/* Generated by Cython 0.20.2 on Tue Jun 17 01:36:29 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 #define CYTHON_ABI "0_20_2" #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 CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 #define Py_OptimizeFlag 0 #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_As_int(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+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #define __Pyx_DefaultClassType PyClass_Type #else #define __Pyx_BUILTIN_MODULE_NAME "builtins" #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #define __Pyx_DefaultClassType PyType_Type #endif #if PY_VERSION_HEX < 0x02060000 #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 < 0x02060000 && !defined(Py_TPFLAGS_IS_ABSTRACT) #define Py_TPFLAGS_IS_ABSTRACT 0 #endif #if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE) #define Py_TPFLAGS_HAVE_FINALIZE 0 #endif #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) #define CYTHON_PEP393_ENABLED 1 #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ 0 : _PyUnicode_Ready((PyObject *)(op))) #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) #else #define CYTHON_PEP393_ENABLED 0 #define __Pyx_PyUnicode_READY(op) (0) #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) #endif #if CYTHON_COMPILING_IN_PYPY #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) #else #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \ PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) #endif #define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) #define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b) #else #define __Pyx_PyString_Format(a, b) PyString_Format(a, b) #endif #if PY_MAJOR_VERSION >= 3 #define PyBaseString_Type PyUnicode_Type #define PyStringObject PyUnicodeObject #define PyString_Type PyUnicode_Type #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact #endif #if PY_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) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj)) #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 #define PyNumber_Int PyNumber_Long #endif #if PY_MAJOR_VERSION >= 3 #define PyBoolObject PyLongObject #endif #if PY_VERSION_HEX < 0x030200A4 typedef long Py_hash_t; #define __Pyx_PyInt_FromHash_t PyInt_FromLong #define __Pyx_PyInt_AsHash_t PyInt_AsLong #else #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t #endif #if (PY_MAJOR_VERSION < 3) || (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) && _MSC_VER >= 1400 #define CYTHON_RESTRICT __restrict #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L #define CYTHON_RESTRICT restrict #else #define CYTHON_RESTRICT #endif #endif #ifdef NAN #define __PYX_NAN() ((float) NAN) #else static CYTHON_INLINE float __PYX_NAN() { /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is a quiet NaN. */ float value; memset(&value, 0xFF, sizeof(value)); return value; } #endif #ifdef __cplusplus template void __Pyx_call_destructor(T* x) { x->~T(); } #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__IO__cCallPeakUnit #define __PYX_HAVE_API__MACS2__IO__cCallPeakUnit #include "string.h" #include "stdio.h" #include "stdlib.h" #include "numpy/arrayobject.h" #include "numpy/ufuncobject.h" #include "pythread.h" #include "stdint.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 #define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \ (sizeof(type) < sizeof(Py_ssize_t)) || \ (sizeof(type) > sizeof(Py_ssize_t) && \ likely(v < (type)PY_SSIZE_T_MAX || \ v == (type)PY_SSIZE_T_MAX) && \ (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \ v == (type)PY_SSIZE_T_MIN))) || \ (sizeof(type) == sizeof(Py_ssize_t) && \ (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \ v == (type)PY_SSIZE_T_MAX))) ) static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); #define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) #define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) #define __Pyx_PyBytes_FromString PyBytes_FromString #define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); #if PY_MAJOR_VERSION < 3 #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize #else #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize #endif #define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) #define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) #define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((const char*)s) #define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((const char*)s) #define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((const char*)s) #define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((const char*)s) #define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((const char*)s) #if PY_MAJOR_VERSION < 3 static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { const Py_UNICODE *u_end = u; while (*u_end++) ; return (size_t)(u_end - u - 1); } #else #define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen #endif #define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) #define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode #define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None) #define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); #if CYTHON_COMPILING_IN_CPYTHON #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) #else #define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) #endif #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII static int __Pyx_sys_getdefaultencoding_not_ascii; static int __Pyx_init_sys_getdefaultencoding_params(void) { PyObject* sys; PyObject* default_encoding = NULL; PyObject* ascii_chars_u = NULL; PyObject* ascii_chars_b = NULL; const char* default_encoding_c; sys = PyImport_ImportModule("sys"); if (!sys) goto bad; default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); Py_DECREF(sys); if (!default_encoding) goto bad; default_encoding_c = PyBytes_AsString(default_encoding); if (!default_encoding_c) goto bad; if (strcmp(default_encoding_c, "ascii") == 0) { __Pyx_sys_getdefaultencoding_not_ascii = 0; } else { char ascii_chars[128]; int c; for (c = 0; c < 128; c++) { ascii_chars[c] = c; } __Pyx_sys_getdefaultencoding_not_ascii = 1; ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); if (!ascii_chars_u) goto bad; ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { PyErr_Format( PyExc_ValueError, "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", default_encoding_c); goto bad; } Py_DECREF(ascii_chars_u); Py_DECREF(ascii_chars_b); } Py_DECREF(default_encoding); return 0; bad: Py_XDECREF(default_encoding); Py_XDECREF(ascii_chars_u); Py_XDECREF(ascii_chars_b); return -1; } #endif #if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3 #define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL) #else #define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL) #if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT static char* __PYX_DEFAULT_STRING_ENCODING; static int __Pyx_init_sys_getdefaultencoding_params(void) { PyObject* sys; PyObject* default_encoding = NULL; char* default_encoding_c; sys = PyImport_ImportModule("sys"); if (!sys) goto bad; default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); Py_DECREF(sys); if (!default_encoding) goto bad; default_encoding_c = PyBytes_AsString(default_encoding); if (!default_encoding_c) goto bad; __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c)); if (!__PYX_DEFAULT_STRING_ENCODING) goto bad; strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); Py_DECREF(default_encoding); return 0; bad: Py_XDECREF(default_encoding); return -1; } #endif #endif /* Test for GCC > 2.95 */ #if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))) #define likely(x) __builtin_expect(!!(x), 1) #define unlikely(x) __builtin_expect(!!(x), 0) #else /* !__GNUC__ or GCC < 2.95 */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ */ static PyObject *__pyx_m; static PyObject *__pyx_d; static PyObject *__pyx_b; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; static int __pyx_lineno; static int __pyx_clineno = 0; static const char * __pyx_cfilenm= __FILE__; static const char *__pyx_filename; #if !defined(CYTHON_CCOMPLEX) #if defined(__cplusplus) #define CYTHON_CCOMPLEX 1 #elif defined(_Complex_I) #define CYTHON_CCOMPLEX 1 #else #define CYTHON_CCOMPLEX 0 #endif #endif #if CYTHON_CCOMPLEX #ifdef __cplusplus #include #else #include #endif #endif #if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__) #undef _Complex_I #define _Complex_I 1.0fj #endif static const char *__pyx_f[] = { "cCallPeakUnit.pyx", "__init__.pxd", "type.pxd", "bool.pxd", "complex.pxd", }; #define IS_UNSIGNED(type) (((type) -1) > 0) struct __Pyx_StructField_; #define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0) typedef struct { const char* name; /* for error messages only */ struct __Pyx_StructField_* fields; size_t size; /* sizeof(type) */ size_t arraysize[8]; /* length of array in each dimension */ int ndim; char typegroup; /* _R_eal, _C_omplex, Signed _I_nt, _U_nsigned int, _S_truct, _P_ointer, _O_bject, c_H_ar */ char is_unsigned; int flags; } __Pyx_TypeInfo; typedef struct __Pyx_StructField_ { __Pyx_TypeInfo* type; const char* name; size_t offset; } __Pyx_StructField; typedef struct { __Pyx_StructField* field; size_t parent_offset; } __Pyx_BufFmt_StackElem; typedef struct { __Pyx_StructField root; __Pyx_BufFmt_StackElem* head; size_t fmt_offset; size_t new_count, enc_count; size_t struct_alignment; int is_complex; char enc_type; char new_packmode; char enc_packmode; char is_valid_array; } __Pyx_BufFmt_Context; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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_2IO_13cCallPeakUnit_CallerFromAlignments; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; /* "/Library/Python/2.7/site-packages/Cython/Includes/numpy/__init__.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; struct __pyx_opt_args_5MACS2_5cProb_poisson_cdf; struct __pyx_opt_args_5MACS2_5cProb_poisson_cdf_inv; struct __pyx_opt_args_5MACS2_5cProb_poisson_cdf_Q_inv; struct __pyx_opt_args_5MACS2_5cProb_binomial_cdf; /* "MACS2/cProb.pxd":5 * cpdef factorial ( unsigned int n ) * * cpdef double poisson_cdf ( unsigned int n, double lam, bool lower = ?, bool log10 = ? ) # <<<<<<<<<<<<<< * * cdef inline double __poisson_cdf ( unsigned int k, double a ) */ struct __pyx_opt_args_5MACS2_5cProb_poisson_cdf { int __pyx_n; PyBoolObject *lower; PyBoolObject *log10; }; /* "MACS2/cProb.pxd":21 * cdef inline double logspace_add ( double logx, double logy ) * * cpdef poisson_cdf_inv ( double cdf, double lam, int maximum = ? ) # <<<<<<<<<<<<<< * * cpdef poisson_cdf_Q_inv ( double cdf, double lam, int maximum = ? ) */ struct __pyx_opt_args_5MACS2_5cProb_poisson_cdf_inv { int __pyx_n; int maximum; }; /* "MACS2/cProb.pxd":23 * cpdef poisson_cdf_inv ( double cdf, double lam, int maximum = ? ) * * cpdef poisson_cdf_Q_inv ( double cdf, double lam, int maximum = ? ) # <<<<<<<<<<<<<< * * cpdef poisson_pdf ( unsigned int k, double a ) */ struct __pyx_opt_args_5MACS2_5cProb_poisson_cdf_Q_inv { int __pyx_n; int maximum; }; /* "MACS2/cProb.pxd":29 * cdef binomial_coef ( long n, long k ) * * cpdef binomial_cdf ( long x, long a, double b, bool lower = ? ) # <<<<<<<<<<<<<< * * cdef _binomial_cdf_r ( long x, long a, double b ) */ struct __pyx_opt_args_5MACS2_5cProb_binomial_cdf { int __pyx_n; PyBoolObject *lower; }; struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments_call_peaks; struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments___close_peak_wo_subpeaks; struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments___close_peak_with_subpeaks; struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments_call_broadpeaks; struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments___close_peak_for_broad_region; struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments_refine_peak_from_tags_distribution; /* "MACS2/IO/cCallPeakUnit.pyx":556 * return self.pqtable * * cpdef call_peaks ( self, list scoring_function_symbols, list score_cutoff_s, int min_length = 200, # <<<<<<<<<<<<<< * int max_gap = 50, bool call_summits = False ): * """Call peaks for all chromosomes. Return a PeakIO object. */ struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments_call_peaks { int __pyx_n; int min_length; int max_gap; PyBoolObject *call_summits; }; /* "MACS2/IO/cCallPeakUnit.pyx":703 * return peaks * * cdef bool __close_peak_wo_subpeaks (self, list peak_content, peaks, int min_length, # <<<<<<<<<<<<<< * str