self.logLR_table.n_buckets * * cpdef double get_logLR_sym ( self, double x, double y ): # <<<<<<<<<<<<<< * cdef: * khiter_t k # index got in the table; translated from hash key */ static PyObject *__pyx_pw_5MACS2_7Poisson_9LogLR_Sym_9get_logLR_sym(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static double __pyx_f_5MACS2_7Poisson_9LogLR_Sym_get_logLR_sym(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *__pyx_v_self, double __pyx_v_x, double __pyx_v_y, int __pyx_skip_dispatch) { khiter_t __pyx_v_k; int __pyx_v_ret; double __pyx_v_val; long __pyx_v_key_value; double __pyx_r; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; double __pyx_t_5; Py_hash_t __pyx_t_6; int __pyx_t_7; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("get_logLR_sym", 0); /* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s__get_logLR_sym); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_5MACS2_7Poisson_9LogLR_Sym_9get_logLR_sym)) { __pyx_t_2 = PyFloat_FromDouble(__pyx_v_x); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = PyFloat_FromDouble(__pyx_v_y); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_2 = 0; __pyx_t_3 = 0; __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_t_5 = __pyx_PyFloat_AsDouble(__pyx_t_3); if (unlikely((__pyx_t_5 == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_r = __pyx_t_5; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L0; } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } /* "MACS2/Poisson.pyx":148 * cdef: * khiter_t k # index got in the table; translated from hash key * int ret = 0 # <<<<<<<<<<<<<< * double val * long key_value # hash key */ __pyx_v_ret = 0; /* "MACS2/Poisson.pyx":151 * double val * long key_value # hash key * key_value = hash( (x, y) ) # <<<<<<<<<<<<<< * k = kh_get_int64(self.logLR_table, key_value) # translate hash key to index * if k != self.logLR_table.n_buckets: #kh_exist_int64( self.pscore_table, k ): */ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_x); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_3 = PyFloat_FromDouble(__pyx_v_y); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_1 = 0; __pyx_t_3 = 0; __pyx_t_6 = PyObject_Hash(((PyObject *)__pyx_t_4)); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_v_key_value = __pyx_t_6; /* "MACS2/Poisson.pyx":152 * long key_value # hash key * key_value = hash( (x, y) ) * k = kh_get_int64(self.logLR_table, key_value) # translate hash key to index # <<<<<<<<<<<<<< * if k != self.logLR_table.n_buckets: #kh_exist_int64( self.pscore_table, k ): * return self.logLR_table.vals[k] */ __pyx_v_k = kh_get_int64(__pyx_v_self->logLR_table, __pyx_v_key_value); /* "MACS2/Poisson.pyx":153 * key_value = hash( (x, y) ) * k = kh_get_int64(self.logLR_table, key_value) # translate hash key to index * if k != self.logLR_table.n_buckets: #kh_exist_int64( self.pscore_table, k ): # <<<<<<<<<<<<<< * return self.logLR_table.vals[k] * else: */ __pyx_t_7 = ((__pyx_v_k != __pyx_v_self->logLR_table->n_buckets) != 0); if (__pyx_t_7) { /* "MACS2/Poisson.pyx":154 * k = kh_get_int64(self.logLR_table, key_value) # translate hash key to index * if k != self.logLR_table.n_buckets: #kh_exist_int64( self.pscore_table, k ): * return self.logLR_table.vals[k] # <<<<<<<<<<<<<< * else: * # calculate and cache */ __pyx_r = (__pyx_v_self->logLR_table->vals[__pyx_v_k]); goto __pyx_L0; goto __pyx_L3; } /*else*/ { /* "MACS2/Poisson.pyx":157 * else: * # calculate and cache * if x > y: # <<<<<<<<<<<<<< * val = (x*(log10(x)-log10(y))+y-x) * elif y > x: */ __pyx_t_7 = ((__pyx_v_x > __pyx_v_y) != 0); if (__pyx_t_7) { /* "MACS2/Poisson.pyx":158 * # calculate and cache * if x > y: * val = (x*(log10(x)-log10(y))+y-x) # <<<<<<<<<<<<<< * elif y > x: * val = (y*(log10(x)-log10(y))+y-x) */ __pyx_v_val = (((__pyx_v_x * (log10(__pyx_v_x) - log10(__pyx_v_y))) + __pyx_v_y) - __pyx_v_x); goto __pyx_L4; } /* "MACS2/Poisson.pyx":159 * if x > y: * val = (x*(log10(x)-log10(y))+y-x) * elif y > x: # <<<<<<<<<<<<<< * val = (y*(log10(x)-log10(y))+y-x) * else: */ __pyx_t_7 = ((__pyx_v_y > __pyx_v_x) != 0); if (__pyx_t_7) { /* "MACS2/Poisson.pyx":160 * val = (x*(log10(x)-log10(y))+y-x) * elif y > x: * val = (y*(log10(x)-log10(y))+y-x) # <<<<<<<<<<<<<< * else: * val = 0 */ __pyx_v_val = (((__pyx_v_y * (log10(__pyx_v_x) - log10(__pyx_v_y))) + __pyx_v_y) - __pyx_v_x); goto __pyx_L4; } /*else*/ { /* "MACS2/Poisson.pyx":162 * val = (y*(log10(x)-log10(y))+y-x) * else: * val = 0 # <<<<<<<<<<<<<< * * k = kh_put_int64( self.logLR_table, key_value, &ret ) */ __pyx_v_val = 0.0; } __pyx_L4:; /* "MACS2/Poisson.pyx":164 * val = 0 * * k = kh_put_int64( self.logLR_table, key_value, &ret ) # <<<<<<<<<<<<<< * self.logLR_table.keys[ k ] = key_value * self.logLR_table.vals[ k ] = val */ __pyx_v_k = kh_put_int64(__pyx_v_self->logLR_table, __pyx_v_key_value, (&__pyx_v_ret)); /* "MACS2/Poisson.pyx":165 * * k = kh_put_int64( self.logLR_table, key_value, &ret ) * self.logLR_table.keys[ k ] = key_value # <<<<<<<<<<<<<< * self.logLR_table.vals[ k ] = val * return val */ (__pyx_v_self->logLR_table->keys[__pyx_v_k]) = __pyx_v_key_value; /* "MACS2/Poisson.pyx":166 * k = kh_put_int64( self.logLR_table, key_value, &ret ) * self.logLR_table.keys[ k ] = key_value * self.logLR_table.vals[ k ] = val # <<<<<<<<<<<<<< * return val * */ (__pyx_v_self->logLR_table->vals[__pyx_v_k]) = __pyx_v_val; /* "MACS2/Poisson.pyx":167 * self.logLR_table.keys[ k ] = key_value * self.logLR_table.vals[ k ] = val * return val # <<<<<<<<<<<<<< * * */ __pyx_r = __pyx_v_val; goto __pyx_L0; } __pyx_L3:; __pyx_r = 0; goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); __Pyx_WriteUnraisable("MACS2.Poisson.LogLR_Sym.get_logLR_sym", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static PyObject *__pyx_pw_5MACS2_7Poisson_9LogLR_Sym_9get_logLR_sym(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static PyObject *__pyx_pw_5MACS2_7Poisson_9LogLR_Sym_9get_logLR_sym(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { double __pyx_v_x; double __pyx_v_y; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("get_logLR_sym (wrapper)", 0); { static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__x,&__pyx_n_s__y,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__x)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__y)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("get_logLR_sym", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "get_logLR_sym") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; } else { values[0] = PyTuple_GET_ITEM(__pyx_args, 0); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); } __pyx_v_x = __pyx_PyFloat_AsDouble(values[0]); if (unlikely((__pyx_v_x == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_y = __pyx_PyFloat_AsDouble(values[1]); if (unlikely((__pyx_v_y == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("get_logLR_sym", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MACS2.Poisson.LogLR_Sym.get_logLR_sym", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; __pyx_r = __pyx_pf_5MACS2_7Poisson_9LogLR_Sym_8get_logLR_sym(((struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *)__pyx_v_self), __pyx_v_x, __pyx_v_y); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":145 * return k != self.logLR_table.n_buckets * * cpdef double get_logLR_sym ( self, double x, double y ): # <<<<<<<<<<<<<< * cdef: * khiter_t k # index got in the table; translated from hash key */ static PyObject *__pyx_pf_5MACS2_7Poisson_9LogLR_Sym_8get_logLR_sym(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *__pyx_v_self, double __pyx_v_x, double __pyx_v_y) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("get_logLR_sym", 0); __Pyx_XDECREF(__pyx_r); __pyx_t_1 = PyFloat_FromDouble(((struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Sym *)__pyx_v_self->__pyx_vtab)->get_logLR_sym(__pyx_v_self, __pyx_v_x, __pyx_v_y, 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_AddTraceback("MACS2.Poisson.LogLR_Sym.get_logLR_sym", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static int __pyx_pw_5MACS2_7Poisson_10LogLR_Diff_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static int __pyx_pw_5MACS2_7Poisson_10LogLR_Diff_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_size_hint = 0; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); { static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__size_hint,0}; PyObject* values[1] = {0}; values[0] = ((PyObject *)__pyx_int_1); if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: if (kw_args > 0) { PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__size_hint); if (value) { values[0] = value; kw_args--; } } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } } __pyx_v_size_hint = values[0]; } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("__init__", 0, 0, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MACS2.Poisson.LogLR_Diff.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; __pyx_r = __pyx_pf_5MACS2_7Poisson_10LogLR_Diff___init__(((struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *)__pyx_v_self), __pyx_v_size_hint); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":179 * kh_int64_t *logLR_table # a hash where key is integr, value is float * * def __init__ ( self, size_hint = 1 ): # <<<<<<<<<<<<<< * if size_hint is not None: * kh_resize_int64( self.logLR_table, size_hint ) */ static int __pyx_pf_5MACS2_7Poisson_10LogLR_Diff___init__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *__pyx_v_self, PyObject *__pyx_v_size_hint) { int __pyx_r; __Pyx_RefNannyDeclarations int __pyx_t_1; int __pyx_t_2; khint_t __pyx_t_3; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__init__", 0); /* "MACS2/Poisson.pyx":180 * * def __init__ ( self, size_hint = 1 ): * if size_hint is not None: # <<<<<<<<<<<<<< * kh_resize_int64( self.logLR_table, size_hint ) * */ __pyx_t_1 = (__pyx_v_size_hint != Py_None); __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { /* "MACS2/Poisson.pyx":181 * def __init__ ( self, size_hint = 1 ): * if size_hint is not None: * kh_resize_int64( self.logLR_table, size_hint ) # <<<<<<<<<<<<<< * * def __cinit__( self ): */ __pyx_t_3 = __Pyx_PyInt_from_py_npy_uint32(__pyx_v_size_hint); if (unlikely((__pyx_t_3 == (khint_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} kh_resize_int64(__pyx_v_self->logLR_table, __pyx_t_3); goto __pyx_L3; } __pyx_L3:; __pyx_r = 0; goto __pyx_L0; __pyx_L1_error:; __Pyx_AddTraceback("MACS2.Poisson.LogLR_Diff.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = -1; __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static int __pyx_pw_5MACS2_7Poisson_10LogLR_Diff_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static int __pyx_pw_5MACS2_7Poisson_10LogLR_Diff_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0); if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) { __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;} if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 0))) return -1; __pyx_r = __pyx_pf_5MACS2_7Poisson_10LogLR_Diff_2__cinit__(((struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":183 * kh_resize_int64( self.logLR_table, size_hint ) * * def __cinit__( self ): # <<<<<<<<<<<<<< * self.logLR_table = kh_init_int64() * */ static int __pyx_pf_5MACS2_7Poisson_10LogLR_Diff_2__cinit__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *__pyx_v_self) { int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__cinit__", 0); /* "MACS2/Poisson.pyx":184 * * def __cinit__( self ): * self.logLR_table = kh_init_int64() # <<<<<<<<<<<<<< * * def __dealloc__( self ): */ __pyx_v_self->logLR_table = kh_init_int64(); __pyx_r = 0; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static void __pyx_pw_5MACS2_7Poisson_10LogLR_Diff_5__dealloc__(PyObject *__pyx_v_self); /*proto*/ static void __pyx_pw_5MACS2_7Poisson_10LogLR_Diff_5__dealloc__(PyObject *__pyx_v_self) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0); __pyx_pf_5MACS2_7Poisson_10LogLR_Diff_4__dealloc__(((struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *)__pyx_v_self)); __Pyx_RefNannyFinishContext(); } /* "MACS2/Poisson.pyx":186 * self.logLR_table = kh_init_int64() * * def __dealloc__( self ): # <<<<<<<<<<<<<< * kh_destroy_int64(self.logLR_table) * */ static void __pyx_pf_5MACS2_7Poisson_10LogLR_Diff_4__dealloc__(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *__pyx_v_self) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__dealloc__", 