chrom, int smoothlen=0, list score_cutoff_s=[]): * """Close the peak region, output peak boundaries, peak summit */ struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments___close_peak_wo_subpeaks { int __pyx_n; int smoothlen; PyObject *score_cutoff_s; }; /* "MACS2/IO/cCallPeakUnit.pyx":763 * return True * * cdef bool __close_peak_with_subpeaks (self, list peak_content, peaks, int min_length, # <<<<<<<<<<<<<< * str chrom, int smoothlen=51, list score_cutoff_s=[], * float min_valley = 0.9 ): */ struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments___close_peak_with_subpeaks { int __pyx_n; int smoothlen; PyObject *score_cutoff_s; float min_valley; }; /* "MACS2/IO/cCallPeakUnit.pyx":964 * return True * * cpdef call_broadpeaks (self, list scoring_function_symbols, list lvl1_cutoff_s, list lvl2_cutoff_s, int min_length=200, int lvl1_max_gap=50, int lvl2_max_gap=400): # <<<<<<<<<<<<<< * """This function try to find enriched regions within which, * scores are continuously higher than a given cutoff for level */ struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments_call_broadpeaks { int __pyx_n; int min_length; int lvl1_max_gap; int lvl2_max_gap; }; /* "MACS2/IO/cCallPeakUnit.pyx":1173 * return * * cdef bool __close_peak_for_broad_region (self, list peak_content, peaks, int min_length, # <<<<<<<<<<<<<< * str chrom, int smoothlen=0, list score_cutoff_s=[]): * """Close the broad peak region, output peak boundaries, peak summit */ struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments___close_peak_for_broad_region { int __pyx_n; int smoothlen; PyObject *score_cutoff_s; }; /* "MACS2/IO/cCallPeakUnit.pyx":1276 * return bpeaks * * cpdef refine_peak_from_tags_distribution ( self, peaks, int window_size = 100, float cutoff = 5 ): # <<<<<<<<<<<<<< * """Extract tags in peak, then apply func on extracted tags. * */ struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments_refine_peak_from_tags_distribution { int __pyx_n; int window_size; float cutoff; }; /* "MACS2/IO/cCallPeakUnit.pyx":203 * # Classes * # ------------------------------------ * cdef class CallerFromAlignments: # <<<<<<<<<<<<<< * """A unit to calculate scores and call peaks from alignments -- * FWTrackIII or PETrackI objects. */ struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments { PyObject_HEAD struct __pyx_vtabstruct_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *__pyx_vtab; PyObject *treat; PyObject *ctrl; int d; PyObject *ctrl_d_s; float treat_scaling_factor; PyObject *ctrl_scaling_factor_s; float lambda_bg; PyObject *chromosomes; float pseudocount; PyObject *bedGraph_filename_prefix; int end_shift; PyBoolObject *trackline; PyBoolObject *save_bedGraph; PyBoolObject *save_SPMR; PyBoolObject *no_lambda_flag; PyBoolObject *PE_mode; PyObject *chrom; PyObject *chr_pos_treat_ctrl; PyObject *bedGraph_treat_filename; PyObject *bedGraph_control_filename; PyObject *bedGraph_treat; PyObject *bedGraph_ctrl; PyObject *pqtable; PyBoolObject *pvalue_all_done; double test_time; }; struct __pyx_vtabstruct_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments { PyObject *(*set_pseudocount)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, float, int __pyx_skip_dispatch); PyObject *(*enable_trackline)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, int __pyx_skip_dispatch); PyObject *(*__pyx___pileup_treat_ctrl_a_chromosome)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *); PyObject *(*__pyx___chrom_pair_treat_ctrl)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, PyObject *); PyArrayObject *(*__pyx___cal_score)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, PyObject *, PyObject *); PyObject *(*__pyx___cal_pvalue_qvalue_table)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *); PyObject *(*call_peaks)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments_call_peaks *__pyx_optional_args); PyObject *(*__pyx___chrom_call_peak_using_certain_criteria)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, PyObject *, PyObject *, PyObject *, int, int, PyBoolObject *, PyBoolObject *); PyBoolObject *(*__pyx___close_peak_wo_subpeaks)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, PyObject *, int, PyObject *, struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments___close_peak_wo_subpeaks *__pyx_optional_args); PyBoolObject *(*__pyx___close_peak_with_subpeaks)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, PyObject *, int, PyObject *, struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments___close_peak_with_subpeaks *__pyx_optional_args); PyArrayObject *(*__pyx___cal_pscore)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, PyObject *); PyArrayObject *(*__pyx___cal_qscore)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, PyObject *); PyArrayObject *(*__pyx___cal_logLR)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, PyObject *); PyArrayObject *(*__pyx___cal_logFE)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, PyObject *); PyArrayObject *(*__pyx___cal_FE)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, PyObject *); PyArrayObject *(*__pyx___cal_subtraction)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, PyObject *); PyBoolObject *(*__pyx___write_bedGraph_for_a_chromosome)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *); PyObject *(*call_broadpeaks)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, PyObject *, PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments_call_broadpeaks *__pyx_optional_args); PyObject *(*__pyx___chrom_call_broadpeak_using_certain_criteria)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, PyObject *, PyObject *, PyObject *, PyObject *, PyObject *, int, int, int, PyBoolObject *); PyBoolObject *(*__pyx___close_peak_for_broad_region)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, PyObject *, int, PyObject *, struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments___close_peak_for_broad_region *__pyx_optional_args); PyObject *(*__pyx___add_broadpeak)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, PyObject *, PyObject *, PyObject *); PyObject *(*refine_peak_from_tags_distribution)(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *, PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments_refine_peak_from_tags_distribution *__pyx_optional_args); }; static struct __pyx_vtabstruct_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *__pyx_vtabptr_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments; #ifndef CYTHON_REFNANNY #define CYTHON_REFNANNY 0 #endif #if CYTHON_REFNANNY typedef struct { void (*INCREF)(void*, PyObject*, int); 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(PyErr_SetString(PyExc_IndexError, "list assignment index out of range"), -1) : \ __Pyx_SetItemInt_Generic(o, to_py_func(i), v))) static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v); static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v, int is_list, int wraparound, int boundscheck); #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { PyListObject* L = (PyListObject*) list; Py_ssize_t len = Py_SIZE(list); if (likely(L->allocated > len)) { Py_INCREF(x); PyList_SET_ITEM(list, len, x); Py_SIZE(list) = len+1; return 0; } return PyList_Append(list, x); } #else #define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) #endif static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*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 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 CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact); /*proto*/ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/ #if PY_VERSION_HEX < 0x02050000 #ifndef PyAnySet_CheckExact #define PyAnySet_CheckExact(ob) \ ((ob)->ob_type == &PySet_Type || \ (ob)->ob_type == &PyFrozenSet_Type) #define PySet_New(iterable) \ PyObject_CallFunctionObjArgs((PyObject *)&PySet_Type, (iterable), NULL) #define PyFrozenSet_New(iterable) \ PyObject_CallFunctionObjArgs((PyObject *)&PyFrozenSet_Type, (iterable), NULL) #define PySet_Size(anyset) \ PyObject_Size((anyset)) #define PySet_GET_SIZE(anyset) \ PyObject_Size((anyset)) #define PySet_Contains(anyset, key) \ PySequence_Contains((anyset), (key)) #define PySet_Pop(set) \ PyObject_CallMethod((set), (char*)"pop", NULL) static CYTHON_INLINE int PySet_Clear(PyObject *set) { PyObject *ret = PyObject_CallMethod(set, (char*)"clear", NULL); if (!ret) return -1; Py_DECREF(ret); return 0; } static CYTHON_INLINE int PySet_Discard(PyObject *set, PyObject *key) { PyObject *ret = PyObject_CallMethod(set, (char*)"discard", (char*)"(O)", key); if (!ret) return -1; Py_DECREF(ret); return 0; } static CYTHON_INLINE int PySet_Add(PyObject *set, PyObject *key) { PyObject *ret = PyObject_CallMethod(set, (char*)"add", (char*)"(O)", key); if (!ret) return -1; Py_DECREF(ret); return 0; } #endif /* PyAnySet_CheckExact (<= Py2.4) */ #endif /* < Py2.5 */ static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) { int result = PySequence_Contains(seq, item); return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); } static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice( PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop, PyObject** py_start, PyObject** py_stop, PyObject** py_slice, int has_cstart, int has_cstop, int wraparound); static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); #if PY_MAJOR_VERSION >= 3 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { PyObject *value; value = PyDict_GetItemWithError(d, key); if (unlikely(!value)) { if (!PyErr_Occurred()) { PyObject* args = PyTuple_Pack(1, key); if (likely(args)) PyErr_SetObject(PyExc_KeyError, args); Py_XDECREF(args); } return NULL; } Py_INCREF(value); return value; } #else #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) #endif static PyObject* __Pyx_PyObject_CallMethodTuple(PyObject* obj, PyObject* method_name, PyObject* args) { PyObject *method, *result = NULL; if (unlikely(!args)) return NULL; method = __Pyx_PyObject_GetAttrStr(obj, method_name); if (unlikely(!method)) goto bad; result = __Pyx_PyObject_Call(method, args, NULL); Py_DECREF(method); bad: Py_DECREF(args); return result; } #define __Pyx_PyObject_CallMethod3(obj, name, arg1, arg2, arg3) \ __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(3, arg1, arg2, arg3)) #define __Pyx_PyObject_CallMethod2(obj, name, arg1, arg2) \ __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(2, arg1, arg2)) #define __Pyx_PyObject_CallMethod1(obj, name, arg1) \ __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(1, arg1)) #define __Pyx_PyObject_CallMethod0(obj, name) \ __Pyx_PyObject_CallMethodTuple(obj, name, (Py_INCREF(__pyx_empty_tuple), __pyx_empty_tuple)) static CYTHON_INLINE PyObject* __Pyx_PyDict_Values(PyObject* d); /*proto*/ static CYTHON_INLINE PyObject* __Pyx_PyDict_Keys(PyObject* d); /*proto*/ #include static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/ static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/ #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals #else #define __Pyx_PyString_Equals __Pyx_PyBytes_Equals #endif static CYTHON_INLINE long __Pyx_div_long(long, long); /* proto */ static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */ static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); static void __Pyx_RaiseBufferFallbackError(void); /*proto*/ #define __Pyx_PyObject_DelSlice(obj, cstart, cstop, py_start, py_stop, py_slice, has_cstart, has_cstop, wraparound) \ __Pyx_PyObject_SetSlice(obj, (PyObject*)NULL, cstart, cstop, py_start, py_stop, py_slice, has_cstart, has_cstop, wraparound) static CYTHON_INLINE int __Pyx_PyObject_SetSlice( PyObject* obj, PyObject* value, Py_ssize_t cstart, Py_ssize_t cstop, PyObject** py_start, PyObject** py_stop, PyObject** py_slice, int has_cstart, int has_cstop, int wraparound); static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ #if PY_MAJOR_VERSION < 3 #define __Pyx_PyString_Join __Pyx_PyBytes_Join #define __Pyx_PyBaseString_Join(s, v) (PyUnicode_CheckExact(s) ? PyUnicode_Join(s, v) : __Pyx_PyBytes_Join(s, v)) #else #define __Pyx_PyString_Join PyUnicode_Join #define __Pyx_PyBaseString_Join PyUnicode_Join #endif #if CYTHON_COMPILING_IN_CPYTHON #if PY_MAJOR_VERSION < 3 #define __Pyx_PyBytes_Join _PyString_Join #else #define __Pyx_PyBytes_Join _PyBytes_Join #endif #else static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values); /*proto*/ #endif static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/ static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); /*proto*/ typedef struct { Py_ssize_t shape, strides, suboffsets; } __Pyx_Buf_DimInfo; typedef struct { size_t refcount; Py_buffer pybuffer; } __Pyx_Buffer; typedef struct { __Pyx_Buffer *rcbuffer; char *data; __Pyx_Buf_DimInfo diminfo[8]; } __Pyx_LocalBuf_ND; #if PY_MAJOR_VERSION < 3 static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); static void __Pyx_ReleaseBuffer(Py_buffer *view); #else #define __Pyx_GetBuffer PyObject_GetBuffer #define __Pyx_ReleaseBuffer PyBuffer_Release #endif static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0}; static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); static CYTHON_INLINE int32_t __Pyx_PyInt_As_int32_t(PyObject *); static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int32_t(int32_t value); static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value); #if CYTHON_CCOMPLEX #ifdef __cplusplus #define __Pyx_CREAL(z) ((z).real()) #define __Pyx_CIMAG(z) ((z).imag()) #else #define __Pyx_CREAL(z) (__real__(z)) #define __Pyx_CIMAG(z) (__imag__(z)) #endif #else #define __Pyx_CREAL(z) ((z).real) #define __Pyx_CIMAG(z) ((z).imag) #endif #if (defined(_WIN32) || defined(__clang__)) && defined(__cplusplus) && CYTHON_CCOMPLEX #define __Pyx_SET_CREAL(z,x) ((z).real(x)) #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) #else #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) #endif static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); #if CYTHON_CCOMPLEX #define __Pyx_c_eqf(a, b) ((a)==(b)) #define __Pyx_c_sumf(a, b) ((a)+(b)) #define __Pyx_c_difff(a, b) ((a)-(b)) #define __Pyx_c_prodf(a, b) ((a)*(b)) #define __Pyx_c_quotf(a, b) ((a)/(b)) #define __Pyx_c_negf(a) (-(a)) #ifdef __cplusplus #define __Pyx_c_is_zerof(z) ((z)==(float)0) #define __Pyx_c_conjf(z) (::std::conj(z)) #if 1 #define __Pyx_c_absf(z) (::std::abs(z)) #define __Pyx_c_powf(a, b) (::std::pow(a, b)) #endif #else #define __Pyx_c_is_zerof(z) ((z)==0) #define __Pyx_c_conjf(z) (conjf(z)) #if 1 #define __Pyx_c_absf(z) (cabsf(z)) #define __Pyx_c_powf(a, b) (cpowf(a, b)) #endif #endif #else static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex); static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex); #if 1 static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex); static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex); #endif #endif static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); #if CYTHON_CCOMPLEX #define __Pyx_c_eq(a, b) ((a)==(b)) #define __Pyx_c_sum(a, b) ((a)+(b)) #define __Pyx_c_diff(a, b) ((a)-(b)) #define __Pyx_c_prod(a, b) ((a)*(b)) #define __Pyx_c_quot(a, b) ((a)/(b)) #define __Pyx_c_neg(a) (-(a)) #ifdef __cplusplus #define __Pyx_c_is_zero(z) ((z)==(double)0) #define __Pyx_c_conj(z) (::std::conj(z)) #if 1 #define __Pyx_c_abs(z) (::std::abs(z)) #define __Pyx_c_pow(a, b) (::std::pow(a, b)) #endif #else #define __Pyx_c_is_zero(z) ((z)==0) #define __Pyx_c_conj(z) (conj(z)) #if 1 #define __Pyx_c_abs(z) (cabs(z)) #define __Pyx_c_pow(a, b) (cpow(a, b)) #endif #endif #else static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex, __pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex, __pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex, __pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex, __pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex); static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex); #if 1 static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex); static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex); #endif #endif static int __Pyx_check_binary_version(void); #if !defined(__Pyx_PyIdentifier_FromString) #if PY_MAJOR_VERSION < 3 #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) #else #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) #endif #endif static PyObject *__Pyx_ImportModule(const char *name); /*proto*/ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**f)(void), const char *sig); /*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.buffer' */ /* Module declarations from 'cpython.ref' */ /* Module declarations from 'libc.string' */ /* Module declarations from 'libc.stdio' */ /* Module declarations from 'cpython.object' */ /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.type' */ static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; /* Module declarations from 'libc.stdlib' */ /* Module declarations from 'numpy' */ /* Module declarations from 'numpy' */ static PyTypeObject *__pyx_ptype_5numpy_dtype = 0; static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0; static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0; static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ /* Module declarations from 'cpython.version' */ /* 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 'cpython.sequence' */ /* Module declarations from 'cpython.mapping' */ /* Module declarations from 'cpython.iterator' */ /* 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.bytes' */ /* Module declarations from 'cpython.pycapsule' */ /* Module declarations from 'cpython' */ /* Module declarations from 'libc.stdint' */ /* Module declarations from 'cython' */ /* Module declarations from 'libc.math' */ /* Module declarations from 'MACS2.cProb' */ static double (*__pyx_f_5MACS2_5cProb_poisson_cdf)(unsigned int, double, int __pyx_skip_dispatch, struct __pyx_opt_args_5MACS2_5cProb_poisson_cdf *__pyx_optional_args); /*proto*/ /* Module declarations from 'MACS2.IO.cCallPeakUnit' */ static PyTypeObject *__pyx_ptype_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments = 0; static CYTHON_INLINE PyArrayObject *__pyx_f_5MACS2_2IO_13cCallPeakUnit_apply_multiple_cutoffs(PyObject *, PyObject *); /*proto*/ static CYTHON_INLINE PyObject *__pyx_f_5MACS2_2IO_13cCallPeakUnit_get_from_multiple_scores(PyObject *, int); /*proto*/ static CYTHON_INLINE double __pyx_f_5MACS2_2IO_13cCallPeakUnit_get_logFE(float, float); /*proto*/ static CYTHON_INLINE PyObject *__pyx_f_5MACS2_2IO_13cCallPeakUnit_getitem_then_subtract(PyObject *, int); /*proto*/ static CYTHON_INLINE int32_t __pyx_f_5MACS2_2IO_13cCallPeakUnit_left_sum(PyObject *, int, int); /*proto*/ static CYTHON_INLINE int32_t __pyx_f_5MACS2_2IO_13cCallPeakUnit_right_sum(PyObject *, int, int); /*proto*/ static CYTHON_INLINE int32_t __pyx_f_5MACS2_2IO_13cCallPeakUnit_left_forward(PyObject *, int, int); /*proto*/ static CYTHON_INLINE int32_t __pyx_f_5MACS2_2IO_13cCallPeakUnit_right_forward(PyObject *, int, int); /*proto*/ static PyObject *__pyx_f_5MACS2_2IO_13cCallPeakUnit_wtd_find_summit(PyObject *, PyArrayObject *, PyArrayObject *, int32_t, int32_t, int32_t, float); /*proto*/ static float __pyx_f_5MACS2_2IO_13cCallPeakUnit_mean_from_value_length(PyArrayObject *, PyObject *); /*proto*/ static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t = { "float32_t", NULL, sizeof(__pyx_t_5numpy_float32_t), { 0 }, 0, 'R', 0, 0 }; static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int32_t = { "int32_t", NULL, sizeof(__pyx_t_5numpy_int32_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int32_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_int32_t), 0 }; #define __Pyx_MODULE_NAME "MACS2.IO.cCallPeakUnit" int __pyx_module_is_main_MACS2__IO__cCallPeakUnit = 0; /* Implementation of 'MACS2.IO.cCallPeakUnit' */ static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_map; static PyObject *__pyx_builtin_sum; static PyObject *__pyx_builtin_sorted; static PyObject *__pyx_builtin_zip; static PyObject *__pyx_builtin_Exception; static PyObject *__pyx_builtin_StopIteration; static PyObject *__pyx_builtin_open; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_RuntimeError; static PyObject *__pyx_pf_5MACS2_2IO_13cCallPeakUnit_do_nothing(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_args, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */ static int __pyx_pf_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments___init__(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *__pyx_v_self, PyObject *__pyx_v_treat, PyObject *__pyx_v_ctrl, int __pyx_v_d, PyObject *__pyx_v_ctrl_d_s, float __pyx_v_treat_scaling_factor, PyObject *__pyx_v_ctrl_scaling_factor_s, CYTHON_UNUSED PyBoolObject *__pyx_v_stderr_on, float __pyx_v_pseudocount, int __pyx_v_end_shift, float __pyx_v_lambda_bg, PyBoolObject *__pyx_v_save_bedGraph, PyObject *__pyx_v_bedGraph_filename_prefix, PyObject *__pyx_v_bedGraph_treat_filename, PyObject *__pyx_v_bedGraph_control_filename, PyBoolObject *__pyx_v_save_SPMR); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments_2set_pseudocount(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *__pyx_v_self, float __pyx_v_pseudocount); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments_4enable_trackline(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *__pyx_v_self); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments_6call_peaks(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *__pyx_v_self, PyObject *__pyx_v_scoring_function_symbols, PyObject *__pyx_v_score_cutoff_s, int __pyx_v_min_length, int __pyx_v_max_gap, PyBoolObject *__pyx_v_call_summits); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments_8call_broadpeaks(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *__pyx_v_self, PyObject *__pyx_v_scoring_function_symbols, PyObject *__pyx_v_lvl1_cutoff_s, PyObject *__pyx_v_lvl2_cutoff_s, int __pyx_v_min_length, int __pyx_v_lvl1_max_gap, int __pyx_v_lvl2_max_gap); /* proto */ static PyObject *__pyx_pf_5MACS2_2IO_13cCallPeakUnit_20CallerFromAlignments_10refine_peak_from_tags_distribution(struct __pyx_obj_5MACS2_2IO_13cCallPeakUnit_CallerFromAlignments *__pyx_v_self, PyObject *__pyx_v_peaks, int __pyx_v_window_size, float __pyx_v_cutoff); /* 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_2IO_13cCallPeakUnit_CallerFromAlignments(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static char __pyx_k_0[] = "0,"; static char __pyx_k_1[] = "1,"; 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_p[] = "p"; static char __pyx_k_q[] = "q"; static char __pyx_k_s[] = "s"; static char __pyx_k_w[] = "w"; static char __pyx_k_Zd[] = "Zd"; static char __pyx_k_Zf[] = "Zf"; static char __pyx_k_Zg[] = "Zg"; static char __pyx_k__4[] = ""; static char __pyx_k_fc[] = "fc"; static char __pyx_k_np[] = "np"; static char __pyx_k_1_1[] = "1,1"; static char __pyx_k_1_2[] = ",1"; static char __pyx_k__25[] = ","; static char __pyx_k_add[] = "add"; static char __pyx_k_doc[] = "__doc__"; static char __pyx_k_end[] = "end"; static char __pyx_k_get[] = "get"; static char __pyx_k_map[] = "map"; static char __pyx_k_sum[] = "sum"; static char __pyx_k_zip[] = "zip"; static char __pyx_k_args[] = "args"; static char __pyx_k_copy[] = "copy"; static char __pyx_k_ctrl[] = "ctrl"; static char __pyx_k_info[] = "info"; static char __pyx_k_join[] = "join"; static char __pyx_k_keys[] = "keys"; static char __pyx_k_main[] = "__main__"; static char __pyx_k_next[] = "next"; static char __pyx_k_open[] = "open"; static char __pyx_k_size[] = "size"; static char __pyx_k_sort[] = "sort"; static char __pyx_k_test[] = "__test__"; static char __pyx_k_time[] = "time"; static char __pyx_k_BYTE4[] = "BYTE4"; static char __pyx_k_array[] = "array"; static char __pyx_k_close[] = "close"; static char __pyx_k_debug[] = "debug"; static char __pyx_k_dtype[] = "dtype"; static char __pyx_k_int32[] = "int32"; static char __pyx_k_numpy[] = "numpy"; static char __pyx_k_peaks[] = "peaks"; static char __pyx_k_range[] = "range"; static char __pyx_k_right[] = "right"; static char __pyx_k_score[] = "score"; static char __pyx_k_shape[] = "shape"; static char __pyx_k_start[] = "start"; static char __pyx_k_total[] = "total"; static char __pyx_k_treat[] = "treat"; static char __pyx_k_ttime[] = "ttime"; static char __pyx_k_write[] = "write"; static char __pyx_k_zeros[] = "zeros"; static char __pyx_k_FBYTE4[] = "FBYTE4"; static char __pyx_k_PeakIO[] = "PeakIO"; static char __pyx_k_arange[] = "arange"; static char __pyx_k_author[] = "__author__"; static char __pyx_k_cutoff[] = "cutoff"; static char __pyx_k_import[] = "__import__"; static char __pyx_k_kwargs[] = "kwargs"; static char __pyx_k_length[] = "length"; static char __pyx_k_maxima[] = "maxima"; static char __pyx_k_pileup[] = "pileup"; static char __pyx_k_pscore[] = "pscore"; static char __pyx_k_qscore[] = "qscore"; static char __pyx_k_resize[] = "resize"; static char __pyx_k_sorted[] = "sorted"; static char __pyx_k_summit[] = "summit"; static char __pyx_k_values[] = "values"; static char __pyx_k_Counter[] = "Counter"; static char __pyx_k_LOG10_E[] = "LOG10_E"; static char __pyx_k_float32[] = "float32"; static