0); /* "MACS2/Poisson.pyx":187 * * def __dealloc__( self ): * kh_destroy_int64(self.logLR_table) # <<<<<<<<<<<<<< * * cpdef bint check_cache ( self, double x, double y ): */ kh_destroy_int64(__pyx_v_self->logLR_table); __Pyx_RefNannyFinishContext(); } /* "MACS2/Poisson.pyx":189 * kh_destroy_int64(self.logLR_table) * * cpdef bint check_cache ( self, double x, double y ): # <<<<<<<<<<<<<< * """Check if the logLR of enrich:x background:y; has been * calculated and cached. */ static PyObject *__pyx_pw_5MACS2_7Poisson_10LogLR_Diff_7check_cache(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static int __pyx_f_5MACS2_7Poisson_10LogLR_Diff_check_cache(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *__pyx_v_self, double __pyx_v_x, double __pyx_v_y, int __pyx_skip_dispatch) { khiter_t __pyx_v_k; long __pyx_v_key_value; int __pyx_r; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; int __pyx_t_5; Py_hash_t __pyx_t_6; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("check_cache", 0); /* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s__check_cache); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_5MACS2_7Poisson_10LogLR_Diff_7check_cache)) { __pyx_t_2 = PyFloat_FromDouble(__pyx_v_x); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = PyFloat_FromDouble(__pyx_v_y); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_2 = 0; __pyx_t_3 = 0; __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_r = __pyx_t_5; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L0; } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } /* "MACS2/Poisson.pyx":198 * long key_value * * key_value = hash( (x, y) ) # <<<<<<<<<<<<<< * k = kh_get_int64( self.logLR_table, key_value ) * return k != self.logLR_table.n_buckets */ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_x); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_3 = PyFloat_FromDouble(__pyx_v_y); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_1 = 0; __pyx_t_3 = 0; __pyx_t_6 = PyObject_Hash(((PyObject *)__pyx_t_4)); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_v_key_value = __pyx_t_6; /* "MACS2/Poisson.pyx":199 * * key_value = hash( (x, y) ) * k = kh_get_int64( self.logLR_table, key_value ) # <<<<<<<<<<<<<< * return k != self.logLR_table.n_buckets * */ __pyx_v_k = kh_get_int64(__pyx_v_self->logLR_table, __pyx_v_key_value); /* "MACS2/Poisson.pyx":200 * key_value = hash( (x, y) ) * k = kh_get_int64( self.logLR_table, key_value ) * return k != self.logLR_table.n_buckets # <<<<<<<<<<<<<< * * cpdef double get_logLR_diff ( self, double x, double y ): */ __pyx_r = (__pyx_v_k != __pyx_v_self->logLR_table->n_buckets); goto __pyx_L0; __pyx_r = 0; goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); __Pyx_WriteUnraisable("MACS2.Poisson.LogLR_Diff.check_cache", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static PyObject *__pyx_pw_5MACS2_7Poisson_10LogLR_Diff_7check_cache(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static char __pyx_doc_5MACS2_7Poisson_10LogLR_Diff_6check_cache[] = "Check if the logLR of enrich:x background:y; has been\n calculated and cached.\n \n "; static PyObject *__pyx_pw_5MACS2_7Poisson_10LogLR_Diff_7check_cache(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { double __pyx_v_x; double __pyx_v_y; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("check_cache (wrapper)", 0); { static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__x,&__pyx_n_s__y,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__x)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__y)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("check_cache", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "check_cache") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; } else { values[0] = PyTuple_GET_ITEM(__pyx_args, 0); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); } __pyx_v_x = __pyx_PyFloat_AsDouble(values[0]); if (unlikely((__pyx_v_x == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_y = __pyx_PyFloat_AsDouble(values[1]); if (unlikely((__pyx_v_y == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("check_cache", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MACS2.Poisson.LogLR_Diff.check_cache", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; __pyx_r = __pyx_pf_5MACS2_7Poisson_10LogLR_Diff_6check_cache(((struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *)__pyx_v_self), __pyx_v_x, __pyx_v_y); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":189 * kh_destroy_int64(self.logLR_table) * * cpdef bint check_cache ( self, double x, double y ): # <<<<<<<<<<<<<< * """Check if the logLR of enrich:x background:y; has been * calculated and cached. */ static PyObject *__pyx_pf_5MACS2_7Poisson_10LogLR_Diff_6check_cache(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *__pyx_v_self, double __pyx_v_x, double __pyx_v_y) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("check_cache", 0); __Pyx_XDECREF(__pyx_r); __pyx_t_1 = __Pyx_PyBool_FromLong(((struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Diff *)__pyx_v_self->__pyx_vtab)->check_cache(__pyx_v_self, __pyx_v_x, __pyx_v_y, 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_AddTraceback("MACS2.Poisson.LogLR_Diff.check_cache", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":202 * return k != self.logLR_table.n_buckets * * cpdef double get_logLR_diff ( self, double x, double y ): # <<<<<<<<<<<<<< * cdef: * khiter_t k # index got in the table; translated from hash key */ static PyObject *__pyx_pw_5MACS2_7Poisson_10LogLR_Diff_9get_logLR_diff(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static double __pyx_f_5MACS2_7Poisson_10LogLR_Diff_get_logLR_diff(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *__pyx_v_self, double __pyx_v_x, double __pyx_v_y, int __pyx_skip_dispatch) { khiter_t __pyx_v_k; int __pyx_v_ret; double __pyx_v_val; long __pyx_v_key_value; double __pyx_r; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; double __pyx_t_5; Py_hash_t __pyx_t_6; int __pyx_t_7; double __pyx_t_8; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("get_logLR_diff", 0); /* Check if called by wrapper */ if (unlikely(__pyx_skip_dispatch)) ; /* Check if overridden in Python */ else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) { __pyx_t_1 = __Pyx_PyObject_GetAttrStr(((PyObject *)__pyx_v_self), __pyx_n_s__get_logLR_diff); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_5MACS2_7Poisson_10LogLR_Diff_9get_logLR_diff)) { __pyx_t_2 = PyFloat_FromDouble(__pyx_v_x); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_3 = PyFloat_FromDouble(__pyx_v_y); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_2 = 0; __pyx_t_3 = 0; __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_t_5 = __pyx_PyFloat_AsDouble(__pyx_t_3); if (unlikely((__pyx_t_5 == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_r = __pyx_t_5; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; goto __pyx_L0; } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } /* "MACS2/Poisson.pyx":205 * cdef: * khiter_t k # index got in the table; translated from hash key * int ret = 0 # <<<<<<<<<<<<<< * double val * long key_value # hash key */ __pyx_v_ret = 0; /* "MACS2/Poisson.pyx":208 * double val * long key_value # hash key * key_value = hash( (x, y) ) # <<<<<<<<<<<<<< * k = kh_get_int64(self.logLR_table, key_value) # translate hash key to index * if k != self.logLR_table.n_buckets: #kh_exist_int64( self.pscore_table, k ): */ __pyx_t_1 = PyFloat_FromDouble(__pyx_v_x); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_t_3 = PyFloat_FromDouble(__pyx_v_y); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_1 = 0; __pyx_t_3 = 0; __pyx_t_6 = PyObject_Hash(((PyObject *)__pyx_t_4)); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __pyx_v_key_value = __pyx_t_6; /* "MACS2/Poisson.pyx":209 * long key_value # hash key * key_value = hash( (x, y) ) * k = kh_get_int64(self.logLR_table, key_value) # translate hash key to index # <<<<<<<<<<<<<< * if k != self.logLR_table.n_buckets: #kh_exist_int64( self.pscore_table, k ): * return self.logLR_table.vals[k] */ __pyx_v_k = kh_get_int64(__pyx_v_self->logLR_table, __pyx_v_key_value); /* "MACS2/Poisson.pyx":210 * key_value = hash( (x, y) ) * k = kh_get_int64(self.logLR_table, key_value) # translate hash key to index * if k != self.logLR_table.n_buckets: #kh_exist_int64( self.pscore_table, k ): # <<<<<<<<<<<<<< * return self.logLR_table.vals[k] * else: */ __pyx_t_7 = ((__pyx_v_k != __pyx_v_self->logLR_table->n_buckets) != 0); if (__pyx_t_7) { /* "MACS2/Poisson.pyx":211 * k = kh_get_int64(self.logLR_table, key_value) # translate hash key to index * if k != self.logLR_table.n_buckets: #kh_exist_int64( self.pscore_table, k ): * return self.logLR_table.vals[k] # <<<<<<<<<<<<<< * else: * # calculate and cache */ __pyx_r = (__pyx_v_self->logLR_table->vals[__pyx_v_k]); goto __pyx_L0; goto __pyx_L3; } /*else*/ { /* "MACS2/Poisson.pyx":214 * else: * # calculate and cache * if y > x: y, x = x, y # <<<<<<<<<<<<<< * if x == y: * val = 0 */ __pyx_t_7 = ((__pyx_v_y > __pyx_v_x) != 0); if (__pyx_t_7) { __pyx_t_5 = __pyx_v_x; __pyx_t_8 = __pyx_v_y; __pyx_v_y = __pyx_t_5; __pyx_v_x = __pyx_t_8; goto __pyx_L4; } __pyx_L4:; /* "MACS2/Poisson.pyx":215 * # calculate and cache * if y > x: y, x = x, y * if x == y: # <<<<<<<<<<<<<< * val = 0 * else: */ __pyx_t_7 = ((__pyx_v_x == __pyx_v_y) != 0); if (__pyx_t_7) { /* "MACS2/Poisson.pyx":216 * if y > x: y, x = x, y * if x == y: * val = 0 # <<<<<<<<<<<<<< * else: * val = (x*(log10(x)-log10(y))+y-x) */ __pyx_v_val = 0.0; goto __pyx_L5; } /*else*/ { /* "MACS2/Poisson.pyx":218 * val = 0 * else: * val = (x*(log10(x)-log10(y))+y-x) # <<<<<<<<<<<<<< * * k = kh_put_int64( self.logLR_table, key_value, &ret ) */ __pyx_v_val = (((__pyx_v_x * (log10(__pyx_v_x) - log10(__pyx_v_y))) + __pyx_v_y) - __pyx_v_x); } __pyx_L5:; /* "MACS2/Poisson.pyx":220 * val = (x*(log10(x)-log10(y))+y-x) * * k = kh_put_int64( self.logLR_table, key_value, &ret ) # <<<<<<<<<<<<<< * self.logLR_table.keys[ k ] = key_value * self.logLR_table.vals[ k ] = val */ __pyx_v_k = kh_put_int64(__pyx_v_self->logLR_table, __pyx_v_key_value, (&__pyx_v_ret)); /* "MACS2/Poisson.pyx":221 * * k = kh_put_int64( self.logLR_table, key_value, &ret ) * self.logLR_table.keys[ k ] = key_value # <<<<<<<<<<<<<< * self.logLR_table.vals[ k ] = val * return val */ (__pyx_v_self->logLR_table->keys[__pyx_v_k]) = __pyx_v_key_value; /* "MACS2/Poisson.pyx":222 * k = kh_put_int64( self.logLR_table, key_value, &ret ) * self.logLR_table.keys[ k ] = key_value * self.logLR_table.vals[ k ] = val # <<<<<<<<<<<<<< * return val */ (__pyx_v_self->logLR_table->vals[__pyx_v_k]) = __pyx_v_val; /* "MACS2/Poisson.pyx":223 * self.logLR_table.keys[ k ] = key_value * self.logLR_table.vals[ k ] = val * return val # <<<<<<<<<<<<<< */ __pyx_r = __pyx_v_val; goto __pyx_L0; } __pyx_L3:; __pyx_r = 0; goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); __Pyx_WriteUnraisable("MACS2.Poisson.LogLR_Diff.get_logLR_diff", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static PyObject *__pyx_pw_5MACS2_7Poisson_10LogLR_Diff_9get_logLR_diff(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ static PyObject *__pyx_pw_5MACS2_7Poisson_10LogLR_Diff_9get_logLR_diff(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { double __pyx_v_x; double __pyx_v_y; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("get_logLR_diff (wrapper)", 0); { static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__x,&__pyx_n_s__y,0}; PyObject* values[2] = {0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); case 0: break; default: goto __pyx_L5_argtuple_error; } kw_args = PyDict_Size(__pyx_kwds); switch (pos_args) { case 0: if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__x)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__y)) != 0)) kw_args--; else { __Pyx_RaiseArgtupleInvalid("get_logLR_diff", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "get_logLR_diff") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; } else { values[0] = PyTuple_GET_ITEM(__pyx_args, 0); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); } __pyx_v_x = __pyx_PyFloat_AsDouble(values[0]); if (unlikely((__pyx_v_x == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_y = __pyx_PyFloat_AsDouble(values[1]); if (unlikely((__pyx_v_y == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; __Pyx_RaiseArgtupleInvalid("get_logLR_diff", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("MACS2.Poisson.LogLR_Diff.get_logLR_diff", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; __pyx_r = __pyx_pf_5MACS2_7Poisson_10LogLR_Diff_8get_logLR_diff(((struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *)__pyx_v_self), __pyx_v_x, __pyx_v_y); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "MACS2/Poisson.pyx":202 * return k != self.logLR_table.n_buckets * * cpdef double get_logLR_diff ( self, double x, double y ): # <<<<<<<<<<<<<< * cdef: * khiter_t k # index got in the table; translated from hash key */ static PyObject *__pyx_pf_5MACS2_7Poisson_10LogLR_Diff_8get_logLR_diff(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *__pyx_v_self, double __pyx_v_x, double __pyx_v_y) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("get_logLR_diff", 0); __Pyx_XDECREF(__pyx_r); __pyx_t_1 = PyFloat_FromDouble(((struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Diff *)__pyx_v_self->__pyx_vtab)->get_logLR_diff(__pyx_v_self, __pyx_v_x, __pyx_v_y, 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_AddTraceback("MACS2.Poisson.LogLR_Diff.get_logLR_diff", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static CYTHON_UNUSED int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ static CYTHON_UNUSED int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__getbuffer__ (wrapper)", 0); __pyx_r = __pyx_pf_5numpy_7ndarray___getbuffer__(((PyArrayObject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info), ((int)__pyx_v_flags)); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "numpy.pxd":194 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< * # This implementation of getbuffer is geared towards Cython * # requirements, and does not yet fullfill the PEP. */ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) { int __pyx_v_copy_shape; int __pyx_v_i; int __pyx_v_ndim; int __pyx_v_endian_detector; int __pyx_v_little_endian; int __pyx_v_t; char *__pyx_v_f; PyArray_Descr *__pyx_v_descr = 0; int __pyx_v_offset; int __pyx_v_hasfields; int __pyx_r; __Pyx_RefNannyDeclarations int __pyx_t_1; int __pyx_t_2; int __pyx_t_3; PyObject *__pyx_t_4 = NULL; int __pyx_t_5; int __pyx_t_6; int __pyx_t_7; PyObject *__pyx_t_8 = NULL; char *__pyx_t_9; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__getbuffer__", 0); if (__pyx_v_info != NULL) { __pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None); __Pyx_GIVEREF(__pyx_v_info->obj); } /* "numpy.pxd":200 * # of flags * * if info == NULL: return # <<<<<<<<<<<<<< * * cdef int copy_shape, i, ndim */ __pyx_t_1 = ((__pyx_v_info == NULL) != 0); if (__pyx_t_1) { __pyx_r = 0; goto __pyx_L0; goto __pyx_L3; } __pyx_L3:; /* "numpy.pxd":203 * * cdef int copy_shape, i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< * cdef bint little_endian = ((&endian_detector)[0] != 0) * */ __pyx_v_endian_detector = 1; /* "numpy.pxd":204 * cdef int copy_shape, i, ndim * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< * * ndim = PyArray_NDIM(self) */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); /* "numpy.pxd":206 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< * * if sizeof(npy_intp) != sizeof(Py_ssize_t): */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); /* "numpy.pxd":208 * ndim = PyArray_NDIM(self) * * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< * copy_shape = 1 * else: */ __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { /* "numpy.pxd":209 * * if sizeof(npy_intp) != sizeof(Py_ssize_t): * copy_shape = 1 # <<<<<<<<<<<<<< * else: * copy_shape = 0 */ __pyx_v_copy_shape = 1; goto __pyx_L4; } /*else*/ { /* "numpy.pxd":211 * copy_shape = 1 * else: * copy_shape = 0 # <<<<<<<<<<<<<< * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) */ __pyx_v_copy_shape = 0; } __pyx_L4:; /* "numpy.pxd":213 * copy_shape = 0 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") */ __pyx_t_1 = (((__pyx_v_flags & PyBUF_C_CONTIGUOUS) == PyBUF_C_CONTIGUOUS) != 0); if (__pyx_t_1) { /* "numpy.pxd":214 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< * raise ValueError(u"ndarray is not C contiguous") * */ __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS) != 0)) != 0); __pyx_t_3 = __pyx_t_2; } else { __pyx_t_3 = __pyx_t_1; } if (__pyx_t_3) { /* "numpy.pxd":215 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) */ __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L5; } __pyx_L5:; /* "numpy.pxd":217 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") */ __pyx_t_3 = (((__pyx_v_flags & PyBUF_F_CONTIGUOUS) == PyBUF_F_CONTIGUOUS) != 0); if (__pyx_t_3) { /* "numpy.pxd":218 * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< * raise ValueError(u"ndarray is not Fortran contiguous") * */ __pyx_t_1 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0); __pyx_t_2 = __pyx_t_1; } else { __pyx_t_2 = __pyx_t_3; } if (__pyx_t_2) { /* "numpy.pxd":219 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< * * info.buf = PyArray_DATA(self) */ __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_4), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L6; } __pyx_L6:; /* "numpy.pxd":221 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< * info.ndim = ndim * if copy_shape: */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); /* "numpy.pxd":222 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< * if copy_shape: * # Allocate new buffer for strides and shape info. */ __pyx_v_info->ndim = __pyx_v_ndim; /* "numpy.pxd":223 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if copy_shape: # <<<<<<<<<<<<<< * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. */ __pyx_t_2 = (__pyx_v_copy_shape != 0); if (__pyx_t_2) { /* "numpy.pxd":226 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) # <<<<<<<<<<<<<< * info.shape = info.strides + ndim * for i in range(ndim): */ __pyx_v_info->strides = ((Py_ssize_t *)malloc((((sizeof(Py_ssize_t)) * ((size_t)__pyx_v_ndim)) * 2))); /* "numpy.pxd":227 * # This is allocated as one block, strides first. * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); /* "numpy.pxd":228 * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] */ __pyx_t_5 = __pyx_v_ndim; for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_i = __pyx_t_6; /* "numpy.pxd":229 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< * info.shape[i] = PyArray_DIMS(self)[i] * else: */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); /* "numpy.pxd":230 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< * else: * info.strides = PyArray_STRIDES(self) */ (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } goto __pyx_L7; } /*else*/ { /* "numpy.pxd":232 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL */ __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); /* "numpy.pxd":233 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) */ __pyx_v_info->shape = ((Py_ssize_t *)PyArray_DIMS(__pyx_v_self)); } __pyx_L7:; /* "numpy.pxd":234 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) */ __pyx_v_info->suboffsets = NULL; /* "numpy.pxd":235 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< * info.readonly = not PyArray_ISWRITEABLE(self) * */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); /* "numpy.pxd":236 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< * * cdef int t */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); /* "numpy.pxd":239 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< * cdef dtype descr = self.descr * cdef list stack */ __pyx_v_f = NULL; /* "numpy.pxd":240 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< * cdef list stack * cdef int offset */ __pyx_t_4 = ((PyObject *)__pyx_v_self->descr); __Pyx_INCREF(__pyx_t_4); __pyx_v_descr = ((PyArray_Descr *)__pyx_t_4); __pyx_t_4 = 0; /* "numpy.pxd":244 * cdef int offset * * cdef bint hasfields = PyDataType_HASFIELDS(descr) # <<<<<<<<<<<<<< * * if not hasfields and not copy_shape: */ __pyx_v_hasfields = PyDataType_HASFIELDS(__pyx_v_descr); /* "numpy.pxd":246 * cdef bint hasfields = PyDataType_HASFIELDS(descr) * * if not hasfields and not copy_shape: # <<<<<<<<<<<<<< * # do not call releasebuffer * info.obj = None */ __pyx_t_2 = ((!(__pyx_v_hasfields != 0)) != 0); if (__pyx_t_2) { __pyx_t_3 = ((!(__pyx_v_copy_shape != 0)) != 0); __pyx_t_1 = __pyx_t_3; } else { __pyx_t_1 = __pyx_t_2; } if (__pyx_t_1) { /* "numpy.pxd":248 * if not hasfields and not copy_shape: * # do not call releasebuffer * info.obj = None # <<<<<<<<<<<<<< * else: * # need to call releasebuffer */ __Pyx_INCREF(Py_None); __Pyx_GIVEREF(Py_None); __Pyx_GOTREF(__pyx_v_info->obj); __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = Py_None; goto __pyx_L10; } /*else*/ { /* "numpy.pxd":251 * else: * # need to call releasebuffer * info.obj = self # <<<<<<<<<<<<<< * * if not hasfields: */ __Pyx_INCREF(((PyObject *)__pyx_v_self)); __Pyx_GIVEREF(((PyObject *)__pyx_v_self)); __Pyx_GOTREF(__pyx_v_info->obj); __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = ((PyObject *)__pyx_v_self); } __pyx_L10:; /* "numpy.pxd":253 * info.obj = self * * if not hasfields: # <<<<<<<<<<<<<< * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or */ __pyx_t_1 = ((!(__pyx_v_hasfields != 0)) != 0); if (__pyx_t_1) { /* "numpy.pxd":254 * * if not hasfields: * t = descr.type_num # <<<<<<<<<<<<<< * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): */ __pyx_t_5 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_5; /* "numpy.pxd":255 * if not hasfields: * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") */ __pyx_t_1 = ((__pyx_v_descr->byteorder == '>') != 0); if (__pyx_t_1) { __pyx_t_2 = (__pyx_v_little_endian != 0); } else { __pyx_t_2 = __pyx_t_1; } if (!__pyx_t_2) { /* "numpy.pxd":256 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" */ __pyx_t_1 = ((__pyx_v_descr->byteorder == '<') != 0); if (__pyx_t_1) { __pyx_t_3 = ((!(__pyx_v_little_endian != 0)) != 0); __pyx_t_7 = __pyx_t_3; } else { __pyx_t_7 = __pyx_t_1; } __pyx_t_1 = __pyx_t_7; } else { __pyx_t_1 = __pyx_t_2; } if (__pyx_t_1) { /* "numpy.pxd":257 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" */ __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_6), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L12; } __pyx_L12:; /* "numpy.pxd":274 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) */ switch (__pyx_v_t) { /* "numpy.pxd":258 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" */ case NPY_BYTE: __pyx_v_f = __pyx_k__b; break; /* "numpy.pxd":259 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" */ case NPY_UBYTE: __pyx_v_f = __pyx_k__B; break; /* "numpy.pxd":260 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" */ case NPY_SHORT: __pyx_v_f = __pyx_k__h; break; /* "numpy.pxd":261 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" */ case NPY_USHORT: __pyx_v_f = __pyx_k__H; break; /* "numpy.pxd":262 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" */ case NPY_INT: __pyx_v_f = __pyx_k__i; break; /* "numpy.pxd":263 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" */ case NPY_UINT: __pyx_v_f = __pyx_k__I; break; /* "numpy.pxd":264 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" */ case NPY_LONG: __pyx_v_f = __pyx_k__l; break; /* "numpy.pxd":265 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" */ case NPY_ULONG: __pyx_v_f = __pyx_k__L; break; /* "numpy.pxd":266 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" */ case NPY_LONGLONG: __pyx_v_f = __pyx_k__q; break; /* "numpy.pxd":267 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" */ case NPY_ULONGLONG: __pyx_v_f = __pyx_k__Q; break; /* "numpy.pxd":268 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" */ case NPY_FLOAT: __pyx_v_f = __pyx_k__f; break; /* "numpy.pxd":269 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" */ case NPY_DOUBLE: __pyx_v_f = __pyx_k__d; break; /* "numpy.pxd":270 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" */ case NPY_LONGDOUBLE: __pyx_v_f = __pyx_k__g; break; /* "numpy.pxd":271 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" */ case NPY_CFLOAT: __pyx_v_f = __pyx_k__Zf; break; /* "numpy.pxd":272 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" */ case NPY_CDOUBLE: __pyx_v_f = __pyx_k__Zd; break; /* "numpy.pxd":273 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< * elif