char __pyx_k_logging[] = "logging"; static char __pyx_k_max_gap[] = "max_gap"; static char __pyx_k_nonzero[] = "nonzero"; static char __pyx_k_pyarray[] = "pyarray"; static char __pyx_k_reverse[] = "reverse"; static char __pyx_k_version[] = "__version__"; static char __pyx_k_PETrackI[] = "PETrackI"; static char __pyx_k_blockNum[] = "blockNum"; static char __pyx_k_ctrl_d_s[] = "ctrl_d_s"; static char __pyx_k_deepcopy[] = "deepcopy"; static char __pyx_k_operator[] = "operator"; static char __pyx_k_refcheck[] = "refcheck"; static char __pyx_k_s_d_d_5f[] = "%s\t%d\t%d\t%.5f\n"; static char __pyx_k_sorted_2[] = "__sorted"; static char __pyx_k_thickEnd[] = "thickEnd"; static char __pyx_k_Exception[] = "Exception"; static char __pyx_k_end_shift[] = "end_shift"; static char __pyx_k_lambda_bg[] = "lambda_bg"; static char __pyx_k_locations[] = "__locations"; static char __pyx_k_save_SPMR[] = "save_SPMR"; static char __pyx_k_stderr_on[] = "stderr_on"; static char __pyx_k_FWTrackIII[] = "FWTrackIII"; static char __pyx_k_LogLR_Asym[] = "LogLR_Asym"; static char __pyx_k_ValueError[] = "ValueError"; static char __pyx_k_blockSizes[] = "blockSizes"; static char __pyx_k_call_peaks[] = "call_peaks"; static char __pyx_k_do_nothing[] = "do_nothing"; static char __pyx_k_get_pscore[] = "get_pscore"; static char __pyx_k_itemgetter[] = "itemgetter"; static char __pyx_k_min_length[] = "min_length"; static char __pyx_k_peak_score[] = "peak_score"; static char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; static char __pyx_k_thickStart[] = "thickStart"; static char __pyx_k_BroadPeakIO[] = "BroadPeakIO"; static char __pyx_k_blockStarts[] = "blockStarts"; static char __pyx_k_collections[] = "collections"; static char __pyx_k_directional[] = "directional"; static char __pyx_k_fold_change[] = "fold_change"; static char __pyx_k_logLR_table[] = "logLR_table"; static char __pyx_k_pseudocount[] = "pseudocount"; static char __pyx_k_window_size[] = "window_size"; static char __pyx_k_RuntimeError[] = "RuntimeError"; static char __pyx_k_call_summits[] = "call_summits"; static char __pyx_k_intersection[] = "intersection"; static char __pyx_k_lvl1_max_gap[] = "lvl1_max_gap"; static char __pyx_k_lvl2_max_gap[] = "lvl2_max_gap"; static char __pyx_k_pscore_table[] = "pscore_table"; static char __pyx_k_searchsorted[] = "searchsorted"; static char __pyx_k_MACS2_Poisson[] = "MACS2.Poisson"; static char __pyx_k_MACS2_cSignal[] = "MACS2.cSignal"; static char __pyx_k_StopIteration[] = "StopIteration"; static char __pyx_k_get_chr_names[] = "get_chr_names"; static char __pyx_k_lvl1_cutoff_s[] = "lvl1_cutoff_s"; static char __pyx_k_lvl2_cutoff_s[] = "lvl2_cutoff_s"; static char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; static char __pyx_k_save_bedGraph[] = "save_bedGraph"; static char __pyx_k_baseline_value[] = "baseline_value"; static char __pyx_k_get_logLR_asym[] = "get_logLR_asym"; static char __pyx_k_parse_peakname[] = "parse_peakname"; static char __pyx_k_score_cutoff_s[] = "score_cutoff_s"; static char __pyx_k_MACS2_Constants[] = "MACS2.Constants"; static char __pyx_k_MACS2_hashtable[] = "MACS2.hashtable"; static char __pyx_k_add_PeakContent[] = "add_PeakContent"; static char __pyx_k_call_broadpeaks[] = "call_broadpeaks"; static char __pyx_k_enforce_valleys[] = "enforce_valleys"; static char __pyx_k_set_pseudocount[] = "set_pseudocount"; static char __pyx_k_Float64HashTable[] = "Float64HashTable"; static char __pyx_k_MACS2_IO_cPeakIO[] = "MACS2.IO.cPeakIO"; static char __pyx_k_enable_trackline[] = "enable_trackline"; static char __pyx_k_treat_pileup_bdg[] = "_treat_pileup.bdg"; static char __pyx_k_enforce_peakyness[] = "enforce_peakyness"; static char __pyx_k_pyx_releasebuffer[] = "__pyx_releasebuffer"; static char __pyx_k_P_Score_Upper_Tail[] = "P_Score_Upper_Tail"; static char __pyx_k_control_lambda_bdg[] = "_control_lambda.bdg"; static char __pyx_k_get_data_from_chrom[] = "get_data_from_chrom"; static char __pyx_k_pileup_a_chromosome[] = "pileup_a_chromosome"; static char __pyx_k_scoreTrackI_classes[] = "scoreTrackI classes"; static char __pyx_k_treat_scaling_factor[] = "treat_scaling_factor"; static char __pyx_k_ctrl_scaling_factor_s[] = "ctrl_scaling_factor_s"; static char __pyx_k_pileup_a_chromosome_c[] = "pileup_a_chromosome_c"; static char __pyx_k_MACS2_IO_cCallPeakUnit[] = "MACS2.IO.cCallPeakUnit"; static char __pyx_k_MACS2_IO_cFixWidthTrack[] = "MACS2.IO.cFixWidthTrack"; static char __pyx_k_bedGraph_treat_filename[] = "bedGraph_treat_filename"; static char __pyx_k_scoreCalculate_Revision[] = "scoreCalculate $Revision$"; static char __pyx_k_MACS2_IO_cPairedEndTrack[] = "MACS2.IO.cPairedEndTrack"; static char __pyx_k_bedGraph_filename_prefix[] = "bedGraph_filename_prefix"; static char __pyx_k_scoring_function_symbols[] = "scoring_function_symbols"; static char __pyx_k_bedGraph_control_filename[] = "bedGraph_control_filename"; static char __pyx_k_chromosome_s_is_not_valid[] = "chromosome %s is not valid."; static char __pyx_k_access_pq_hash_for_d_times[] = "access pq hash for %d times"; static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; static char __pyx_k_3_In_the_peak_calling_step_the[] = "#3 In the peak calling step, the following will be performed simultaneously:"; static char __pyx_k_Start_to_calculate_pvalue_stat[] = "Start to calculate pvalue stat..."; static char __pyx_k_Tao_Liu_vladimir_liu_gmail_com[] = "Tao Liu "; static char __pyx_k_3_Call_peaks_for_each_chromosom[] = "#3 Call peaks for each chromosome..."; static char __pyx_k_3_Pileup_will_be_based_on_seque[] = "#3 Pileup will be based on sequencing depth in treatment."; static char __pyx_k_3_Pre_compute_pvalue_qvalue_tab[] = "#3 Pre-compute pvalue-qvalue table..."; static char __pyx_k_3_SPMR_is_requested_so_pileup_w[] = "#3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads."; static char __pyx_k_3_Write_bedGraph_files_for_cont[] = "#3 Write bedGraph files for control lambda (after scaling if necessary)... %s"; static char __pyx_k_3_Write_bedGraph_files_for_trea[] = "#3 Write bedGraph files for treatment pileup (after scaling if necessary)... %s"; static char __pyx_k_Users_taoliu_Dropbox_UB_Dropbox[] = "/Users/taoliu/Dropbox-UB/Dropbox/Projects/MACS2/MACS/MACS2/IO/cCallPeakUnit.pyx"; static char __pyx_k_number_of_functions_and_cutoffs[] = "number of functions and cutoffs should be the same!"; static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; static char __pyx_k_Module_for_Calculate_Scores_Copy[] = "Module for Calculate Scores.\n\nCopyright (c) 2013 Tao Liu \n\nThis code is free software; you can redistribute it and/or modify it\nunder the terms of the BSD License (see the file COPYING included\nwith the distribution).\n\n@status: experimental\n@version: $Revision$\n@author: Tao Liu\n@contact: vladimir.liu@gmail.com\n"; static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; static char __pyx_k_Should_be_FWTrackIII_or_PETrackI[] = "Should be FWTrackIII or PETrackI object!"; static char __pyx_k_calculate_pvalue_access_hash_for[] = "calculate pvalue/access hash for %d times"; static char __pyx_k_chromosome_s_can_t_be_found_in_t[] = "chromosome %s can't be found in the FWTrackIII object. %s"; static char __pyx_k_make_pvalue_stat_cost_5f_seconds[] = "make pvalue_stat cost %.5f seconds"; 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"" : "s"); } static CYTHON_INLINE int __Pyx_IterFinish(void) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); PyObject* exc_type = tstate->curexc_type; if (unlikely(exc_type)) { if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) { PyObject *exc_value, *exc_tb; exc_value = tstate->curexc_value; exc_tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; Py_DECREF(exc_type); Py_XDECREF(exc_value); Py_XDECREF(exc_tb); return 0; } else { return -1; } } return 0; #else if (unlikely(PyErr_Occurred())) { if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { PyErr_Clear(); return 0; } else { return -1; } } return 0; #endif } static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { if (unlikely(retval)) { Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); return -1; } else { return __Pyx_IterFinish(); } return 0; } static void __Pyx_RaiseArgtupleInvalid( const char* func_name, int exact, Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found) { Py_ssize_t num_expected; const char *more_or_less; if (num_found < num_min) { num_expected = num_min; more_or_less = "at least"; } else { num_expected = num_max; more_or_less = "at most"; } if (exact) { more_or_less = "exactly"; } PyErr_Format(PyExc_TypeError, "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", func_name, more_or_less, num_expected, (num_expected == 1) ? "" : "s", num_found); } static void __Pyx_RaiseDoubleKeywordsError( const char* func_name, PyObject* kw_name) { PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION >= 3 "%s() got multiple values for keyword argument '%U'", func_name, kw_name); #else "%s() got multiple values for keyword argument '%s'", func_name, PyString_AsString(kw_name)); #endif } static int __Pyx_ParseOptionalKeywords( PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name) { PyObject *key = 0, *value = 0; Py_ssize_t pos = 0; PyObject*** name; PyObject*** first_kw_arg = argnames + num_pos_args; while (PyDict_Next(kwds, &pos, &key, &value)) { name = first_kw_arg; while (*name && (**name != key)) name++; if (*name) { values[name-argnames] = value; continue; } name = first_kw_arg; #if PY_MAJOR_VERSION < 3 if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { while (*name) { if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) && _PyString_Eq(**name, key)) { values[name-argnames] = value; break; } name++; } if (*name) continue; else { PyObject*** argname = argnames; while (argname != first_kw_arg) { if ((**argname == key) || ( (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) && _PyString_Eq(**argname, key))) { goto arg_passed_twice; } argname++; } } } else #endif if (likely(PyUnicode_Check(key))) { while (*name) { int cmp = (**name == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : #endif PyUnicode_Compare(**name, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; if (cmp == 0) { values[name-argnames] = value; break; } name++; } if (*name) continue; else { PyObject*** argname = argnames; while (argname != first_kw_arg) { int cmp = (**argname == key) ? 0 : #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : #endif PyUnicode_Compare(**argname, key); if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; if (cmp == 0) goto arg_passed_twice; argname++; } } } else goto invalid_keyword_type; if (kwds2) { if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; } else { goto invalid_keyword; } } return 0; arg_passed_twice: __Pyx_RaiseDoubleKeywordsError(function_name, key); goto bad; invalid_keyword_type: PyErr_Format(PyExc_TypeError, "%.200s() keywords must be strings", function_name); goto bad; invalid_keyword: PyErr_Format(PyExc_TypeError, #if PY_MAJOR_VERSION < 3 "%.200s() got an unexpected keyword argument '%.200s'", function_name, PyString_AsString(key)); #else "%s() got an unexpected keyword argument '%U'", function_name, key); #endif bad: return -1; } static void __Pyx_RaiseArgumentTypeInvalid(const char* name, PyObject *obj, PyTypeObject *type) { PyErr_Format(PyExc_TypeError, "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", name, type->tp_name, Py_TYPE(obj)->tp_name); } static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact) { if (unlikely(!type)) { PyErr_SetString(PyExc_SystemError, "Missing type object"); return 0; } if (none_allowed && obj == Py_None) return 1; else if (exact) { if (likely(Py_TYPE(obj) == type)) return 1; #if PY_MAJOR_VERSION == 2 else if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; #endif } else { if (likely(PyObject_TypeCheck(obj, type))) return 1; } __Pyx_RaiseArgumentTypeInvalid(name, obj, type); return 0; } #if 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 *instance_class = NULL; if (value && PyExceptionInstance_Check(value)) { instance_class = (PyObject*) Py_TYPE(value); if (instance_class != type) { if (PyObject_IsSubclass(instance_class, type)) { type = instance_class; } else { instance_class = NULL; } } } if (!instance_class) { PyObject *args; if (!value) args = PyTuple_New(0); else if (PyTuple_Check(value)) { Py_INCREF(value); args = value; } else args = PyTuple_Pack(1, value); if (!args) goto bad; owned_instance = PyObject_Call(type, args, NULL); Py_DECREF(args); if (!owned_instance) goto bad; value = owned_instance; if (!PyExceptionInstance_Check(value)) { PyErr_Format(PyExc_TypeError, "calling %R should have returned an instance of " "BaseException, not %R", type, Py_TYPE(value)); goto bad; } } } else { PyErr_SetString(PyExc_TypeError, "raise: exception class must be a subclass of BaseException"); goto bad; } #if PY_VERSION_HEX >= 0x03030000 if (cause) { #else if (cause && cause != Py_None) { #endif PyObject *fixed_cause; if (cause == Py_None) { fixed_cause = NULL; } else if (PyExceptionClass_Check(cause)) { fixed_cause = PyObject_CallObject(cause, NULL); if (fixed_cause == NULL) goto bad; } else if (PyExceptionInstance_Check(cause)) { fixed_cause = cause; Py_INCREF(fixed_cause); } else { PyErr_SetString(PyExc_TypeError, "exception causes must derive from " "BaseException"); goto bad; } PyException_SetCause(value, fixed_cause); } PyErr_SetObject(type, value); if (tb) { 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 PyObject* __Pyx_PyObject_GetSlice( PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop, PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice, int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) { #if CYTHON_COMPILING_IN_CPYTHON PyMappingMethods* mp; #if PY_MAJOR_VERSION < 3 PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence; if (likely(ms && ms->sq_slice)) { if (!has_cstart) { if (_py_start && (*_py_start != Py_None)) { cstart = __Pyx_PyIndex_AsSsize_t(*_py_start); if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; } else cstart = 0; } if (!has_cstop) { if (_py_stop && (*_py_stop != Py_None)) { cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop); if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; } else cstop = PY_SSIZE_T_MAX; } if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) { Py_ssize_t l = ms->sq_length(obj); if (likely(l >= 0)) { if (cstop < 0) { cstop += l; if (cstop < 0) cstop = 0; } if (cstart < 0) { cstart += l; if (cstart < 0) cstart = 0; } } else { if (PyErr_ExceptionMatches(PyExc_OverflowError)) PyErr_Clear(); else goto bad; } } return ms->sq_slice(obj, cstart, cstop); } #endif mp = Py_TYPE(obj)->tp_as_mapping; if (likely(mp && mp->mp_subscript)) #endif { PyObject* result; PyObject *py_slice, *py_start, *py_stop; if (_py_slice) { py_slice = *_py_slice; } else { PyObject* owned_start = NULL; PyObject* owned_stop = NULL; if (_py_start) { py_start = *_py_start; } else { if (has_cstart) { owned_start = py_start = PyInt_FromSsize_t(cstart); if (unlikely(!py_start)) goto bad; } else py_start = Py_None; } if (_py_stop) { py_stop = *_py_stop; } else { if (has_cstop) { owned_stop = py_stop = PyInt_FromSsize_t(cstop); if (unlikely(!py_stop)) { Py_XDECREF(owned_start); goto bad; } } else py_stop = Py_None; } py_slice = PySlice_New(py_start, py_stop, Py_None); Py_XDECREF(owned_start); Py_XDECREF(owned_stop); if (unlikely(!py_slice)) goto bad; } #if CYTHON_COMPILING_IN_CPYTHON result = mp->mp_subscript(obj, py_slice); #else result = PyObject_GetItem(obj, py_slice); #endif if (!_py_slice) { Py_DECREF(py_slice); } return result; } PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name); bad: return NULL; } static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { #if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); *type = tstate->exc_type; *value = tstate->exc_value; *tb = tstate->exc_traceback; Py_XINCREF(*type); Py_XINCREF(*value); Py_XINCREF(*tb); #else PyErr_GetExcInfo(type, value, tb); #endif } static void __Pyx_ExceptionReset(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->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = type; tstate->exc_value = value; tstate->exc_traceback = tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_SetExcInfo(type, value, tb); #endif } static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); } static CYTHON_INLINE PyObject* __Pyx_PyDict_Values(PyObject* d) { if (PY_MAJOR_VERSION >= 3) return __Pyx_PyObject_CallMethod1((PyObject*)&PyDict_Type, __pyx_n_s_values, d); else return PyDict_Values(d); } static CYTHON_INLINE PyObject* __Pyx_PyDict_Keys(PyObject* d) { if (PY_MAJOR_VERSION >= 3) return __Pyx_PyObject_CallMethod1((PyObject*)&PyDict_Type, __pyx_n_s_keys, d); else return PyDict_Keys(d); } static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { #if CYTHON_COMPILING_IN_PYPY return PyObject_RichCompareBool(s1, s2, equals); #else if (s1 == s2) { return (equals == Py_EQ); } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { const char *ps1, *ps2; Py_ssize_t length = PyBytes_GET_SIZE(s1); if (length != PyBytes_GET_SIZE(s2)) return (equals == Py_NE); ps1 = PyBytes_AS_STRING(s1); ps2 = PyBytes_AS_STRING(s2); if (ps1[0] != ps2[0]) { return (equals == Py_NE); } else if (length == 1) { return (equals == Py_EQ); } else { int result = memcmp(ps1, ps2, (size_t)length); return (equals == Py_EQ) ? (result == 0) : (result != 0); } } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { return (equals == Py_NE); } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { return (equals == Py_NE); } else { int result; PyObject* py_result = PyObject_RichCompare(s1, s2, equals); if (!py_result) return -1; result = __Pyx_PyObject_IsTrue(py_result); Py_DECREF(py_result); return result; } #endif } static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { #if CYTHON_COMPILING_IN_PYPY return PyObject_RichCompareBool(s1, s2, equals); #else #if PY_MAJOR_VERSION < 3 PyObject* owned_ref = NULL; #endif int s1_is_unicode, s2_is_unicode; if (s1 == s2) { goto return_eq; } s1_is_unicode = PyUnicode_CheckExact(s1); s2_is_unicode = PyUnicode_CheckExact(s2); #if PY_MAJOR_VERSION < 3 if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { owned_ref = PyUnicode_FromObject(s2); if (unlikely(!owned_ref)) return -1; s2 = owned_ref; s2_is_unicode = 1; } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { owned_ref = PyUnicode_FromObject(s1); if (unlikely(!owned_ref)) return -1; s1 = owned_ref; s1_is_unicode = 1; } else if (((!s2_is_unicode) & (!s1_is_unicode))) { return __Pyx_PyBytes_Equals(s1, s2, equals); } #endif if (s1_is_unicode & s2_is_unicode) { Py_ssize_t length; int kind; void *data1, *data2; #if CYTHON_PEP393_ENABLED if (unlikely(PyUnicode_READY(s1) < 0) || unlikely(PyUnicode_READY(s2) < 0)) return -1; #endif length = __Pyx_PyUnicode_GET_LENGTH(s1); if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { goto return_ne; } kind = __Pyx_PyUnicode_KIND(s1); if (kind != __Pyx_PyUnicode_KIND(s2)) { goto return_ne; } data1 = __Pyx_PyUnicode_DATA(s1); data2 = __Pyx_PyUnicode_DATA(s2); if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { goto return_ne; } else if (length == 1) { goto return_eq; } else { int result = memcmp(data1, data2, (size_t)(length * kind)); #if PY_MAJOR_VERSION < 3 Py_XDECREF(owned_ref); #endif return (equals == Py_EQ) ? (result == 0) : (result != 0); } } else if ((s1 == Py_None) & s2_is_unicode) { goto return_ne; } else if ((s2 == Py_None) & s1_is_unicode) { goto return_ne; } else { int result; PyObject* py_result = PyObject_RichCompare(s1, s2, equals); if (!py_result) return -1; result = __Pyx_PyObject_IsTrue(py_result); Py_DECREF(py_result); return result; } return_eq: #if PY_MAJOR_VERSION < 3 Py_XDECREF(owned_ref); #endif return (equals == Py_EQ); return_ne: #if PY_MAJOR_VERSION < 3 Py_XDECREF(owned_ref); #endif return (equals == Py_NE); #endif } static CYTHON_INLINE long __Pyx_div_long(long a, long b) { long q = a / b; long r = a - q*b; q -= ((r != 0) & ((r ^ b) < 0)); return q; } static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); } static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { Py_ssize_t q = a / b; Py_ssize_t r = a - q*b; q -= ((r != 0) & ((r ^ b) < 0)); return q; } static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { unsigned int n = 1; return *(unsigned char*)(&n) != 0; } static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, __Pyx_BufFmt_StackElem* stack, __Pyx_TypeInfo* type) { stack[0].field = &ctx->root; stack[0].parent_offset = 0; ctx->root.type = type; ctx->root.name = "buffer dtype"; ctx->root.offset = 0; ctx->head = stack; ctx->head->field = &ctx->root; ctx->fmt_offset = 0; ctx->head->parent_offset = 0; ctx->new_packmode = '@'; ctx->enc_packmode = '@'; ctx->new_count = 1; ctx->enc_count = 0; ctx->enc_type = 0; ctx->is_complex = 0; ctx->is_valid_array = 0; ctx->struct_alignment = 0; while (type->typegroup == 'S') { ++ctx->head; ctx->head->field = type->fields; ctx->head->parent_offset = 0; type = type->fields->type; } } static int __Pyx_BufFmt_ParseNumber(const char** ts) { int count; const char* t = *ts; if (*t < '0' || *t > '9') { return -1; } else { count = *t++ - '0'; while (*t >= '0' && *t < '9') { count *= 10; count += *t++ - '0'; } } *ts = t; return count; } static int __Pyx_BufFmt_ExpectNumber(const char **ts) { int number = __Pyx_BufFmt_ParseNumber(ts); if (number == -1) /* First char was not a digit */ PyErr_Format(PyExc_ValueError,\ "Does not understand character buffer dtype format string ('%c')", **ts); return number; } static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { PyErr_Format(PyExc_ValueError, "Unexpected format string character: '%c'", ch); } static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { switch (ch) { case 'c': return "'char'"; case 'b': return "'signed char'"; case 'B': return "'unsigned char'"; case 'h': return "'short'"; case 'H': return "'unsigned short'"; case 'i': return "'int'"; case 'I': return "'unsigned int'"; case 'l': return "'long'"; case 'L': return "'unsigned long'"; case 'q': return "'long long'"; case 'Q': return "'unsigned long long'"; case 'f': return (is_complex ? "'complex float'" : "'float'"); case 'd': return (is_complex ? "'complex double'" : "'double'"); case 'g': return (is_complex ? "'complex long double'" : "'long double'"); case 'T': return "a struct"; case 'O': return "Python object"; case 'P': return "a pointer"; case 's': case 'p': return "a string"; case 0: return "end"; default: return "unparseable format string"; } } static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { switch (ch) { case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return 2; case 'i': case 'I': case 'l': case 'L': return 4; case 'q': case 'Q': return 8; case 'f': return (is_complex ? 8 : 4); case 'd': return (is_complex ? 16 : 8); case 'g': { PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); return 0; } case 'O': case 'P': return sizeof(void*); default: __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { switch (ch) { case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return sizeof(short); case 'i': case 'I': return sizeof(int); case 'l': case 'L': return sizeof(long); #ifdef HAVE_LONG_LONG case 'q': case 'Q': return sizeof(PY_LONG_LONG); #endif case 'f': return sizeof(float) * (is_complex ? 2 : 1); case 'd': return sizeof(double) * (is_complex ? 2 : 1); case 'g': return sizeof(long double) * (is_complex ? 2 : 1); case 'O': case 'P': return sizeof(void*); default: { __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } } typedef struct { char c; short x; } __Pyx_st_short; typedef struct { char c; int x; } __Pyx_st_int; typedef struct { char c; long x; } __Pyx_st_long; typedef struct { char c; float x; } __Pyx_st_float; typedef struct { char c; double x; } __Pyx_st_double; typedef struct { char c; long double x; } __Pyx_st_longdouble; typedef struct { char c; void *x; } __Pyx_st_void_p; #ifdef HAVE_LONG_LONG typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; #endif static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { switch (ch) { case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); #ifdef HAVE_LONG_LONG case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); #endif case 'f': return sizeof(__Pyx_st_float) - sizeof(float); case 'd': return sizeof(__Pyx_st_double) - sizeof(double); case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); default: __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } /* These are for computing the padding at the end of the struct to align on the first member of the struct. This will probably the same as above, but we don't have any guarantees. */ typedef struct { short x; char c; } __Pyx_pad_short; typedef struct { int x; char c; } __Pyx_pad_int; typedef struct { long x; char c; } __Pyx_pad_long; typedef struct { float x; char c; } __Pyx_pad_float; typedef struct { double x; char c; } __Pyx_pad_double; typedef struct { long double x; char c; } __Pyx_pad_longdouble; typedef struct { void *x; char c; } __Pyx_pad_void_p; #ifdef HAVE_LONG_LONG typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; #endif static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { switch (ch) { case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); #ifdef HAVE_LONG_LONG case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); #endif case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); default: __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { switch (ch) { case 'c': return 'H'; case 'b': case 'h': case 'i': case 'l': case 'q': case 's': case 'p': return 'I'; case 'B': case 'H': case 'I': case 'L': case 'Q': return 'U'; case 'f': case 'd': case 'g': return (is_complex ? 