t == NPY_OBJECT: f = "O" * else: */ case NPY_CLONGDOUBLE: __pyx_v_f = __pyx_k__Zg; break; /* "numpy.pxd":274 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) */ case NPY_OBJECT: __pyx_v_f = __pyx_k__O; break; default: /* "numpy.pxd":276 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< * info.format = f * return */ __pyx_t_4 = PyInt_FromLong(__pyx_v_t); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_u_7), __pyx_t_4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_8)); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_8)); __Pyx_GIVEREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0; __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_8); __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0; __Pyx_Raise(__pyx_t_8, 0, 0, 0); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;} break; } /* "numpy.pxd":277 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< * return * else: */ __pyx_v_info->format = __pyx_v_f; /* "numpy.pxd":278 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< * else: * info.format = stdlib.malloc(_buffer_format_string_len) */ __pyx_r = 0; goto __pyx_L0; goto __pyx_L11; } /*else*/ { /* "numpy.pxd":280 * return * else: * info.format = stdlib.malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 */ __pyx_v_info->format = ((char *)malloc(255)); /* "numpy.pxd":281 * else: * info.format = stdlib.malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< * offset = 0 * f = _util_dtypestring(descr, info.format + 1, */ (__pyx_v_info->format[0]) = '^'; /* "numpy.pxd":282 * info.format = stdlib.malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< * f = _util_dtypestring(descr, info.format + 1, * info.format + _buffer_format_string_len, */ __pyx_v_offset = 0; /* "numpy.pxd":285 * f = _util_dtypestring(descr, info.format + 1, * info.format + _buffer_format_string_len, * &offset) # <<<<<<<<<<<<<< * f[0] = c'\0' # Terminate format string * */ __pyx_t_9 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 255), (&__pyx_v_offset)); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_f = __pyx_t_9; /* "numpy.pxd":286 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< * * def __releasebuffer__(ndarray self, Py_buffer* info): */ (__pyx_v_f[0]) = '\x00'; } __pyx_L11:; __pyx_r = 0; goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_8); __Pyx_AddTraceback("numpy.ndarray.__getbuffer__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = -1; if (__pyx_v_info != NULL && __pyx_v_info->obj != NULL) { __Pyx_GOTREF(__pyx_v_info->obj); __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = NULL; } goto __pyx_L2; __pyx_L0:; if (__pyx_v_info != NULL && __pyx_v_info->obj == Py_None) { __Pyx_GOTREF(Py_None); __Pyx_DECREF(Py_None); __pyx_v_info->obj = NULL; } __pyx_L2:; __Pyx_XDECREF((PyObject *)__pyx_v_descr); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* Python wrapper */ static CYTHON_UNUSED void __pyx_pw_5numpy_7ndarray_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info); /*proto*/ static CYTHON_UNUSED void __pyx_pw_5numpy_7ndarray_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__releasebuffer__ (wrapper)", 0); __pyx_pf_5numpy_7ndarray_2__releasebuffer__(((PyArrayObject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info)); __Pyx_RefNannyFinishContext(); } /* "numpy.pxd":288 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< * if PyArray_HASFIELDS(self): * stdlib.free(info.format) */ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info) { __Pyx_RefNannyDeclarations int __pyx_t_1; __Pyx_RefNannySetupContext("__releasebuffer__", 0); /* "numpy.pxd":289 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< * stdlib.free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): */ __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); if (__pyx_t_1) { /* "numpy.pxd":290 * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): * stdlib.free(info.format) # <<<<<<<<<<<<<< * if sizeof(npy_intp) != sizeof(Py_ssize_t): * stdlib.free(info.strides) */ free(__pyx_v_info->format); goto __pyx_L3; } __pyx_L3:; /* "numpy.pxd":291 * if PyArray_HASFIELDS(self): * stdlib.free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< * stdlib.free(info.strides) * # info.shape was stored after info.strides in the same block */ __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { /* "numpy.pxd":292 * stdlib.free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): * stdlib.free(info.strides) # <<<<<<<<<<<<<< * # info.shape was stored after info.strides in the same block * */ free(__pyx_v_info->strides); goto __pyx_L4; } __pyx_L4:; __Pyx_RefNannyFinishContext(); } /* "numpy.pxd":768 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(1, a) * */ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__pyx_v_a) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 0); /* "numpy.pxd":769 * * cdef inline object PyArray_MultiIterNew1(a): * return PyArray_MultiIterNew(1, a) # <<<<<<<<<<<<<< * * cdef inline object PyArray_MultiIterNew2(a, b): */ __Pyx_XDECREF(__pyx_r); __pyx_t_1 = PyArray_MultiIterNew(1, ((void *)__pyx_v_a)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_AddTraceback("numpy.PyArray_MultiIterNew1", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "numpy.pxd":771 * return PyArray_MultiIterNew(1, a) * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(2, a, b) * */ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__pyx_v_a, PyObject *__pyx_v_b) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew2", 0); /* "numpy.pxd":772 * * cdef inline object PyArray_MultiIterNew2(a, b): * return PyArray_MultiIterNew(2, a, b) # <<<<<<<<<<<<<< * * cdef inline object PyArray_MultiIterNew3(a, b, c): */ __Pyx_XDECREF(__pyx_r); __pyx_t_1 = PyArray_MultiIterNew(2, ((void *)__pyx_v_a), ((void *)__pyx_v_b)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_AddTraceback("numpy.PyArray_MultiIterNew2", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "numpy.pxd":774 * return PyArray_MultiIterNew(2, a, b) * * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(3, a, b, c) * */ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew3", 0); /* "numpy.pxd":775 * * cdef inline object PyArray_MultiIterNew3(a, b, c): * return PyArray_MultiIterNew(3, a, b, c) # <<<<<<<<<<<<<< * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): */ __Pyx_XDECREF(__pyx_r); __pyx_t_1 = PyArray_MultiIterNew(3, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_AddTraceback("numpy.PyArray_MultiIterNew3", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "numpy.pxd":777 * return PyArray_MultiIterNew(3, a, b, c) * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(4, a, b, c, d) * */ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew4", 0); /* "numpy.pxd":778 * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): * return PyArray_MultiIterNew(4, a, b, c, d) # <<<<<<<<<<<<<< * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): */ __Pyx_XDECREF(__pyx_r); __pyx_t_1 = PyArray_MultiIterNew(4, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_AddTraceback("numpy.PyArray_MultiIterNew4", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "numpy.pxd":780 * return PyArray_MultiIterNew(4, a, b, c, d) * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< * return PyArray_MultiIterNew(5, a, b, c, d, e) * */ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__pyx_v_a, PyObject *__pyx_v_b, PyObject *__pyx_v_c, PyObject *__pyx_v_d, PyObject *__pyx_v_e) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew5", 0); /* "numpy.pxd":781 * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): * return PyArray_MultiIterNew(5, a, b, c, d, e) # <<<<<<<<<<<<<< * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: */ __Pyx_XDECREF(__pyx_r); __pyx_t_1 = PyArray_MultiIterNew(5, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d), ((void *)__pyx_v_e)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; __pyx_r = Py_None; __Pyx_INCREF(Py_None); goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_AddTraceback("numpy.PyArray_MultiIterNew5", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "numpy.pxd":783 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< * # Recursive utility function used in __getbuffer__ to get format * # string. The new location in the format string is returned. */ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx_v_descr, char *__pyx_v_f, char *__pyx_v_end, int *__pyx_v_offset) { PyArray_Descr *__pyx_v_child = 0; int __pyx_v_endian_detector; int __pyx_v_little_endian; PyObject *__pyx_v_fields = 0; PyObject *__pyx_v_childname = NULL; PyObject *__pyx_v_new_offset = NULL; PyObject *__pyx_v_t = NULL; char *__pyx_r; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; Py_ssize_t __pyx_t_2; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; PyObject *__pyx_t_5 = NULL; PyObject *(*__pyx_t_6)(PyObject *); int __pyx_t_7; int __pyx_t_8; int __pyx_t_9; int __pyx_t_10; long __pyx_t_11; char *__pyx_t_12; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("_util_dtypestring", 0); /* "numpy.pxd":790 * cdef int delta_offset * cdef tuple i * cdef int endian_detector = 1 # <<<<<<<<<<<<<< * cdef bint little_endian = ((&endian_detector)[0] != 0) * cdef tuple fields */ __pyx_v_endian_detector = 1; /* "numpy.pxd":791 * cdef tuple i * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< * cdef tuple fields * */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); /* "numpy.pxd":794 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< * fields = descr.fields[childname] * child, new_offset = fields */ if (unlikely(((PyObject *)__pyx_v_descr->names) == Py_None)) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_1 = ((PyObject *)__pyx_v_descr->names); __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0; for (;;) { if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break; #if CYTHON_COMPILING_IN_CPYTHON __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif __Pyx_XDECREF(__pyx_v_childname); __pyx_v_childname = __pyx_t_3; __pyx_t_3 = 0; /* "numpy.pxd":795 * * for childname in descr.names: * fields = descr.fields[childname] # <<<<<<<<<<<<<< * child, new_offset = fields * */ __pyx_t_3 = PyObject_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (!__pyx_t_3) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); if (!(likely(PyTuple_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected tuple, got %.200s", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_XDECREF(((PyObject *)__pyx_v_fields)); __pyx_v_fields = ((PyObject*)__pyx_t_3); __pyx_t_3 = 0; /* "numpy.pxd":796 * for childname in descr.names: * fields = descr.fields[childname] * child, new_offset = fields # <<<<<<<<<<<<<< * * if (end - f) - (new_offset - offset[0]) < 15: */ if (likely(PyTuple_CheckExact(((PyObject *)__pyx_v_fields)))) { PyObject* sequence = ((PyObject *)__pyx_v_fields); #if CYTHON_COMPILING_IN_CPYTHON Py_ssize_t size = Py_SIZE(sequence); #else Py_ssize_t size = PySequence_Size(sequence); #endif if (unlikely(size != 2)) { if (size > 2) __Pyx_RaiseTooManyValuesError(2); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON __pyx_t_3 = PyTuple_GET_ITEM(sequence, 0); __pyx_t_4 = PyTuple_GET_ITEM(sequence, 1); __Pyx_INCREF(__pyx_t_3); __Pyx_INCREF(__pyx_t_4); #else __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); #endif } else if (1) { __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } else { Py_ssize_t index = -1; __pyx_t_5 = PyObject_GetIter(((PyObject *)__pyx_v_fields)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_6 = Py_TYPE(__pyx_t_5)->tp_iternext; index = 0; __pyx_t_3 = __pyx_t_6(__pyx_t_5); if (unlikely(!__pyx_t_3)) goto __pyx_L5_unpacking_failed; __Pyx_GOTREF(__pyx_t_3); index = 1; __pyx_t_4 = __pyx_t_6(__pyx_t_5); if (unlikely(!