'C' : 'R'); case 'O': return 'O'; case 'P': return 'P'; default: { __Pyx_BufFmt_RaiseUnexpectedChar(ch); return 0; } } } static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { if (ctx->head == NULL || ctx->head->field == &ctx->root) { const char* expected; const char* quote; if (ctx->head == NULL) { expected = "end"; quote = ""; } else { expected = ctx->head->field->type->name; quote = "'"; } PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch, expected %s%s%s but got %s", quote, expected, quote, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); } else { __Pyx_StructField* field = ctx->head->field; __Pyx_StructField* parent = (ctx->head - 1)->field; PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), parent->type->name, field->name); } } static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { char group; size_t size, offset, arraysize = 1; if (ctx->enc_type == 0) return 0; if (ctx->head->field->type->arraysize[0]) { int i, ndim = 0; if (ctx->enc_type == 's' || ctx->enc_type == 'p') { ctx->is_valid_array = ctx->head->field->type->ndim == 1; ndim = 1; if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { PyErr_Format(PyExc_ValueError, "Expected a dimension of size %zu, got %zu", ctx->head->field->type->arraysize[0], ctx->enc_count); return -1; } } if (!ctx->is_valid_array) { PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", ctx->head->field->type->ndim, ndim); return -1; } for (i = 0; i < ctx->head->field->type->ndim; i++) { arraysize *= ctx->head->field->type->arraysize[i]; } ctx->is_valid_array = 0; ctx->enc_count = 1; } group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); do { __Pyx_StructField* field = ctx->head->field; __Pyx_TypeInfo* type = field->type; if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); } else { size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); } if (ctx->enc_packmode == '@') { size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); size_t align_mod_offset; if (align_at == 0) return -1; align_mod_offset = ctx->fmt_offset % align_at; if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; if (ctx->struct_alignment == 0) ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, ctx->is_complex); } if (type->size != size || type->typegroup != group) { if (type->typegroup == 'C' && type->fields != NULL) { size_t parent_offset = ctx->head->parent_offset + field->offset; ++ctx->head; ctx->head->field = type->fields; ctx->head->parent_offset = parent_offset; continue; } if ((type->typegroup == 'H' || group == 'H') && type->size == size) { } else { __Pyx_BufFmt_RaiseExpected(ctx); return -1; } } offset = ctx->head->parent_offset + field->offset; if (ctx->fmt_offset != offset) { PyErr_Format(PyExc_ValueError, "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); return -1; } ctx->fmt_offset += size; if (arraysize) ctx->fmt_offset += (arraysize - 1) * size; --ctx->enc_count; /* Consume from buffer string */ while (1) { if (field == &ctx->root) { ctx->head = NULL; if (ctx->enc_count != 0) { __Pyx_BufFmt_RaiseExpected(ctx); return -1; } break; /* breaks both loops as ctx->enc_count == 0 */ } ctx->head->field = ++field; if (field->type == NULL) { --ctx->head; field = ctx->head->field; continue; } else if (field->type->typegroup == 'S') { size_t parent_offset = ctx->head->parent_offset + field->offset; if (field->type->fields->type == NULL) continue; /* empty struct */ field = field->type->fields; ++ctx->head; ctx->head->field = field; ctx->head->parent_offset = parent_offset; break; } else { break; } } } while (ctx->enc_count); ctx->enc_type = 0; ctx->is_complex = 0; return 0; } static CYTHON_INLINE PyObject * __pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) { const char *ts = *tsp; int i = 0, number; int ndim = ctx->head->field->type->ndim; ; ++ts; if (ctx->new_count != 1) { PyErr_SetString(PyExc_ValueError, "Cannot handle repeated arrays in format string"); return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; while (*ts && *ts != ')') { switch (*ts) { case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; default: break; /* not a 'break' in the loop */ } number = __Pyx_BufFmt_ExpectNumber(&ts); if (number == -1) return NULL; if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) return PyErr_Format(PyExc_ValueError, "Expected a dimension of size %zu, got %d", ctx->head->field->type->arraysize[i], number); if (*ts != ',' && *ts != ')') return PyErr_Format(PyExc_ValueError, "Expected a comma in format string, got '%c'", *ts); if (*ts == ',') ts++; i++; } if (i != ndim) return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", ctx->head->field->type->ndim, i); if (!*ts) { PyErr_SetString(PyExc_ValueError, "Unexpected end of format string, expected ')'"); return NULL; } ctx->is_valid_array = 1; ctx->new_count = 1; *tsp = ++ts; return Py_None; } static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { int got_Z = 0; while (1) { switch(*ts) { case 0: if (ctx->enc_type != 0 && ctx->head == NULL) { __Pyx_BufFmt_RaiseExpected(ctx); return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; if (ctx->head != NULL) { __Pyx_BufFmt_RaiseExpected(ctx); return NULL; } return ts; case ' ': case '\r': case '\n': ++ts; break; case '<': if (!__Pyx_IsLittleEndian()) { PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); return NULL; } ctx->new_packmode = '='; ++ts; break; case '>': case '!': if (__Pyx_IsLittleEndian()) { PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); return NULL; } ctx->new_packmode = '='; ++ts; break; case '=': case '@': case '^': ctx->new_packmode = *ts++; break; case 'T': /* substruct */ { const char* ts_after_sub; size_t i, struct_count = ctx->new_count; size_t struct_alignment = ctx->struct_alignment; ctx->new_count = 1; ++ts; if (*ts != '{') { PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->enc_type = 0; /* Erase processed last struct element */ ctx->enc_count = 0; ctx->struct_alignment = 0; ++ts; ts_after_sub = ts; for (i = 0; i != struct_count; ++i) { ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); if (!ts_after_sub) return NULL; } ts = ts_after_sub; if (struct_alignment) ctx->struct_alignment = struct_alignment; } break; case '}': /* end of substruct; either repeat or move on */ { size_t alignment = ctx->struct_alignment; ++ts; if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->enc_type = 0; /* Erase processed last struct element */ if (alignment && ctx->fmt_offset % alignment) { ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); } } return ts; case 'x': if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->fmt_offset += ctx->new_count; ctx->new_count = 1; ctx->enc_count = 0; ctx->enc_type = 0; ctx->enc_packmode = ctx->new_packmode; ++ts; break; case 'Z': got_Z = 1; ++ts; if (*ts != 'f' && *ts != 'd' && *ts != 'g') { __Pyx_BufFmt_RaiseUnexpectedChar('Z'); return NULL; } case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': case 'l': case 'L': case 'q': case 'Q': case 'f': case 'd': case 'g': case 'O': case 'p': if (ctx->enc_type == *ts && got_Z == ctx->is_complex && ctx->enc_packmode == ctx->new_packmode) { ctx->enc_count += ctx->new_count; ctx->new_count = 1; got_Z = 0; ++ts; break; } case 's': if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; ctx->enc_count = ctx->new_count; ctx->enc_packmode = ctx->new_packmode; ctx->enc_type = *ts; ctx->is_complex = got_Z; ++ts; ctx->new_count = 1; got_Z = 0; break; case ':': ++ts; while(*ts != ':') ++ts; ++ts; break; case '(': if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; break; default: { int number = __Pyx_BufFmt_ExpectNumber(&ts); if (number == -1) return NULL; ctx->new_count = (size_t)number; } } } } static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) { buf->buf = NULL; buf->obj = NULL; buf->strides = __Pyx_zeros; buf->shape = __Pyx_zeros; buf->suboffsets = __Pyx_minusones; } static CYTHON_INLINE int __Pyx_GetBufferAndValidate( Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack) { if (obj == Py_None || obj == NULL) { __Pyx_ZeroBuffer(buf); return 0; } buf->buf = NULL; if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; if (buf->ndim != nd) { PyErr_Format(PyExc_ValueError, "Buffer has wrong number of dimensions (expected %d, got %d)", nd, buf->ndim); goto fail; } if (!cast) { __Pyx_BufFmt_Context ctx; __Pyx_BufFmt_Init(&ctx, stack, dtype); if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; } if ((unsigned)buf->itemsize != dtype->size) { PyErr_Format(PyExc_ValueError, "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", buf->itemsize, (buf->itemsize > 1) ? "s" : "", dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); goto fail; } if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; return 0; fail:; __Pyx_ZeroBuffer(buf); return -1; } static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { if (info->buf == NULL) return; if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; __Pyx_ReleaseBuffer(info); } static void __Pyx_RaiseBufferFallbackError(void) { PyErr_SetString(PyExc_ValueError, "Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!"); } static CYTHON_INLINE int __Pyx_PyObject_SetSlice( PyObject* obj, PyObject* value, Py_ssize_t cstart, Py_ssize_t cstop, PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice, int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) { #if CYTHON_COMPILING_IN_CPYTHON PyMappingMethods* mp; #if PY_MAJOR_VERSION < 3 PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence; if (likely(ms && ms->sq_ass_slice)) { if (!has_cstart) { if (_py_start && (*_py_start != Py_None)) { cstart = __Pyx_PyIndex_AsSsize_t(*_py_start); if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; } else cstart = 0; } if (!has_cstop) { if (_py_stop && (*_py_stop != Py_None)) { cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop); if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad; } else cstop = PY_SSIZE_T_MAX; } if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) { Py_ssize_t l = ms->sq_length(obj); if (likely(l >= 0)) { if (cstop < 0) { cstop += l; if (cstop < 0) cstop = 0; } if (cstart < 0) { cstart += l; if (cstart < 0) cstart = 0; } } else { if (PyErr_ExceptionMatches(PyExc_OverflowError)) PyErr_Clear(); else goto bad; } } return ms->sq_ass_slice(obj, cstart, cstop, value); } #endif mp = Py_TYPE(obj)->tp_as_mapping; if (likely(mp && mp->mp_ass_subscript)) #endif { int result; PyObject *py_slice, *py_start, *py_stop; if (_py_slice) { py_slice = *_py_slice; } else { PyObject* owned_start = NULL; PyObject* owned_stop = NULL; if (_py_start) { py_start = *_py_start; } else { if (has_cstart) { owned_start = py_start = PyInt_FromSsize_t(cstart); if (unlikely(!py_start)) goto bad; } else py_start = Py_None; } if (_py_stop) { py_stop = *_py_stop; } else { if (has_cstop) { owned_stop = py_stop = PyInt_FromSsize_t(cstop); if (unlikely(!py_stop)) { Py_XDECREF(owned_start); goto bad; } } else py_stop = Py_None; } py_slice = PySlice_New(py_start, py_stop, Py_None); Py_XDECREF(owned_start); Py_XDECREF(owned_stop); if (unlikely(!py_slice)) goto bad; } #if CYTHON_COMPILING_IN_CPYTHON result = mp->mp_ass_subscript(obj, py_slice, value); #else result = value ? PyObject_SetItem(obj, py_slice, value) : PyObject_DelItem(obj, py_slice); #endif if (!