__pyx_t_4)) goto __pyx_L5_unpacking_failed; __Pyx_GOTREF(__pyx_t_4); if (__Pyx_IternextUnpackEndCheck(__pyx_t_6(__pyx_t_5), 2) < 0) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_6 = NULL; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; goto __pyx_L6_unpacking_done; __pyx_L5_unpacking_failed:; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_6 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L6_unpacking_done:; } if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_dtype))))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_XDECREF(((PyObject *)__pyx_v_child)); __pyx_v_child = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; __Pyx_XDECREF(__pyx_v_new_offset); __pyx_v_new_offset = __pyx_t_4; __pyx_t_4 = 0; /* "numpy.pxd":798 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * */ __pyx_t_4 = PyInt_FromLong((__pyx_v_end - __pyx_v_f)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_t_3 = PyInt_FromLong((__pyx_v_offset[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_5 = PyNumber_Subtract(__pyx_v_new_offset, __pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_3 = PyNumber_Subtract(__pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_5 = PyObject_RichCompare(__pyx_t_3, __pyx_int_15, Py_LT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_7) { /* "numpy.pxd":799 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< * * if ((child.byteorder == c'>' and little_endian) or */ __pyx_t_5 = PyObject_Call(__pyx_builtin_RuntimeError, ((PyObject *)__pyx_k_tuple_9), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_Raise(__pyx_t_5, 0, 0, 0); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L7; } __pyx_L7:; /* "numpy.pxd":801 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") */ __pyx_t_7 = ((__pyx_v_child->byteorder == '>') != 0); if (__pyx_t_7) { __pyx_t_8 = (__pyx_v_little_endian != 0); } else { __pyx_t_8 = __pyx_t_7; } if (!__pyx_t_8) { /* "numpy.pxd":802 * * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< * raise ValueError(u"Non-native byte order not supported") * # One could encode it in the format string and have Cython */ __pyx_t_7 = ((__pyx_v_child->byteorder == '<') != 0); if (__pyx_t_7) { __pyx_t_9 = ((!(__pyx_v_little_endian != 0)) != 0); __pyx_t_10 = __pyx_t_9; } else { __pyx_t_10 = __pyx_t_7; } __pyx_t_7 = __pyx_t_10; } else { __pyx_t_7 = __pyx_t_8; } if (__pyx_t_7) { /* "numpy.pxd":803 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * # One could encode it in the format string and have Cython * # complain instead, BUT: < and > in format strings also imply */ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_10), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_Raise(__pyx_t_5, 0, 0, 0); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L8; } __pyx_L8:; /* "numpy.pxd":813 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< * f[0] = 120 # "x"; pad byte * f += 1 */ while (1) { __pyx_t_5 = PyInt_FromLong((__pyx_v_offset[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_3 = PyObject_RichCompare(__pyx_t_5, __pyx_v_new_offset, Py_LT); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (!__pyx_t_7) break; /* "numpy.pxd":814 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< * f += 1 * offset[0] += 1 */ (__pyx_v_f[0]) = 120; /* "numpy.pxd":815 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< * offset[0] += 1 * */ __pyx_v_f = (__pyx_v_f + 1); /* "numpy.pxd":816 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< * * offset[0] += child.itemsize */ __pyx_t_11 = 0; (__pyx_v_offset[__pyx_t_11]) = ((__pyx_v_offset[__pyx_t_11]) + 1); } /* "numpy.pxd":818 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< * * if not PyDataType_HASFIELDS(child): */ __pyx_t_11 = 0; (__pyx_v_offset[__pyx_t_11]) = ((__pyx_v_offset[__pyx_t_11]) + __pyx_v_child->elsize); /* "numpy.pxd":820 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< * t = child.type_num * if end - f < 5: */ __pyx_t_7 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_7) { /* "numpy.pxd":821 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") */ __pyx_t_3 = PyInt_FromLong(__pyx_v_child->type_num); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_XDECREF(__pyx_v_t); __pyx_v_t = __pyx_t_3; __pyx_t_3 = 0; /* "numpy.pxd":822 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< * raise RuntimeError(u"Format string allocated too short.") * */ __pyx_t_7 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (__pyx_t_7) { /* "numpy.pxd":823 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< * * # Until ticket #99 is fixed, use integers to avoid warnings */ __pyx_t_3 = PyObject_Call(__pyx_builtin_RuntimeError, ((PyObject *)__pyx_k_tuple_12), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} goto __pyx_L12; } __pyx_L12:; /* "numpy.pxd":826 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" */ __pyx_t_3 = PyInt_FromLong(NPY_BYTE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 98; goto __pyx_L13; } /* "numpy.pxd":827 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" */ __pyx_t_5 = PyInt_FromLong(NPY_UBYTE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 66; goto __pyx_L13; } /* "numpy.pxd":828 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" */ __pyx_t_3 = PyInt_FromLong(NPY_SHORT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 104; goto __pyx_L13; } /* "numpy.pxd":829 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" */ __pyx_t_5 = PyInt_FromLong(NPY_USHORT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 72; goto __pyx_L13; } /* "numpy.pxd":830 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" */ __pyx_t_3 = PyInt_FromLong(NPY_INT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 105; goto __pyx_L13; } /* "numpy.pxd":831 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" */ __pyx_t_5 = PyInt_FromLong(NPY_UINT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 73; goto __pyx_L13; } /* "numpy.pxd":832 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" */ __pyx_t_3 = PyInt_FromLong(NPY_LONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 108; goto __pyx_L13; } /* "numpy.pxd":833 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" */ __pyx_t_5 = PyInt_FromLong(NPY_ULONG); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 76; goto __pyx_L13; } /* "numpy.pxd":834 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" */ __pyx_t_3 = PyInt_FromLong(NPY_LONGLONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 113; goto __pyx_L13; } /* "numpy.pxd":835 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" */ __pyx_t_5 = PyInt_FromLong(NPY_ULONGLONG); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 81; goto __pyx_L13; } /* "numpy.pxd":836 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" */ __pyx_t_3 = PyInt_FromLong(NPY_FLOAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 102; goto __pyx_L13; } /* "numpy.pxd":837 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf */ __pyx_t_5 = PyInt_FromLong(NPY_DOUBLE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 100; goto __pyx_L13; } /* "numpy.pxd":838 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd */ __pyx_t_3 = PyInt_FromLong(NPY_LONGDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 103; goto __pyx_L13; } /* "numpy.pxd":839 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg */ __pyx_t_5 = PyInt_FromLong(NPY_CFLOAT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 90; (__pyx_v_f[1]) = 102; __pyx_v_f = (__pyx_v_f + 1); goto __pyx_L13; } /* "numpy.pxd":840 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" */ __pyx_t_3 = PyInt_FromLong(NPY_CDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 90; (__pyx_v_f[1]) = 100; __pyx_v_f = (__pyx_v_f + 1); goto __pyx_L13; } /* "numpy.pxd":841 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: */ __pyx_t_5 = PyInt_FromLong(NPY_CLONGDOUBLE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 90; (__pyx_v_f[1]) = 103; __pyx_v_f = (__pyx_v_f + 1); goto __pyx_L13; } /* "numpy.pxd":842 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) */ __pyx_t_3 = PyInt_FromLong(NPY_OBJECT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (__pyx_t_7) { (__pyx_v_f[0]) = 79; goto __pyx_L13; } /*else*/ { /* "numpy.pxd":844 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< * f += 1 * else: */ __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_u_7), __pyx_v_t); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_5)); __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_5)); __Pyx_GIVEREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0; __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; __Pyx_Raise(__pyx_t_5, 0, 0, 0); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_L13:; /* "numpy.pxd":845 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * f += 1 # <<<<<<<<<<<<<< * else: * # Cython ignores struct boundary information ("T{...}"), */ __pyx_v_f = (__pyx_v_f + 1); goto __pyx_L11; } /*else*/ { /* "numpy.pxd":849 * # Cython ignores struct boundary information ("T{...}"), * # so don't output it * f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<< * return f * */ __pyx_t_12 = __pyx_f_5numpy__util_dtypestring(__pyx_v_child, __pyx_v_f, __pyx_v_end, __pyx_v_offset); if (unlikely(__pyx_t_12 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_f = __pyx_t_12; } __pyx_L11:; } __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; /* "numpy.pxd":850 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< * * */ __pyx_r = __pyx_v_f; goto __pyx_L0; __pyx_r = 0; goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); __Pyx_XDECREF(__pyx_t_5); __Pyx_AddTraceback("numpy._util_dtypestring", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = NULL; __pyx_L0:; __Pyx_XDECREF((PyObject *)__pyx_v_child); __Pyx_XDECREF(__pyx_v_fields); __Pyx_XDECREF(__pyx_v_childname); __Pyx_XDECREF(__pyx_v_new_offset); __Pyx_XDECREF(__pyx_v_t); __Pyx_RefNannyFinishContext(); return __pyx_r; } /* "numpy.pxd":965 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< * cdef PyObject* baseptr * if base is None: */ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_arr, PyObject *__pyx_v_base) { PyObject *__pyx_v_baseptr; __Pyx_RefNannyDeclarations int __pyx_t_1; int __pyx_t_2; __Pyx_RefNannySetupContext("set_array_base", 0); /* "numpy.pxd":967 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< * baseptr = NULL * else: */ __pyx_t_1 = (__pyx_v_base == Py_None); __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { /* "numpy.pxd":968 * cdef PyObject* baseptr * if base is None: * baseptr = NULL # <<<<<<<<<<<<<< * else: * Py_INCREF(base) # important to do this before decref below! */ __pyx_v_baseptr = NULL; goto __pyx_L3; } /*else*/ { /* "numpy.pxd":970 * baseptr = NULL * else: * Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<< * baseptr = base * Py_XDECREF(arr.base) */ Py_INCREF(__pyx_v_base); /* "numpy.pxd":971 * else: * Py_INCREF(base) # important to do this before decref below! * baseptr = base # <<<<<<<<<<<<<< * Py_XDECREF(arr.base) * arr.base = baseptr */ __pyx_v_baseptr = ((PyObject *)__pyx_v_base); } __pyx_L3:; /* "numpy.pxd":972 * Py_INCREF(base) # important to do this before decref below! * baseptr = base * Py_XDECREF(arr.base) # <<<<<<<<<<<<<< * arr.base = baseptr * */ Py_XDECREF(__pyx_v_arr->base); /* "numpy.pxd":973 * baseptr = base * Py_XDECREF(arr.base) * arr.base = baseptr # <<<<<<<<<<<<<< * * cdef inline object get_array_base(ndarray arr): */ __pyx_v_arr->base = __pyx_v_baseptr; __Pyx_RefNannyFinishContext(); } /* "numpy.pxd":975 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< * if arr.base is NULL: * return None */ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__pyx_v_arr) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations int __pyx_t_1; __Pyx_RefNannySetupContext("get_array_base", 0); /* "numpy.pxd":976 * * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: # <<<<<<<<<<<<<< * return None * else: */ __pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0); if (__pyx_t_1) { /* "numpy.pxd":977 * cdef inline object get_array_base(ndarray arr): * if arr.base is NULL: * return None # <<<<<<<<<<<<<< * else: * return arr.base */ __Pyx_XDECREF(__pyx_r); __Pyx_INCREF(Py_None); __pyx_r = Py_None; goto __pyx_L0; goto __pyx_L3; } /*else*/ { /* "numpy.pxd":979 * return None * else: * return arr.base # <<<<<<<<<<<<<< */ __Pyx_XDECREF(__pyx_r); __Pyx_INCREF(((PyObject *)__pyx_v_arr->base)); __pyx_r = ((PyObject *)__pyx_v_arr->base); goto __pyx_L0; } __pyx_L3:; __pyx_r = Py_None; __Pyx_INCREF(Py_None); __pyx_L0:; __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } static struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Asym __pyx_vtable_5MACS2_7Poisson_LogLR_Asym; static PyObject *__pyx_tp_new_5MACS2_7Poisson_LogLR_Asym(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *p; PyObject *o; o = (*t->tp_alloc)(t, 0); if (unlikely(!o)) return 0; p = ((struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *)o); p->__pyx_vtab = __pyx_vtabptr_5MACS2_7Poisson_LogLR_Asym; if (unlikely(__pyx_pw_5MACS2_7Poisson_10LogLR_Asym_3__cinit__(o, __pyx_empty_tuple, NULL) < 0)) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5MACS2_7Poisson_LogLR_Asym(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5MACS2_7Poisson_10LogLR_Asym_5__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } (*Py_TYPE(o)->tp_free)(o); } static PyMethodDef __pyx_methods_5MACS2_7Poisson_LogLR_Asym[] = { {__Pyx_NAMESTR("check_cache"), (PyCFunction)__pyx_pw_5MACS2_7Poisson_10LogLR_Asym_7check_cache, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5MACS2_7Poisson_10LogLR_Asym_6check_cache)}, {__Pyx_NAMESTR("get_logLR_asym"), (PyCFunction)__pyx_pw_5MACS2_7Poisson_10LogLR_Asym_9get_logLR_asym, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; static PyTypeObject __pyx_type_5MACS2_7Poisson_LogLR_Asym = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("MACS2.Poisson.LogLR_Asym"), /*tp_name*/ sizeof(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5MACS2_7Poisson_LogLR_Asym, /*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, /*tp_flags*/ __Pyx_DOCSTR("Unit to calculate asymmetric log likelihood, and cache\n results in a hashtable.