_py_slice) { Py_DECREF(py_slice); } return result; } PyErr_Format(PyExc_TypeError, "'%.200s' object does not support slice %.10s", Py_TYPE(obj)->tp_name, value ? "assignment" : "deletion"); bad: return -1; } static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { PyObject *local_type, *local_value, *local_tb; #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; PyThreadState *tstate = PyThreadState_GET(); local_type = tstate->curexc_type; local_value = tstate->curexc_value; local_tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; #else PyErr_Fetch(&local_type, &local_value, &local_tb); #endif PyErr_NormalizeException(&local_type, &local_value, &local_tb); #if CYTHON_COMPILING_IN_CPYTHON if (unlikely(tstate->curexc_type)) #else if (unlikely(PyErr_Occurred())) #endif goto bad; #if PY_MAJOR_VERSION >= 3 if (local_tb) { if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) goto bad; } #endif Py_XINCREF(local_tb); Py_XINCREF(local_type); Py_XINCREF(local_value); *type = local_type; *value = local_value; *tb = local_tb; #if CYTHON_COMPILING_IN_CPYTHON tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = local_type; tstate->exc_value = local_value; tstate->exc_traceback = local_tb; Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); #else PyErr_SetExcInfo(local_type, local_value, local_tb); #endif return 0; bad: *type = 0; *value = 0; *tb = 0; Py_XDECREF(local_type); Py_XDECREF(local_value); Py_XDECREF(local_tb); return -1; } #if !CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values) { return PyObject_CallMethodObjArgs(sep, __pyx_n_s_join, values, NULL); } #endif 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 PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) { PyObject* value = __Pyx_PyObject_GetAttrStr(module, name); if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) { PyErr_Format(PyExc_ImportError, #if PY_MAJOR_VERSION < 3 "cannot import name %.230s", PyString_AS_STRING(name)); #else "cannot import name %S", name); #endif } return value; } #if PY_MAJOR_VERSION < 3 static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { #if PY_VERSION_HEX >= 0x02060000 if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); #endif if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); #if PY_VERSION_HEX < 0x02060000 if (obj->ob_type->tp_dict) { PyObject *getbuffer_cobj = PyObject_GetItem( obj->ob_type->tp_dict, __pyx_n_s_pyx_getbuffer); if (getbuffer_cobj) { getbufferproc func = (getbufferproc) PyCObject_AsVoidPtr(getbuffer_cobj); Py_DECREF(getbuffer_cobj); if (!func) goto fail; return func(obj, view, flags); } else { PyErr_Clear(); } } #endif PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); #if PY_VERSION_HEX < 0x02060000 fail: #endif return -1; } static void __Pyx_ReleaseBuffer(Py_buffer *view) { PyObject *obj = view->obj; if (!obj) return; #if PY_VERSION_HEX >= 0x02060000 if (PyObject_CheckBuffer(obj)) { PyBuffer_Release(view); return; } #endif if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } #if PY_VERSION_HEX < 0x02060000 if (obj->ob_type->tp_dict) { PyObject *releasebuffer_cobj = PyObject_GetItem( obj->ob_type->tp_dict, __pyx_n_s_pyx_releasebuffer); if (releasebuffer_cobj) { releasebufferproc func = (releasebufferproc) PyCObject_AsVoidPtr(releasebuffer_cobj); Py_DECREF(releasebuffer_cobj); if (!func) goto fail; func(obj, view); return; } else { PyErr_Clear(); } } #endif goto nofail; #if PY_VERSION_HEX < 0x02060000 fail: #endif PyErr_WriteUnraisable(obj); nofail: Py_DECREF(obj); view->obj = NULL; } #endif /* PY_MAJOR_VERSION < 3 */ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { PyObject *empty_list = 0; PyObject *module = 0; PyObject *global_dict = 0; PyObject *empty_dict = 0; PyObject *list; #if PY_VERSION_HEX < 0x03030000 PyObject *py_import; py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); if (!py_import) goto bad; #endif if (from_list) list = from_list; else { empty_list = PyList_New(0); if (!empty_list) goto bad; list = empty_list; } global_dict = PyModule_GetDict(__pyx_m); if (!global_dict) goto bad; empty_dict = PyDict_New(); if (!empty_dict) goto bad; #if PY_VERSION_HEX >= 0x02050000 { #if PY_MAJOR_VERSION >= 3 if (level == -1) { if (strchr(__Pyx_MODULE_NAME, '.')) { #if PY_VERSION_HEX < 0x03030000 PyObject *py_level = PyInt_FromLong(1); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); #else module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, 1); #endif if (!module) { if (!PyErr_ExceptionMatches(PyExc_ImportError)) goto bad; PyErr_Clear(); } } level = 0; /* try absolute import on failure */ } #endif if (!module) { #if PY_VERSION_HEX < 0x03030000 PyObject *py_level = PyInt_FromLong(level); if (!py_level) goto bad; module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, py_level, NULL); Py_DECREF(py_level); #else module = PyImport_ImportModuleLevelObject( name, global_dict, empty_dict, list, level); #endif } } #else if (level>0) { PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4."); goto bad; } module = PyObject_CallFunctionObjArgs(py_import, name, global_dict, empty_dict, list, NULL); #endif bad: #if PY_VERSION_HEX < 0x03030000 Py_XDECREF(py_import); #endif Py_XDECREF(empty_list); Py_XDECREF(empty_dict); return module; } #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func) \ { \ func_type value = func(x); \ if (sizeof(target_type) < sizeof(func_type)) { \ if (unlikely(value != (func_type) (target_type) value)) { \ func_type zero = 0; \ PyErr_SetString(PyExc_OverflowError, \ (is_unsigned && unlikely(value < zero)) ? \ "can't convert negative value to " #target_type : \ "value too large to convert to " #target_type); \ return (target_type) -1; \ } \ } \ return (target_type) value; \ } #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS #include "longintrepr.h" #endif #endif static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { const int neg_one = (int) -1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { if (sizeof(int) < sizeof(long)) { __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG) } else { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to int"); return (int) -1; } return (int) val; } } else #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(int)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return (int) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to int"); return (int) -1; } if (sizeof(int) <= sizeof(unsigned long)) { __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong) } else if (sizeof(int) <= sizeof(unsigned long long)) { __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong) } } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(int)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return +(int) ((PyLongObject*)x)->ob_digit[0]; case -1: return -(int) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif if (sizeof(int) <= sizeof(long)) { __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong) } else if (sizeof(int) <= sizeof(long long)) { __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong) } } { #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else int val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_MAJOR_VERSION < 3 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int one = 1; int is_little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; int ret = _PyLong_AsByteArray((PyLongObject *)v, bytes, sizeof(val), is_little, !is_unsigned); Py_DECREF(v); if (likely(!ret)) return val; } #endif return (int) -1; } } else { int val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (int) -1; val = __Pyx_PyInt_As_int(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { const long neg_one = (long) -1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { if (sizeof(long) < sizeof(long)) { return PyInt_FromLong((long) value); } else if (sizeof(long) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); } else if (sizeof(long) <= sizeof(unsigned long long)) { return PyLong_FromUnsignedLongLong((unsigned long long) value); } } else { if (sizeof(long) <= sizeof(long)) { return PyInt_FromLong((long) value); } else if (sizeof(long) <= sizeof(long long)) { return PyLong_FromLongLong((long long) value); } } { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; return _PyLong_FromByteArray(bytes, sizeof(long), little, !is_unsigned); } } static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { const int neg_one = (int) -1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { if (sizeof(int) < sizeof(long)) { return PyInt_FromLong((long) value); } else if (sizeof(int) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); } else if (sizeof(int) <= sizeof(unsigned long long)) { return PyLong_FromUnsignedLongLong((unsigned long long) value); } } else { if (sizeof(int) <= sizeof(long)) { return PyInt_FromLong((long) value); } else if (sizeof(int) <= sizeof(long long)) { return PyLong_FromLongLong((long long) value); } } { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; return _PyLong_FromByteArray(bytes, sizeof(int), little, !is_unsigned); } } #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS #include "longintrepr.h" #endif #endif static CYTHON_INLINE int32_t __Pyx_PyInt_As_int32_t(PyObject *x) { const int32_t neg_one = (int32_t) -1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { if (sizeof(int32_t) < sizeof(long)) { __PYX_VERIFY_RETURN_INT(int32_t, long, PyInt_AS_LONG) } else { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to int32_t"); return (int32_t) -1; } return (int32_t) 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(int32_t)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return (int32_t) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif if (unlikely(Py_SIZE(x) < 0)) { PyErr_SetString(PyExc_OverflowError, "can't convert negative value to int32_t"); return (int32_t) -1; } if (sizeof(int32_t) <= sizeof(unsigned long)) { __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, PyLong_AsUnsignedLong) } else if (sizeof(int32_t) <= sizeof(unsigned long long)) { __PYX_VERIFY_RETURN_INT(int32_t, unsigned long long, PyLong_AsUnsignedLongLong) } } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS if (sizeof(digit) <= sizeof(int32_t)) { switch (Py_SIZE(x)) { case 0: return 0; case 1: return +(int32_t) ((PyLongObject*)x)->ob_digit[0]; case -1: return -(int32_t) ((PyLongObject*)x)->ob_digit[0]; } } #endif #endif if (sizeof(int32_t) <= sizeof(long)) { __PYX_VERIFY_RETURN_INT(int32_t, long, PyLong_AsLong) } else if (sizeof(int32_t) <= sizeof(long long)) { __PYX_VERIFY_RETURN_INT(int32_t, long long, PyLong_AsLongLong) } } { #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else int32_t 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 (int32_t) -1; } } else { int32_t val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (int32_t) -1; val = __Pyx_PyInt_As_int32_t(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int32_t(int32_t value) { const int32_t neg_one = (int32_t) -1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { if (sizeof(int32_t) < sizeof(long)) { return PyInt_FromLong((long) value); } else if (sizeof(int32_t) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); } else if (sizeof(int32_t) <= sizeof(unsigned long long)) { return PyLong_FromUnsignedLongLong((unsigned long long) value); } } else { if (sizeof(int32_t) <= sizeof(long)) { return PyInt_FromLong((long) value); } else if (sizeof(int32_t) <= sizeof(long long)) { return PyLong_FromLongLong((long long) value); } } { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; return _PyLong_FromByteArray(bytes, sizeof(int32_t), little, !is_unsigned); } } #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_As_long(PyObject *x) { const long neg_one = (long) -1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { if (sizeof(long) < sizeof(long)) { __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG) } else { 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; } if (sizeof(long) <= sizeof(unsigned long)) { __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong) } else if (sizeof(long) <= sizeof(unsigned long long)) { __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong) } } 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 if (sizeof(long) <= sizeof(long)) { __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong) } else if (sizeof(long) <= sizeof(long long)) { __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong) } } { #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) PyErr_SetString(PyExc_RuntimeError, "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); #else long val; PyObject *v = __Pyx_PyNumber_Int(x); #if PY_MAJOR_VERSION < 3 if (likely(v) && !PyLong_Check(v)) { PyObject *tmp = v; v = PyNumber_Long(tmp); Py_DECREF(tmp); } #endif if (likely(v)) { int one = 1; int is_little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&val; int ret = _PyLong_AsByteArray((PyLongObject *)v, bytes, sizeof(val), is_little, !is_unsigned); Py_DECREF(v); if (likely(!ret)) return val; } #endif return (long) -1; } } else { long val; PyObject *tmp = __Pyx_PyNumber_Int(x); if (!tmp) return (long) -1; val = __Pyx_PyInt_As_long(tmp); Py_DECREF(tmp); return val; } } static CYTHON_INLINE PyObject* __Pyx_PyInt_From_Py_intptr_t(Py_intptr_t value) { const Py_intptr_t neg_one = (Py_intptr_t) -1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { if (sizeof(Py_intptr_t) < sizeof(long)) { return PyInt_FromLong((long) value); } else if (sizeof(Py_intptr_t) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); } else if (sizeof(Py_intptr_t) <= sizeof(unsigned long long)) { return PyLong_FromUnsignedLongLong((unsigned long long) value); } } else { if (sizeof(Py_intptr_t) <= sizeof(long)) { return PyInt_FromLong((long) value); } else if (sizeof(Py_intptr_t) <= sizeof(long long)) { return PyLong_FromLongLong((long long) value); } } { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; return _PyLong_FromByteArray(bytes, sizeof(Py_intptr_t), little, !is_unsigned); } } #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { return ::std::complex< float >(x, y); } #else static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { return x + y*(__pyx_t_float_complex)_Complex_I; } #endif #else static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { __pyx_t_float_complex z; z.real = x; z.imag = y; return z; } #endif #if CYTHON_CCOMPLEX #else static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { return (a.real == b.real) && (a.imag == b.imag); } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real + b.real; z.imag = a.imag + b.imag; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real - b.real; z.imag = a.imag - b.imag; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real * b.real - a.imag * b.imag; z.imag = a.real * b.imag + a.imag * b.real; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; float denom = b.real * b.real + b.imag * b.imag; z.real = (a.real * b.real + a.imag * b.imag) / denom; z.imag = (a.imag * b.real - a.real * b.imag) / denom; return z; } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { __pyx_t_float_complex z; z.real = -a.real; z.imag = -a.imag; return z; } static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { return (a.real == 0) && (a.imag == 0); } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { __pyx_t_float_complex z; z.real = a.real; z.imag = -a.imag; return z; } #if 1 static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { #if !defined(HAVE_HYPOT) || defined(_MSC_VER) return sqrtf(z.real*z.real + z.imag*z.imag); #else return hypotf(z.real, z.imag); #endif } static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; float r, lnr, theta, z_r, z_theta; if (b.imag == 0 && b.real == (int)b.real) { if (b.real < 0) { float denom = a.real * a.real + a.imag * a.imag; a.real = a.real / denom; a.imag = -a.imag / denom; b.real = -b.real; } switch ((int)b.real) { case 0: z.real = 1; z.imag = 0; return z; case 1: return a; case 2: z = __Pyx_c_prodf(a, a); return __Pyx_c_prodf(a, a); case 3: z = __Pyx_c_prodf(a, a); return __Pyx_c_prodf(z, a); case 4: z = __Pyx_c_prodf(a, a); return __Pyx_c_prodf(z, z); } } if (a.imag == 0) { if (a.real == 0) { return a; } r = a.real; theta = 0; } else { r = __Pyx_c_absf(a); theta = atan2f(a.imag, a.real); } lnr = logf(r); z_r = expf(lnr * b.real - theta * b.imag); z_theta = theta * b.real + lnr * b.imag; z.real = z_r * cosf(z_theta); z.imag = z_r * sinf(z_theta); return z; } #endif #endif #if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { return ::std::complex< double >(x, y); } #else static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { return x + y*(__pyx_t_double_complex)_Complex_I; } #endif #else static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { __pyx_t_double_complex z; z.real = x; z.imag = y; return z; } #endif #if CYTHON_CCOMPLEX #else static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { return (a.real == b.real) && (a.imag == b.imag); } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real + b.real; z.imag = a.imag + b.imag; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real - b.real; z.imag = a.imag - b.imag; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real * b.real - a.imag * b.imag; z.imag = a.real * b.imag + a.imag * b.real; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; double denom = b.real * b.real + b.imag * b.imag; z.real = (a.real * b.real + a.imag * b.imag) / denom; z.imag = (a.imag * b.real - a.real * b.imag) / denom; return z; } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { __pyx_t_double_complex z; z.real = -a.real; z.imag = -a.imag; return z; } static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { return (a.real == 0) && (a.imag == 0); } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { __pyx_t_double_complex z; z.real = a.real; z.imag = -a.imag; return z; } #if 1 static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { #if !defined(HAVE_HYPOT) || defined(_MSC_VER) return sqrt(z.real*z.real + z.imag*z.imag); #else return hypot(z.real, z.imag); #endif } static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; double r, lnr, theta, z_r, z_theta; if (b.imag == 0 && b.real == (int)b.real) { if (b.real < 0) { double denom = a.real * a.real + a.imag * a.imag; a.real = a.real / denom; a.imag = -a.imag / denom; b.real = -b.real; } switch ((int)b.real) { case 0: z.real = 1; z.imag = 0; return z; case 1: return a; case 2: z = __Pyx_c_prod(a, a); return __Pyx_c_prod(a, a); case 3: z = __Pyx_c_prod(a, a); return __Pyx_c_prod(z, a); case 4: z = __Pyx_c_prod(a, a); return __Pyx_c_prod(z, z); } } if (a.imag == 0) { if (a.real == 0) { return a; } r = a.real; theta = 0; } else { r = __Pyx_c_abs(a); theta = atan2(a.imag, a.real); } lnr = log(r); z_r = exp(lnr * b.real - theta * b.imag); z_theta = theta * b.real + lnr * b.imag; z.real = z_r * cos(z_theta); z.imag = z_r * sin(z_theta); return z; } #endif #endif static int __Pyx_check_binary_version(void) { char ctversion[4], rtversion[4]; PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { char message[200]; PyOS_snprintf(message, sizeof(message), "compiletime version %s of module '%.100s' " "does not match runtime version %s", ctversion, __Pyx_MODULE_NAME, rtversion); #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, "%.200s.%.200s is not a type object", module_name, class_name); goto bad; } #ifndef Py_LIMITED_API basicsize = ((PyTypeObject *)result)->tp_basicsize; #else py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); if (!py_basicsize) goto bad; basicsize = PyLong_AsSsize_t(py_basicsize); Py_DECREF(py_basicsize); py_basicsize = 0; if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) goto bad; #endif if (!strict && (size_t)basicsize > size) { PyOS_snprintf(warning, sizeof(warning), "%s.%s size changed, may indicate binary incompatibility", module_name, class_name); #if 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, "%.200s.%.200s has the wrong size, try recompiling", module_name, class_name); goto bad; } return (PyTypeObject *)result; bad: Py_XDECREF(py_module); Py_XDECREF(result); return NULL; } #endif #ifndef __PYX_HAVE_RT_ImportFunction #define __PYX_HAVE_RT_ImportFunction static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**f)(void), const char *sig) { PyObject *d = 0; PyObject *cobj = 0; union { void (*fp)(void); void *p; } tmp; d = PyObject_GetAttrString(module, (char *)"__pyx_capi__"); if (!d) goto bad; cobj = PyDict_GetItemString(d, funcname); if (!cobj) { PyErr_Format(PyExc_ImportError, "%.200s does not export expected C function %.200s", PyModule_GetName(module), funcname); goto bad; } #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3 && PY_MINOR_VERSION==0) if (!PyCapsule_IsValid(cobj, sig)) { PyErr_Format(PyExc_TypeError, "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)", PyModule_GetName(module), funcname, sig, PyCapsule_GetName(cobj)); goto bad; } tmp.p = PyCapsule_GetPointer(cobj, sig); #else {const char *desc, *s1, *s2; desc = (const char *)PyCObject_GetDesc(cobj); if (!desc) goto bad; s1 = desc; s2 = sig; while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; } if (*s1 != *s2) { PyErr_Format(PyExc_TypeError, "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)", PyModule_GetName(module), funcname, sig, desc); goto bad; } tmp.p = PyCObject_AsVoidPtr(cobj);} #endif *f = tmp.fp; if (!(*f)) goto bad; Py_DECREF(d); return 0; bad: Py_XDECREF(d); return -1; } #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, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); if (unlikely(!entries)) { return; } __pyx_code_cache.entries = entries; __pyx_code_cache.max_count = new_max; } for (i=__pyx_code_cache.count; i>pos; i--) { entries[i] = entries[i-1]; } entries[pos].code_line = code_line; entries[pos].code_object = code_object; __pyx_code_cache.count++; Py_INCREF(code_object); } #include "compile.h" #include "frameobject.h" #include "traceback.h" static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( const char *funcname, int c_line, int py_line, const char *filename) { PyCodeObject *py_code = 0; PyObject *py_srcfile = 0; PyObject *py_funcname = 0; #if PY_MAJOR_VERSION < 3 py_srcfile = PyString_FromString(filename); #else py_srcfile = PyUnicode_FromString(filename); #endif if (!py_srcfile) goto bad; if (c_line) { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #else py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); #endif } else { #if PY_MAJOR_VERSION < 3 py_funcname = PyString_FromString(funcname); #else py_funcname = PyUnicode_FromString(funcname); #endif } if (!py_funcname) goto bad; py_code = __Pyx_PyCode_New( 0, /*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(const char* c_str) { return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); } static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { Py_ssize_t ignore; return __Pyx_PyObject_AsStringAndSize(o, &ignore); } static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT if ( #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII __Pyx_sys_getdefaultencoding_not_ascii && #endif PyUnicode_Check(o)) { #if PY_VERSION_HEX < 0x03030000 char* defenc_c; PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); if (!defenc) return NULL; defenc_c = PyBytes_AS_STRING(defenc); #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII { char* end = defenc_c + PyBytes_GET_SIZE(defenc); char* c; for (c = defenc_c; c < end; c++) { if ((unsigned char) (*c) >= 128) { PyUnicode_AsASCIIString(o); return NULL; } } } #endif /*__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_LENGTH(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 */ #if !CYTHON_COMPILING_IN_PYPY #if PY_VERSION_HEX >= 0x02060000 if (PyByteArray_Check(o)) { *length = PyByteArray_GET_SIZE(o); return PyByteArray_AS_STRING(o); } else #endif #endif { char* result; int r = PyBytes_AsStringAndSize(o, &result, length); if (unlikely(r < 0)) { return NULL; } else { return result; } } } static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { int is_true = x == Py_True; if (is_true | (x == Py_False) | (x == Py_None)) return is_true; else return PyObject_IsTrue(x); } static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { PyNumberMethods *m; const char *name = NULL; PyObject *res = NULL; #if PY_MAJOR_VERSION < 3 if (PyInt_Check(x) || PyLong_Check(x)) #else if (PyLong_Check(x)) #endif return Py_INCREF(x), x; m = Py_TYPE(x)->tp_as_number; #if PY_MAJOR_VERSION < 3 if (m && m->nb_int) { name = "int"; res = PyNumber_Int(x); } else if (m && m->nb_long) { name = "long"; res = PyNumber_Long(x); } #else if (m && m->nb_int) { name = "int"; res = PyNumber_Long(x); } #endif if (res) { #if PY_MAJOR_VERSION < 3 if (!PyInt_Check(res) && !PyLong_Check(res)) { #else if (!PyLong_Check(res)) { #endif PyErr_Format(PyExc_TypeError, "__%.4s__ returned non-%.4s (type %.200s)", name, name, Py_TYPE(res)->tp_name); Py_DECREF(res); return NULL; } } else if (!PyErr_Occurred()) { PyErr_SetString(PyExc_TypeError, "an integer is required"); } return res; } #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS #include "longintrepr.h" #endif #endif static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_ssize_t ival; PyObject *x; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_CheckExact(b))) return PyInt_AS_LONG(b); #endif if (likely(PyLong_CheckExact(b))) { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS switch (Py_SIZE(b)) { case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0]; case 0: return 0; case 1: return ((PyLongObject*)b)->ob_digit[0]; } #endif #endif #if PY_VERSION_HEX < 0x02060000 return PyInt_AsSsize_t(b); #else return PyLong_AsSsize_t(b); #endif } 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 } #endif /* Py_PYTHON_H */