\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5MACS2_7Poisson_LogLR_Asym, /*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_5MACS2_7Poisson_10LogLR_Asym_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5MACS2_7Poisson_LogLR_Asym, /*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*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5MACS2_7Poisson_P_Score_Upper_Tail __pyx_vtable_5MACS2_7Poisson_P_Score_Upper_Tail; static PyObject *__pyx_tp_new_5MACS2_7Poisson_P_Score_Upper_Tail(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *p; PyObject *o; o = (*t->tp_alloc)(t, 0); if (unlikely(!o)) return 0; p = ((struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *)o); p->__pyx_vtab = __pyx_vtabptr_5MACS2_7Poisson_P_Score_Upper_Tail; if (unlikely(__pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_3__cinit__(o, __pyx_empty_tuple, NULL) < 0)) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5MACS2_7Poisson_P_Score_Upper_Tail(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_5__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } (*Py_TYPE(o)->tp_free)(o); } static PyMethodDef __pyx_methods_5MACS2_7Poisson_P_Score_Upper_Tail[] = { {__Pyx_NAMESTR("check_cache"), (PyCFunction)__pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_7check_cache, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5MACS2_7Poisson_18P_Score_Upper_Tail_6check_cache)}, {__Pyx_NAMESTR("get_pscore"), (PyCFunction)__pyx_pw_5MACS2_7Poisson_18P_Score_Upper_Tail_9get_pscore, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; static PyTypeObject __pyx_type_5MACS2_7Poisson_P_Score_Upper_Tail = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("MACS2.Poisson.P_Score_Upper_Tail"), /*tp_name*/ sizeof(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5MACS2_7Poisson_P_Score_Upper_Tail, /*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, /*tp_flags*/ __Pyx_DOCSTR("Unit to calculate -log10 poisson_CDF of upper tail and cache\n results in a hashtable.\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5MACS2_7Poisson_P_Score_Upper_Tail, /*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_5MACS2_7Poisson_18P_Score_Upper_Tail_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5MACS2_7Poisson_P_Score_Upper_Tail, /*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*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Diff __pyx_vtable_5MACS2_7Poisson_LogLR_Diff; static PyObject *__pyx_tp_new_5MACS2_7Poisson_LogLR_Diff(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *p; PyObject *o; o = (*t->tp_alloc)(t, 0); if (unlikely(!o)) return 0; p = ((struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *)o); p->__pyx_vtab = __pyx_vtabptr_5MACS2_7Poisson_LogLR_Diff; if (unlikely(__pyx_pw_5MACS2_7Poisson_10LogLR_Diff_3__cinit__(o, __pyx_empty_tuple, NULL) < 0)) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5MACS2_7Poisson_LogLR_Diff(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5MACS2_7Poisson_10LogLR_Diff_5__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } (*Py_TYPE(o)->tp_free)(o); } static PyMethodDef __pyx_methods_5MACS2_7Poisson_LogLR_Diff[] = { {__Pyx_NAMESTR("check_cache"), (PyCFunction)__pyx_pw_5MACS2_7Poisson_10LogLR_Diff_7check_cache, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5MACS2_7Poisson_10LogLR_Diff_6check_cache)}, {__Pyx_NAMESTR("get_logLR_diff"), (PyCFunction)__pyx_pw_5MACS2_7Poisson_10LogLR_Diff_9get_logLR_diff, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; static PyTypeObject __pyx_type_5MACS2_7Poisson_LogLR_Diff = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("MACS2.Poisson.LogLR_Diff"), /*tp_name*/ sizeof(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5MACS2_7Poisson_LogLR_Diff, /*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, /*tp_flags*/ __Pyx_DOCSTR("Unit to calculate log likelihood for differential calling, and cache\n results in a hashtable.\n\n here f(x,y) = f(y,x) and f() is always positive.\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5MACS2_7Poisson_LogLR_Diff, /*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_5MACS2_7Poisson_10LogLR_Diff_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5MACS2_7Poisson_LogLR_Diff, /*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*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static struct __pyx_vtabstruct_5MACS2_7Poisson_LogLR_Sym __pyx_vtable_5MACS2_7Poisson_LogLR_Sym; static PyObject *__pyx_tp_new_5MACS2_7Poisson_LogLR_Sym(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) { struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *p; PyObject *o; o = (*t->tp_alloc)(t, 0); if (unlikely(!o)) return 0; p = ((struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *)o); p->__pyx_vtab = __pyx_vtabptr_5MACS2_7Poisson_LogLR_Sym; if (unlikely(__pyx_pw_5MACS2_7Poisson_9LogLR_Sym_3__cinit__(o, __pyx_empty_tuple, NULL) < 0)) { Py_DECREF(o); o = 0; } return o; } static void __pyx_tp_dealloc_5MACS2_7Poisson_LogLR_Sym(PyObject *o) { { PyObject *etype, *eval, *etb; PyErr_Fetch(&etype, &eval, &etb); ++Py_REFCNT(o); __pyx_pw_5MACS2_7Poisson_9LogLR_Sym_5__dealloc__(o); if (PyErr_Occurred()) PyErr_WriteUnraisable(o); --Py_REFCNT(o); PyErr_Restore(etype, eval, etb); } (*Py_TYPE(o)->tp_free)(o); } static PyMethodDef __pyx_methods_5MACS2_7Poisson_LogLR_Sym[] = { {__Pyx_NAMESTR("check_cache"), (PyCFunction)__pyx_pw_5MACS2_7Poisson_9LogLR_Sym_7check_cache, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5MACS2_7Poisson_9LogLR_Sym_6check_cache)}, {__Pyx_NAMESTR("get_logLR_sym"), (PyCFunction)__pyx_pw_5MACS2_7Poisson_9LogLR_Sym_9get_logLR_sym, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)}, {0, 0, 0, 0} }; static PyTypeObject __pyx_type_5MACS2_7Poisson_LogLR_Sym = { PyVarObject_HEAD_INIT(0, 0) __Pyx_NAMESTR("MACS2.Poisson.LogLR_Sym"), /*tp_name*/ sizeof(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym), /*tp_basicsize*/ 0, /*tp_itemsize*/ __pyx_tp_dealloc_5MACS2_7Poisson_LogLR_Sym, /*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, /*tp_flags*/ __Pyx_DOCSTR("Unit to calculate symmetric log likelihood, and cache\n results in a hashtable.\n\n \"symmetric\" means f(x,y) = -f(y,x)\n "), /*tp_doc*/ 0, /*tp_traverse*/ 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ 0, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_5MACS2_7Poisson_LogLR_Sym, /*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_5MACS2_7Poisson_9LogLR_Sym_1__init__, /*tp_init*/ 0, /*tp_alloc*/ __pyx_tp_new_5MACS2_7Poisson_LogLR_Sym, /*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*/ #if PY_VERSION_HEX >= 0x02060000 0, /*tp_version_tag*/ #endif }; static PyMethodDef __pyx_methods[] = { {0, 0, 0, 0} }; #if PY_MAJOR_VERSION >= 3 static struct PyModuleDef __pyx_moduledef = { #if PY_VERSION_HEX < 0x03020000 { PyObject_HEAD_INIT(NULL) NULL, 0, NULL }, #else PyModuleDef_HEAD_INIT, #endif __Pyx_NAMESTR("Poisson"), 0, /* m_doc */ -1, /* m_size */ __pyx_methods /* m_methods */, NULL, /* m_reload */ NULL, /* m_traverse */ NULL, /* m_clear */ NULL /* m_free */ }; #endif static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_u_1, __pyx_k_1, sizeof(__pyx_k_1), 0, 1, 0, 0}, {&__pyx_kp_u_11, __pyx_k_11, sizeof(__pyx_k_11), 0, 1, 0, 0}, {&__pyx_kp_u_3, __pyx_k_3, sizeof(__pyx_k_3), 0, 1, 0, 0}, {&__pyx_kp_u_5, __pyx_k_5, sizeof(__pyx_k_5), 0, 1, 0, 0}, {&__pyx_kp_u_7, __pyx_k_7, sizeof(__pyx_k_7), 0, 1, 0, 0}, {&__pyx_kp_u_8, __pyx_k_8, sizeof(__pyx_k_8), 0, 1, 0, 0}, {&__pyx_n_s__RuntimeError, __pyx_k__RuntimeError, sizeof(__pyx_k__RuntimeError), 0, 0, 1, 1}, {&__pyx_n_s__ValueError, __pyx_k__ValueError, sizeof(__pyx_k__ValueError), 0, 0, 1, 1}, {&__pyx_n_s____main__, __pyx_k____main__, sizeof(__pyx_k____main__), 0, 0, 1, 1}, {&__pyx_n_s____pyx_vtable__, __pyx_k____pyx_vtable__, sizeof(__pyx_k____pyx_vtable__), 0, 0, 1, 1}, {&__pyx_n_s____test__, __pyx_k____test__, sizeof(__pyx_k____test__), 0, 0, 1, 1}, {&__pyx_n_s__check_cache, __pyx_k__check_cache, sizeof(__pyx_k__check_cache), 0, 0, 1, 1}, {&__pyx_n_s__get_logLR_asym, __pyx_k__get_logLR_asym, sizeof(__pyx_k__get_logLR_asym), 0, 0, 1, 1}, {&__pyx_n_s__get_logLR_diff, __pyx_k__get_logLR_diff, sizeof(__pyx_k__get_logLR_diff), 0, 0, 1, 1}, {&__pyx_n_s__get_logLR_sym, __pyx_k__get_logLR_sym, sizeof(__pyx_k__get_logLR_sym), 0, 0, 1, 1}, {&__pyx_n_s__get_pscore, __pyx_k__get_pscore, sizeof(__pyx_k__get_pscore), 0, 0, 1, 1}, {&__pyx_n_s__l, __pyx_k__l, sizeof(__pyx_k__l), 0, 0, 1, 1}, {&__pyx_n_s__range, __pyx_k__range, sizeof(__pyx_k__range), 0, 0, 1, 1}, {&__pyx_n_s__size_hint, __pyx_k__size_hint, sizeof(__pyx_k__size_hint), 0, 0, 1, 1}, {&__pyx_n_s__x, __pyx_k__x, sizeof(__pyx_k__x), 0, 0, 1, 1}, {&__pyx_n_s__y, __pyx_k__y, sizeof(__pyx_k__y), 0, 0, 1, 1}, {0, 0, 0, 0, 0, 0, 0} }; static int __Pyx_InitCachedBuiltins(void) { __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s__range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 228; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s__RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} return 0; __pyx_L1_error:; return -1; } static int __Pyx_InitCachedConstants(void) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); /* "numpy.pxd":215 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) */ __pyx_k_tuple_2 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_u_1)); if (unlikely(!__pyx_k_tuple_2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_2); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_2)); /* "numpy.pxd":219 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< * * info.buf = PyArray_DATA(self) */ __pyx_k_tuple_4 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_u_3)); if (unlikely(!__pyx_k_tuple_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_4); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_4)); /* "numpy.pxd":257 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" */ __pyx_k_tuple_6 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_u_5)); if (unlikely(!__pyx_k_tuple_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_6); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_6)); /* "numpy.pxd":799 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< * * if ((child.byteorder == c'>' and little_endian) or */ __pyx_k_tuple_9 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_u_8)); if (unlikely(!__pyx_k_tuple_9)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_9); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_9)); /* "numpy.pxd":803 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * # One could encode it in the format string and have Cython * # complain instead, BUT: < and > in format strings also imply */ __pyx_k_tuple_10 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_u_5)); if (unlikely(!__pyx_k_tuple_10)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_10); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_10)); /* "numpy.pxd":823 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< * * # Until ticket #99 is fixed, use integers to avoid warnings */ __pyx_k_tuple_12 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_u_11)); if (unlikely(!__pyx_k_tuple_12)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_k_tuple_12); __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_12)); __Pyx_RefNannyFinishContext(); return 0; __pyx_L1_error:; __Pyx_RefNannyFinishContext(); return -1; } static int __Pyx_InitGlobals(void) { if (__Pyx_InitStrings(__pyx_string_tab) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __pyx_int_1 = PyInt_FromLong(1); if (unlikely(!__pyx_int_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; __pyx_int_15 = PyInt_FromLong(15); if (unlikely(!__pyx_int_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; return 0; __pyx_L1_error:; return -1; } #if PY_MAJOR_VERSION < 3 PyMODINIT_FUNC initPoisson(void); /*proto*/ PyMODINIT_FUNC initPoisson(void) #else PyMODINIT_FUNC PyInit_Poisson(void); /*proto*/ PyMODINIT_FUNC PyInit_Poisson(void) #endif { PyObject *__pyx_t_1 = 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_Poisson(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(__Pyx_NAMESTR("Poisson"), __pyx_methods, 0, 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); #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, "MACS2.Poisson")) { if (unlikely(PyDict_SetItemString(modules, "MACS2.Poisson", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } } #endif __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__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 (__Pyx_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_MACS2__Poisson) { if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; } /*--- 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_5MACS2_7Poisson_LogLR_Asym = &__pyx_vtable_5MACS2_7Poisson_LogLR_Asym; __pyx_vtable_5MACS2_7Poisson_LogLR_Asym.check_cache = (int (*)(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *, double, double, int __pyx_skip_dispatch))__pyx_f_5MACS2_7Poisson_10LogLR_Asym_check_cache; __pyx_vtable_5MACS2_7Poisson_LogLR_Asym.get_logLR_asym = (double (*)(struct __pyx_obj_5MACS2_7Poisson_LogLR_Asym *, double, double, int __pyx_skip_dispatch))__pyx_f_5MACS2_7Poisson_10LogLR_Asym_get_logLR_asym; if (PyType_Ready(&__pyx_type_5MACS2_7Poisson_LogLR_Asym) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetVtable(__pyx_type_5MACS2_7Poisson_LogLR_Asym.tp_dict, __pyx_vtabptr_5MACS2_7Poisson_LogLR_Asym) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "LogLR_Asym", (PyObject *)&__pyx_type_5MACS2_7Poisson_LogLR_Asym) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5MACS2_7Poisson_LogLR_Asym = &__pyx_type_5MACS2_7Poisson_LogLR_Asym; __pyx_vtabptr_5MACS2_7Poisson_P_Score_Upper_Tail = &__pyx_vtable_5MACS2_7Poisson_P_Score_Upper_Tail; __pyx_vtable_5MACS2_7Poisson_P_Score_Upper_Tail.check_cache = (int (*)(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *, int, double, int __pyx_skip_dispatch))__pyx_f_5MACS2_7Poisson_18P_Score_Upper_Tail_check_cache; __pyx_vtable_5MACS2_7Poisson_P_Score_Upper_Tail.get_pscore = (double (*)(struct __pyx_obj_5MACS2_7Poisson_P_Score_Upper_Tail *, int, double, int __pyx_skip_dispatch))__pyx_f_5MACS2_7Poisson_18P_Score_Upper_Tail_get_pscore; if (PyType_Ready(&__pyx_type_5MACS2_7Poisson_P_Score_Upper_Tail) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetVtable(__pyx_type_5MACS2_7Poisson_P_Score_Upper_Tail.tp_dict, __pyx_vtabptr_5MACS2_7Poisson_P_Score_Upper_Tail) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "P_Score_Upper_Tail", (PyObject *)&__pyx_type_5MACS2_7Poisson_P_Score_Upper_Tail) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5MACS2_7Poisson_P_Score_Upper_Tail = &__pyx_type_5MACS2_7Poisson_P_Score_Upper_Tail; __pyx_vtabptr_5MACS2_7Poisson_LogLR_Diff = &__pyx_vtable_5MACS2_7Poisson_LogLR_Diff; __pyx_vtable_5MACS2_7Poisson_LogLR_Diff.check_cache = (int (*)(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *, double, double, int __pyx_skip_dispatch))__pyx_f_5MACS2_7Poisson_10LogLR_Diff_check_cache; __pyx_vtable_5MACS2_7Poisson_LogLR_Diff.get_logLR_diff = (double (*)(struct __pyx_obj_5MACS2_7Poisson_LogLR_Diff *, double, double, int __pyx_skip_dispatch))__pyx_f_5MACS2_7Poisson_10LogLR_Diff_get_logLR_diff; if (PyType_Ready(&__pyx_type_5MACS2_7Poisson_LogLR_Diff) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetVtable(__pyx_type_5MACS2_7Poisson_LogLR_Diff.tp_dict, __pyx_vtabptr_5MACS2_7Poisson_LogLR_Diff) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "LogLR_Diff", (PyObject *)&__pyx_type_5MACS2_7Poisson_LogLR_Diff) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5MACS2_7Poisson_LogLR_Diff = &__pyx_type_5MACS2_7Poisson_LogLR_Diff; __pyx_vtabptr_5MACS2_7Poisson_LogLR_Sym = &__pyx_vtable_5MACS2_7Poisson_LogLR_Sym; __pyx_vtable_5MACS2_7Poisson_LogLR_Sym.check_cache = (int (*)(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *, double, double, int __pyx_skip_dispatch))__pyx_f_5MACS2_7Poisson_9LogLR_Sym_check_cache; __pyx_vtable_5MACS2_7Poisson_LogLR_Sym.get_logLR_sym = (double (*)(struct __pyx_obj_5MACS2_7Poisson_LogLR_Sym *, double, double, int __pyx_skip_dispatch))__pyx_f_5MACS2_7Poisson_9LogLR_Sym_get_logLR_sym; if (PyType_Ready(&__pyx_type_5MACS2_7Poisson_LogLR_Sym) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetVtable(__pyx_type_5MACS2_7Poisson_LogLR_Sym.tp_dict, __pyx_vtabptr_5MACS2_7Poisson_LogLR_Sym) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L1_error;} if (__Pyx_SetAttrString(__pyx_m, "LogLR_Sym", (PyObject *)&__pyx_type_5MACS2_7Poisson_LogLR_Sym) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5MACS2_7Poisson_LogLR_Sym = &__pyx_type_5MACS2_7Poisson_LogLR_Sym; /*--- Type import code ---*/ __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type", #if CYTHON_COMPILING_IN_PYPY sizeof(PyTypeObject), #else sizeof(PyHeapTypeObject), #endif 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr), 0); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 169; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Variable import code ---*/ /*--- Function import code ---*/ /*--- Execution code ---*/ /* "MACS2/Poisson.pyx":1 * cdef extern from "cPoisson.h": # <<<<<<<<<<<<<< * double log10_poisson_cdf ( unsigned int n, double lam, short lower ) * double log10_poisson_cdf_P_large_lambda ( unsigned int k, double lbd ) */ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(((PyObject *)__pyx_t_1)); if (PyDict_SetItem(__pyx_d, __pyx_n_s____test__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; /* "numpy.pxd":975 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< * if arr.base is NULL: * return None */ goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); if (__pyx_m) { __Pyx_AddTraceback("init MACS2.Poisson", __pyx_clineno, __pyx_lineno, __pyx_filename); Py_DECREF(__pyx_m); __pyx_m = 0; } else if (!PyErr_Occurred()) { PyErr_SetString(PyExc_ImportError, "init MACS2.Poisson"); } __pyx_L0:; __Pyx_RefNannyFinishContext(); #if PY_MAJOR_VERSION < 3 return; #else return __pyx_m; #endif } /* Runtime support code */ #if CYTHON_REFNANNY static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { PyObject *m = NULL, *p = NULL; void *r = NULL; m = PyImport_ImportModule((char *)modname); if (!m) goto end; p = PyObject_GetAttrString(m, (char *)"RefNannyAPI"); if (!p) goto end; r = PyLong_AsVoidPtr(p); end: Py_XDECREF(p); Py_XDECREF(m); return (__Pyx_RefNannyAPIStruct *)r; } #endif /* CYTHON_REFNANNY */ 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, "%s() keywords must be strings", function_name); goto bad; invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif bad: return -1; } 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, "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)", func_name, more_or_less, num_expected, (num_expected == 1) ? "" : "s", num_found); } static CYTHON_INLINE int __Pyx_CheckKeywordStrings( PyObject *kwdict, const char* function_name, int kw_allowed) { PyObject* key = 0; Py_ssize_t pos = 0; #if CPYTHON_COMPILING_IN_PYPY if (!kw_allowed && PyDict_Next(kwdict, &pos, &key, 0)) goto invalid_keyword; return 1; #else while (PyDict_Next(kwdict, &pos, &key, 0)) { #if PY_MAJOR_VERSION < 3 if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) #endif if (unlikely(!PyUnicode_Check(key))) goto invalid_keyword_type; } if ((!kw_allowed) && unlikely(key)) goto invalid_keyword; return 1; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%s() keywords must be strings", function_name); return 0; #endif invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%s() got an unexpected keyword argument '%s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif return 0; } 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 } static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename) { PyObject *old_exc, *old_val, *old_tb; PyObject *ctx; __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); #if PY_MAJOR_VERSION < 3 ctx = PyString_FromString(name); #else ctx = PyUnicode_FromString(name); #endif __Pyx_ErrRestore(old_exc, old_val, old_tb); if (!ctx) { PyErr_WriteUnraisable(Py_None); } else { PyErr_WriteUnraisable(ctx); Py_DECREF(ctx); } } static PyObject *__Pyx_GetBuiltinName(PyObject *name) { PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name); if (unlikely(!result)) { PyErr_Format(PyExc_NameError, #if PY_MAJOR_VERSION >= 3 "name '%U' is not defined", name); #else "name '%s' is not defined", PyString_AS_STRING(name)); #endif } return result; } #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 PY_VERSION_HEX < 0x02050000 if (PyClass_Check(type)) { #else if (PyType_Check(type)) { #endif #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; #if PY_VERSION_HEX < 0x02050000 if (PyInstance_Check(type)) { type = (PyObject*) ((PyInstanceObject*)type)->in_class; Py_INCREF(type); } else { type = 0; PyErr_SetString(PyExc_TypeError, "raise: exception must be an old-style class or instance"); goto raise_error; } #else 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; } #endif } __Pyx_ErrRestore(type, value, tb); return; raise_error: Py_XDECREF(value); Py_XDECREF(type); Py_XDECREF(tb); return; } #else /* Python 3+ */ 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 *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 = PyEval_CallObject(type, args); 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) { 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); } } bad: Py_XDECREF(owned_instance); return; } #endif 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%s to unpack", index, (index == 1) ? "" : "s"); } static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); } 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 int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { if (unlikely(!type)) { PyErr_Format(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 int __Pyx_SetVtable(PyObject *dict, void *vtable) { #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0) 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 CYTHON_INLINE npy_uint32 __Pyx_PyInt_from_py_npy_uint32(PyObject* x) { const npy_uint32 neg_one = (npy_uint32)-1, const_zero = (npy_uint32)0; const int is_unsigned = const_zero < neg_one; if (sizeof(npy_uint32) == sizeof(char)) { if (is_unsigned) return (npy_uint32)__Pyx_PyInt_AsUnsignedChar(x); else return (npy_uint32)__Pyx_PyInt_AsSignedChar(x); } else if (sizeof(npy_uint32) == sizeof(short)) { if (is_unsigned) return (npy_uint32)__Pyx_PyInt_AsUnsignedShort(x); else return (npy_uint32)__Pyx_PyInt_AsSignedShort(x); } else if (sizeof(npy_uint32) == sizeof(int)) { if (is_unsigned) return (npy_uint32)__Pyx_PyInt_AsUnsignedInt(x); else return (npy_uint32)__Pyx_PyInt_AsSignedInt(x); } else if (sizeof(npy_uint32) == sizeof(long)) { if (is_unsigned) return (npy_uint32)__Pyx_PyInt_AsUnsignedLong(x); else return (npy_uint32)__Pyx_PyInt_AsSignedLong(x); } else if (sizeof(npy_uint32) == sizeof(PY_LONG_LONG)) { if (is_unsigned) return (npy_uint32)__Pyx_PyInt_AsUnsignedLongLong(x); else return (npy_uint32)__Pyx_PyInt_AsSignedLongLong(x); } else { #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else npy_uint32 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 (npy_uint32)-1; } } #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 CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { const unsigned char neg_one = (unsigned char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned char" : "value too large to convert to unsigned char"); } return (unsigned char)-1; } return (unsigned char)val; } return (unsigned char)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { const unsigned short neg_one = (unsigned short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned short" : "value too large to convert to unsigned short"); } return (unsigned short)-1; } return (unsigned short)val; } return (unsigned short)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { const unsigned int neg_one = (unsigned int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(unsigned int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(unsigned int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to unsigned int" : "value too large to convert to unsigned int"); } return (unsigned int)-1; } return (unsigned int)val; } return (unsigned int)__Pyx_PyInt_AsUnsignedLong(x); } static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { const char neg_one = (char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to char" : "value too large to convert to char"); } return (char)-1; } return (char)val; } return (char)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { const short neg_one = (short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to short" : "value too large to convert to short"); } return (short)-1; } return (short)val; } return (short)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { const signed char neg_one = (signed char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed char) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed char)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed char" : "value too large to convert to signed char"); } return (signed char)-1; } return (signed char)val; } return (signed char)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { const signed short neg_one = (signed short)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed short) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed short)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed short" : "value too large to convert to signed short"); } return (signed short)-1; } return (signed short)val; } return (signed short)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { const signed int neg_one = (signed int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(signed int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(signed int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to signed int" : "value too large to convert to signed int"); } return (signed int)-1; } return (signed int)val; } return (signed int)__Pyx_PyInt_AsSignedLong(x); } static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { const int neg_one = (int)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (sizeof(int) < sizeof(long)) { long val = __Pyx_PyInt_AsLong(x); if (unlikely(val != (long)(int)val)) { if (!unlikely(val == -1 && PyErr_Occurred())) { PyErr_SetString(PyExc_OverflowError, (is_unsigned && unlikely(val < 0)) ? "can't convert negative value to int" : "value too large to convert to int"); } return (int)-1; } return (int)val; } return (int)__Pyx_PyInt_AsLong(x); } #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS #include "longintrepr.h" #endif #endif static CYTHON_INLINE unsigned long __Pyx_PyInt_AsUnsignedLong(PyObject* x) { const unsigned long neg_one = (unsigned long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned 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 if (sizeof(digit) <= sizeof(unsigned long)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return (unsigned long) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned long"); return (unsigned long)-1; } return (unsigned long)PyLong_AsUnsignedLong(x); } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(unsigned long)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return +(unsigned long) ((PyLongObject*)x)->ob_digit[0]; case -1: return -(unsigned long) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif return (unsigned long)PyLong_AsLong(x); } } else { unsigned long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned long)-1; val = __Pyx_PyInt_AsUnsignedLong(tmp); Py_DECREF(tmp); return val; } } #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS #include "longintrepr.h" #endif #endif static CYTHON_INLINE unsigned PY_LONG_LONG __Pyx_PyInt_AsUnsignedLongLong(PyObject* x) { const unsigned PY_LONG_LONG neg_one = (unsigned PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_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 if (sizeof(digit) <= sizeof(unsigned PY_LONG_LONG)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return (unsigned PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to unsigned PY_LONG_LONG"); return (unsigned PY_LONG_LONG)-1; } return (unsigned PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(unsigned PY_LONG_LONG)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return +(unsigned PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; case -1: return -(unsigned PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif return (unsigned PY_LONG_LONG)PyLong_AsLongLong(x); } } else { unsigned PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (unsigned PY_LONG_LONG)-1; val = __Pyx_PyInt_AsUnsignedLongLong(tmp); Py_DECREF(tmp); return val; } } #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS #include "longintrepr.h" #endif #endif static CYTHON_INLINE long __Pyx_PyInt_AsLong(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))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } 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 if (sizeof(digit) <= sizeof(long)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return (long) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to long"); return (long)-1; } return (long)PyLong_AsUnsignedLong(x); } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(long)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return +(long) ((PyLongObject*)x)->ob_digit[0]; case -1: return -(long) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif return (long)PyLong_AsLong(x); } } else { long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (long)-1; val = __Pyx_PyInt_AsLong(tmp); Py_DECREF(tmp); return val; } } #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS #include "longintrepr.h" #endif #endif static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { const PY_LONG_LONG neg_one = (PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_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 if (sizeof(digit) <= sizeof(PY_LONG_LONG)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return (PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to PY_LONG_LONG"); return (PY_LONG_LONG)-1; } return (PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(PY_LONG_LONG)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return +(PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; case -1: return -(PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif return (PY_LONG_LONG)PyLong_AsLongLong(x); } } else { PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (PY_LONG_LONG)-1; val = __Pyx_PyInt_AsLongLong(tmp); Py_DECREF(tmp); return val; } } #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS #include "longintrepr.h" #endif #endif static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject* x) { const signed long neg_one = (signed long)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed 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 if (sizeof(digit) <= sizeof(signed long)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return (signed long) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed long"); return (signed long)-1; } return (signed long)PyLong_AsUnsignedLong(x); } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(signed long)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return +(signed long) ((PyLongObject*)x)->ob_digit[0]; case -1: return -(signed long) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif return (signed long)PyLong_AsLong(x); } } else { signed long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed long)-1; val = __Pyx_PyInt_AsSignedLong(tmp); Py_DECREF(tmp); return val; } } #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS #include "longintrepr.h" #endif #endif static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { const signed PY_LONG_LONG neg_one = (signed PY_LONG_LONG)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_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 if (sizeof(digit) <= sizeof(signed PY_LONG_LONG)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return (signed PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to signed PY_LONG_LONG"); return (signed PY_LONG_LONG)-1; } return (signed PY_LONG_LONG)PyLong_AsUnsignedLongLong(x); } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(signed PY_LONG_LONG)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return +(signed PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; case -1: return -(signed PY_LONG_LONG) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif return (signed PY_LONG_LONG)PyLong_AsLongLong(x); } } else { signed PY_LONG_LONG val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (signed PY_LONG_LONG)-1; val = __Pyx_PyInt_AsSignedLongLong(tmp); Py_DECREF(tmp); return val; } } 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); #if PY_VERSION_HEX < 0x02050000 return PyErr_Warn(NULL, message); #else return PyErr_WarnEx(NULL, message, 1); #endif } 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, "%s.%s 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 PY_VERSION_HEX < 0x02050000 if (PyErr_Warn(NULL, warning) < 0) goto bad; #else if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; #endif } else if ((size_t)basicsize != size) { PyErr_Format(PyExc_ValueError, "%s.%s 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_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, 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, /*int argcount,*/ 0, /*int kwonlyargcount,*/ 0, /*int nlocals,*/ 0, /*int stacksize,*/ 0, /*int flags,*/ __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, /*int firstlineno,*/ __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; PyObject *py_globals = 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_globals = PyModule_GetDict(__pyx_m); if (!py_globals) goto bad; py_frame = PyFrame_New( PyThreadState_GET(), /*PyThreadState *tstate,*/ py_code, /*PyCodeObject *code,*/ py_globals, /*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); } 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 /* Python 3+ has unicode identifiers */ 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(char* c_str) { return __Pyx_PyUnicode_FromStringAndSize(c_str, 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 /*__PYX_DEFAULT_STRING_ENCODING_IS_ASCII*/ *length = PyBytes_GET_SIZE(defenc); return defenc_c; #else /* PY_VERSION_HEX < 0x03030000 */ if (PyUnicode_READY(o) == -1) return NULL; #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII if (PyUnicode_IS_ASCII(o)) { *length = PyUnicode_GET_DATA_SIZE(o); return PyUnicode_AsUTF8(o); } else { PyUnicode_AsASCIIString(o); return NULL; } #else /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */ return PyUnicode_AsUTF8AndSize(o, length); #endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */ #endif /* PY_VERSION_HEX < 0x03030000 */ } else #endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT */ { char* result; int r = PyBytes_AsStringAndSize(o, &result, length); if (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, "__%s__ returned non-%s (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 = 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) { #if PY_VERSION_HEX < 0x02050000 if (ival <= LONG_MAX) return PyInt_FromLong((long)ival); else { unsigned char *bytes = (unsigned char *) &ival; int one = 1; int little = (int)*(unsigned char*)&one; return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0); } #else return PyInt_FromSize_t(ival); #endif } static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x); if (unlikely(val != (unsigned PY_LONG_LONG)(size_t)val)) { if ((val != (unsigned PY_LONG_LONG)-1) || !PyErr_Occurred()) PyErr_SetString(PyExc_OverflowError, "value too large to convert to size_t"); return (size_t)-1; } return (size_t)val; } #endif /* Py_PYTHON_H */